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At least 1,009 records · Page 56Linked to original sources
PubMed2006

Chromatin loops are responsible for higher counts of small DNA fragments induced by high-LET radiation, while chromosomal domains do not affect the fragment sizes.

PURPOSE: To apply a polymer model of DNA damage induced by high-LET (linear energy transfer) radiation and determine the influence of chromosomal domains and loops on fragment length distribution. MATERIALS AND METHODS: The yields of DSB (double-strand breaks) induced by high-LET radiation were calculated using a track structure model along with a polymer model of DNA packed in the cell nucleus. The cell nucleus was constructed to include the chromosomal domains and chromatin loops. The latter were generated by the random walk method. RESULTS AND CONCLUSIONS: We present data for DSB yields per track per cell, DNA fragment sizes, the radial distribution of DSB with respect to the track center, and the distribution of 0, 1, 2, and more DSB from a single particle. Calculations were carried out for a range of particles including He (40 keV/microm), N (225 keV/microm), and Fe ions (150 keV/mum). Situations relevant to PFGE (pulsed-field gel electrophoresis) and microbeam experiments with direct irradiation of the cell nucleus were simulated to demonstrate the applicability of the model. Data show that chromosomal domains do not have a significant influence on fragment-size distribution, while the presence of DNA loops increases the frequencies of smaller fragments by nearly 30% for fragment sizes in the range from 2 kbp (bp = base pair) to 20 kbp.

Chromatin↗
PubMed2006

A new paradigm for deriving and analyzing number needed to treat.

The inverse of the risk difference, commonly referred to as the number needed to treat (NNT) has been recently proposed as a useful measure for comparing two treatments. Since its introduction, the method has been used widely to establish comparative treatment benefits, and has also been the subject of extensive discussions among statisticians. In this paper, we examine the assumptions behind the original definition of NNT, and introduce a new formulation of the method based on a random walk model. Using stopping times, we develop a paradigm for NNT that avoids some of the conceptual and inferential difficulties and pitfalls associated with the previous work on NNT. Simulation results are provided to illustrate the bias introduced by using alternative formulations of NNT, and several open problems are suggested for future research.

Clinical Trials as Topic↗
PubMed1993

Unconfined lateral diffusion and an estimate of pericellular matrix viscosity revealed by measuring the mobility of gold-tagged lipids.

Nanovid (video-enhanced) microscopy was used to determine whether lateral diffusion in the plasma membrane of colloidal gold-tagged lipid molecules is confined or is unrestricted. Confinement could be produced by domains within the plane of the plasma membrane or by filamentous barriers within the pericellular matrix. Fluorescein-phosphatidylethanolamine (F1-PE), incorporated into the plasma membranes of cultured fibroblasts, epithelial cells and keratocytes, was labeled with 30-nm colloidal gold conjugated to anti-fluorescein (anti-F1). The trajectories of the gold-labeled lipids were used to compute diffusion coefficients (DG) and to test for restricted motion. On the cell lamella, the gold-labeled lipids diffused freely in the plasma membrane. Since the gold must move through the pericellular matrix as the attached lipid diffuses in the plasma membrane, this result suggests that any extensive filamentous barriers in the pericellular matrix are at least 40 nm from the plasma membrane surface. The average diffusion coefficients ranged from 1.1 to 1.7 x 10(-9) cm2/s. These values were lower than the average diffusion coefficients (DF) (5.4 to 9.5 x 10(-9) cm2/s) obtained by FRAP. The lower DG is partially due to the pericellular matrix as demonstrated by the result that heparinase treatment of keratocytes significantly increased DG to 2.8 x 10(-9) cm2/s, but did not affect DF. Pericellular matrix viscosity was estimated from the frictional coefficients computed from DG and DF and ranged from 0.5 to 0.9 poise for untreated cells. Heparinase treatment of keratocytes decreased the apparent viscosity to approximately 0.1 poise. To evaluate the presence of domains or barriers, the trajectories and corresponding mean square displacement (MSD) plots of gold-labeled lipids were compared to the trajectories and MSD plots resulting from computer simulations of random walks within corrals. Based on these comparisons, we conclude that, if there are domains limiting the diffusion of F1-PE, most are larger than 5 microns in diameter.

Animals↗
PubMed1998

Visualization of melanosome dynamics within wild-type and dilute melanocytes suggests a paradigm for myosin V function In vivo.

Unlike wild-type mouse melanocytes, where melanosomes are concentrated in dendrites and dendritic tips, melanosomes in dilute (myosin Va-) melanocytes are concentrated in the cell center. Here we sought to define the role that myosin Va plays in melanosome transport and distribution. Actin filaments that comprise a cortical shell running the length of the dendrite were found to exhibit a random orientation, suggesting that myosin Va could drive the outward spreading of melanosomes by catalyzing random walks. In contrast to this mechanism, time lapse video microscopy revealed that melanosomes undergo rapid ( approximately 1.5 microm/s) microtubule-dependent movements to the periphery and back again. This bidirectional traffic occurs in both wild-type and dilute melanocytes, but it is more obvious in dilute melanocytes because the only melanosomes in their periphery are those undergoing this movement. While providing an efficient means to transport melanosomes to the periphery, this component does not by itself result in their net accumulation there. These observations, together with previous studies showing extensive colocalization of myosin Va and melanosomes in the actin-rich periphery, suggest a mechanism in which a myosin Va-dