Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Stochastic Processes”

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 631 records · Page 35Linked to original sources

Negative selection of lymphocytes.

Almost by definition, negative selection of T and B lymphocytes cannot be absolute. Given that both sets of receptors are derived by stochastic processes, recognition of epitopes by lymphocyte receptors will not be an all or none affair but a relative one. Too effective a mechanism of negative selection would have resulted in deletion of the whole repertoire, as all specificities would have cross-reacted with some self-epitope at least to some degree. This review has documented some of the influences impacting on emerging T and B cell repertoires that result in a removal of the most dangerous self-reactive cells and the progressive quantitative and qualitative increase, through positive clonal selection, of other cells specific for the actual foreign antigens encountered by each individual. T and B lymphocytes pass through a stage where their natural reaction to antigen is one of negative selection and on to a later stage where the cell is more likely to become activated. Geography plays a role in this; the primary lymphoid organs are designed largely to exclude foreign antigens and to present self-antigens, whereas the secondary lymphoid organs are designed to filter out and concentrate foreign material and to promote costimulatory intercellular immune interactions. Ontogeny of individual cells also plays its role, probably through the progressive assembly of the full receptor signaling machinery, incomplete arrays promoting a negative rather than a positive signal. However, the differing susceptibilities of immature and mature cells to silencing by deletion or anergy are relative rather than absolute. Negative signaling may involve immediate or somewhat delayed death of the anti-self-cell, and in some cases the bad cell may have the chance of editing its receptor to create one lacking anti-self-reactivity. Alternatively, the cell may receive a nonlethal down-regulatory signal and may be induced into a state of anergy. Such anergic cells may have a reduced life span, showing that anergy and deletion may shade into each other. Upon the removal of antigen (an unlikely event for cells anergic to an authentic self-antigen), the state of anergy is reversible. The strength of the receptor cross-linking signal may chiefly determine whether deletion (strong cross-linking) or anergy (weaker cross-linking) supervenes. Some lymphocytes with self-reactivity ignore the self-antigen in question because of low affinity, poor accessibility, lack of suitable presentation, or absence of appropriate help.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

Protein import into nuclei: association and dissociation reactions involving transport substrate, transport factors, and nucleoporins.

The molecular dynamics of nuclear protein import were examined in a solution binding assay by testing for interactions between a protein containing a nuclear localization signal (NLS), the transport factors karyopherin alpha, karyopherin beta, and Ran, and FXFG or GLFG repeat regions of nucleoporins. We found that karyopherins alpha and beta cooperate to bind FXFG but not GLFG repeat regions. Binding of the NLS protein to karyopherin alpha was enhanced by karyopherin beta. Two novel reactions were discovered. First, incubation of a karyopherin heterodimer-NLS protein complex with an FXFG repeat region stimulated the dissociation of the NLS protein from the karyopherin heterodimer. Second, incubation of the karyopherin heterodimer with RanGTP (or with a Ran mutant that cannot hydrolyze GTP) led to the dissociation of karyopherin alpha from beta and to an association of Ran with karyopherin beta; RanGDP had no effect. We propose that movement of NLS proteins across the nuclear pore complex is a stochastic process that operates via repeated association-dissociation reactions.

Amino Acid Sequence↗

Molecular oncogenetics of metastasis.

Metastasis is a complex non-stochastic process that is most likely the result of genetic and epigenetic interactions of a wide variety of genes. The search for a single gene which can encompass such a pleiotropic response as to account for the observed phenotypic characteristics of metastatic tumour populations has been unsuccessful. Particular studies involving gene transfection, subtractive hybridisation and cell fusion are beginning to identify specific genes which contribute to metastasis in some cell types. However, such analyses are complicated by the inherent genetic instability and phenotypic heterogeneity present in tumour populations. A more detailed understanding of the metastatic process may require an abandoning of current generalised approaches to metastasis in favour of concentrating on key components of the metastatic cascade such as adhesion and invasion.

Adenovirus Early Proteins↗

Brainstem control of sensory information: a mechanism for perception.

We have proposed a theory in which pathways ascending from the brainstem reticular formation control sensory centers in the dorsal thalamus and neocortex. We assumed that the sensory messages received at a given level are transformed by a stochastic process, called Alopex, in a way which maximizes responses in central feature analyzers. Perception is seen as a process involving a close cyclic interaction between brainstem and sensory relays. We discuss the specific case of visual information flow and the proposed modification of visual images at the level of the dorsal lateral geniculate nucleus (dLGN). Computer simulations of a simple model, representing the dLGN and reafferent control emanating from the reticular formation, show that sensory features are effectively enhanced and--in the absence of sensory input--quasi-sensory features may be generated by feedback of a simple scalar variable that is formed by the non-linear superposition of the responses of any number of feature analyzers. The model proposes a specific mechanism for such processes as visual imagery, hallucinations, and dreaming, and provides a framework for further studies into the nature of cognitive brain functions.

Afferent Pathways↗

A bootstrap method to compare the shapes of two scalp fields.

A method is described to compare two evoked potential scalp fields in order to decide if the two fields are the same or different. The method uses Efron's bootstrap technique which avoids potential errors due to assumptions about the underlying stochastic process. It is configured to focus only on the shape of the evoked potential scalp field. The method is applied to a simple visually evoked potential paradigm and results are compared to the chi-square test using data from 7 normal subjects.

Evoked Potentials, Visual↗

Projecting the future size and health status of the U.S. elderly population.

"A projection model based on a multivariate continuous state, stochastic process is presented. The model allows multiple time-varying covariates to be used so parameters can be estimated from time series information on health changes and mortality, and their interaction. Health changes are simulated by altering parameters controlling the age trajectory and diffusion of risk factor means, variances, and covariances....By increasing the information used in projections it may be possible to better (a) anticipate the state of health at extreme ages, (b) forecast changes in health at specific ages over time, (c) stimulate the effects of specific interventions, and (d) determine the sensitivity of outcomes to a range of interventions."

Adult↗

Statistical tests of the IBM PC pseudorandom number generator.

The widespread use of IBM personal computers in biomedical research and medical practice is evidenced by a variety of journal articles. Many of the application programs are written in the BASIC language, they model a stochastic process, and they depend on the Microsoft random number generator. Unfortunately, the Microsoft generator has exhibited a number of flaws including, for some seeds, a lack of uniformity of generated sequences of numbers, and serial correlation within such sequences. This paper provides evidence of these problems for several seeds, and provides suggestions for acceptable seeds which ensure that the generated sequences of numbers pass two fundamental statistical tests for randomness.

Computer Simulation↗

Exemplary data: sample size and power in the design of event-time clinical trials.

In planning a complex clinical trial with time to event as the outcome, it is difficult to derive the power of the test statistic analytically. In this paper we describe an algorithm for generating exemplary data from an alternative hypothesis that can be used to compute the expected value of a logrank test statistic and its power under that alternative. Exemplary data are nonrandomly computer-generated data that are constructed from a complex stochastic process and have desirable characteristics such as distributional moments similar to those of the process. An algorithm for generating exemplary timed events data is presented and its use in evaluating power for the planning of clinical trials demonstrated. These data represent "expectations" of outcome, data censoring, and censoring event times. A test statistic, z, such as the logrank can be computed from the data. It is distributed asymptotically, N(mu A, 1), under the alternative hypothesis and its value is used to estimate mu A and the power of the test for a given trial scenario. The results compare favorably to results from analytical methods and Monte Carlo simulations published in the literature. The advantages of the method lie in the degree of flexibility in study design, choice of models that describe the timing of events, and the range of testing methods that can be used. Although Monte Carlo methods may appear to have similar flexibility, the exemplary algorithm is more practical because only one data set need be analyzed and the modifications can be achieved without reprogramming.

Algorithms↗

Electroencephalogram spectral analysis by the direct and indirect methods: a comparison.

An artificially-created electroencephalogram was used to perform a comparison between the indirect and direct analysis methods. The results obtained by Fourier transform of the correlation function and smoothing of Fourier series development differ for a stochastic process in which the correlation functions are not sufficiently damped. Some mathematical framework is also appended in which the difference is worked out from a more theoretical point of view. In order to obtain results independent of inherent conditions, which in the simplest way can be detected by calculating the correlation functions, the indirect method is preferable.

Brain↗

A hypothetical model to explain the 'termination' of chronic myeloid leukemia into blastic crisis.

Chronic myeloid leukemia is characterised by two discrete phases, a 'benign' phase which terminates into an 'acute' phase. Various explanations have been given to explain the cause of 'blastic' crisis in CML. But the consistency and regularity with which blast crisis occurs and the irregularity with which the factors which are ascribed to cause it (e.g. additional chromosomal abnormalities, change in bcr/abl rearrangement, etc. occur, suggests that CML-BC is not a stochastic process in the natural history of CML but is predetermined at the time of the first mutation in the stem cell. A hypothetical model is put forward proposing this. Different points supporting the model are discussed. The most important implication of this model would be to provide an insight that should lead to the development of more selective and appropriate treatment strategies for this disease.

Blast Crisis↗

Temporal distribution of seizures in epilepsy.

A major problem in epileptology is why a seizure occurs at a particular moment in time. An initial step in solving this problem is a detailed analysis of the temporal distribution of seizures. Using methods and theories of stochastic processes, seizure patterns in a group of epileptic outpatients were examined for stationarity, randomness, dependency and periodicity in a prospective study. Sixteen of the 21 seizure diaries included in the study showed stationarity; 2 were non-stationary and 3 inconclusive. Eleven of the 16 stationary diaries were non-Poisson (P less than 0.005), indicating that in the majority of patients seizures did not occur randomly. The most frequently encountered phenomenon was seizure clustering. Clustering was considered when the diaries fulfilled all three criteria: (1) a positive R-test (P less than 0.001); (2) deviation from the fitted Poisson distribution towards clustering; and (3) the feature of an autoregressive process in the autocorrelogram plot. Dependency between seizure events was demonstrated in 8 of the 16 stationary diaries, computing first order transition probabilities. A detailed analysis of seizure occurrence is a major step towards a better understanding of the mechanisms underlying seizure precipitation. This is exemplified by our finding of a relation between seizure frequency and the menstrual cycle.

Adolescent↗

Somatic mutations and cellular aging: two-dimensional DNA typing of rat fibroblast clones.

Aging may be explained, to some extent, as a stochastic process of macromolecular damage. The rate of such a process should then determine longevity and be genetically controlled, as can be derived from the species specificity of maximum lifespan. The genome of the somatic cell is a major candidate to study for loss of DNA sequence integrity during aging. Unfortunately, a lack of adequate techniques has thus far hampered progress in testing the aging genome for changes in its DNA sequence content. Here we discuss recently developed sophisticated technology for studying spontaneous somatic mutations in relation to aging. More specifically, we describe the use of a novel two-dimensional DNA typing technique for the analysis of fibroblast clones derived from primary cultures established from skin biopsies of rats of different ages. Preliminary data are presented indicating the occurrence of DNA sequence changes in mini- and microsatellite regions of the rat genome at an average frequency of 2.7 x 10(-3) per analyzed DNA fragment. Age-related variations in the somatic mutation frequency of these genomic regions were not observed.

Animals↗

Input-output relationship in galvanotactic response of Dictyostelium cells.

Under a direct current electric field, Dictyostelium cells exhibit migration towards the cathode. To determine the input-output relationship of the cell's galvanotactic response, we developed an experimental instrument in which electric signals applied to the cells are highly reproducible and the motile response are analyzed quantitatively. With no electric field, the cells moved randomly in all directions. Upon applying an electric field, cell migration speeds became about 1.3 times faster than those in the absence of an electric field. Such kinetic effects of electric fields on the migration were observed for cells stimulated between 0.25 and 10 V/cm of the field strength. The directions of cell migrations were biased toward the cathode in a positive manner with field strength, showing galvanotactic response in a dose-dependent manner. Quantitative analysis of the relationship between field strengths and directional movements revealed that the biased movements of the cells depend on the square of electric field strength, which can be described by one simple phenomenological equation. The threshold strength for the galvanotaxis was between 0.25 and 1 V/cm. Galvanotactic efficiency reached to half-maximum at 2.6 V/cm, which corresponds to an approximate 8 mV voltage difference between the cathode and anode direction of 10 microm wide, round cells. Based on these results, possible mechanisms of galvanotaxis in Dictyostelium cells were discussed. This development of experimental system, together with its good microscopic accessibility for intracellular signaling molecules, makes Dictyostelium cells attractive as a model organism for elucidating stochastic processes in the signaling systems responsible for cell motility and its regulations.

Animals↗

Genetic and chromatin regulation of Pvt1 monoallelic expression.

While most genes are equivalently expressed on both alleles, genes with random monoallelic expression (RME) stably maintain expression from only one allele, but the mechanisms and consequences of RME remain unclear. We performed allele-specific RNA sequencing (RNA-seq) on ∼100 F1 hybrid neural progenitor cell (NPC) clonal lines to reveal the extent of autosomal RME (aRME). Of the 287 aRME genes, Pvt1, an oncogenic long non-coding RNA, is an aRME with a genetic bias. In the absence of genetic differences, Pvt1 undergoes balanced aRME. Pvt1 monoallelic expression is maintained by allele-specific active and repressive histone modifications, opposed to DNA methylation. Additionally, we provide a two-step mechanism for the initiation of aRME and demonstrate that Pvt1 monoallelic expression results in a growth phenotype due to the interplay with Myc. These findings provide insight into how genetic differences can skew a stochastic process, resulting in monoallelic expression with a phenotypic consequence in early development.

Chromatin↗

Anti-CD3 priming generates heterogeneous antigen-specific memory CD4 T cells.

Anti-CD3 activation of peripheral T cells is used in adoptive immunotherapy for cancer and HIV infection, but the long-term fate of anti-CD3-primed T cells in vivo is not known. In this study, we demonstrate that anti-CD3-mediated activation of influenza hemagglutinin (HA)-specific TCR-transgenic CD4 T cells results in generation of a long-lived HA-specific memory CD4 T cell population when transferred into lymphocyte-deficient and intact mouse hosts. This anti-CD3-primed memory population is indistinguishable from HA peptide-primed memory CD4 T cells in terms of phenotype, rapid recall function, and enhanced proliferative capacity. Moreover, anti-CD3 priming generates phenotypically heterogeneous memory subsets in lymphoid and non-lymphoid sites. Our results suggest that anti-CD3 has potential efficacy in generating memory responses in adoptive immunotherapies and vaccines and that the tissue distribution and maintenance of heterogeneous lymphoid and non-lymphoid memory T cell subsets are a stochastic process that can occur independent of antigen or TCR specificity.

Animals↗

Modelling radionuclide transport for time varying flow in a channel network.

Water flowrates and flow directions may change over time in the subsurface for a number of reasons. In fractured rocks flow takes place in channels within fractures. Solutes are carried by the advective flow. In addition, solutes may diffuse in and out of stagnant waters in the rock matrix and other stagnant water regions. Sorbing species may sorb on fracture surfaces and on the micropore surfaces in the rock matrix. We present a method by which solute particles can be traced in flowing water undergoing changes in flowrate and direction in a complex channel network where the solutes can also interact with the rock by diffusion in the rock matrix. The novelty of this paper is handling of diffusion in the rock matrix under transient flow conditions. The diffusive processes are stochastic and it is not possible to follow a particle deterministically. The method therefore utilises the properties of a probability distribution function for a tracer moving in a fracture where matrix diffusion is active. The method is incorporated in a three dimensional channel network model. Particle tracking is used to trace out a multitude of flowpaths, each of which consists of a large number of channels within fractures. Along each channel the aperture and velocity as well as the matrix sorption properties can vary. An efficient method is presented whereby a particle can be followed along the variable property flowpath. For stationary flow conditions and a network of channels with advective flow and matrix diffusion, a simple analytical solution for the residence time distribution along each pathway can be used. Only two parameter groups need to be integrated along each path. For transient flow conditions, a time stepping procedure that incorporates a stochastic Monte-Carlo like method to follow the particles along the paths when flow conditions change is used. The method is fast and an example is used for illustrative purposes. It is exemplified by a case where land rises due to glacial rebound. It is shown that the effects of changing flowrates and directions can be considerable and that the diffusive migration in the matrix can have a dominating effect on the results.

Computer Simulation↗

The effects of SNR on ADC measurements in diffusion-weighted hyperpolarized He-3 MRI.

The theoretical dependence of the mean and standard deviation of ADC values on signal-to-noise ratio (SNR) was derived and compared to measured values in porous phantoms and the lungs of human subjects using diffusion-weighted hyperpolarized helium-3 MRI. For SNR values below 15, mean ADC values were highly SNR-dependent due to a combination of noise and choice of noise thresholding. Above SNR values of 15 and for mean ADC values within ranges relevant for evaluating lung disease (<0.6 cm2/s), the mean ADC was largely independent of SNR. The standard deviation, by contrast, was highly dependent on SNR over a much larger range, but this dependence was well predicted by theory, suggesting the histogram of ADC values might be corrected for these stochastic processes to more accurately evaluate disease using restricted diffusion measures in the lungs.

Artifacts↗

Factors affecting children's participation and amount of labor on family farms.

METHOD: A two-stage decision-making model is estimated to explain children's participation and labor supply on family farms using unitary and cooperative bargaining frameworks. RESULTS: Results indicate that parents have different preferences about whether their children work and how much they work. The models incorporate non-economic factors and allow for different stochastic processes in the participation and labor supply decisions. CONCLUSIONS: Concerns about children's social development appear to be crucial in deciding children's labor participation, while the child's economic contribution significantly influences both whether they work and how much they work. Some variables affect the two decisions differently. For instance, the higher the parents' education level, the higher the probability children will work but the fewer hours they will work.

Adult↗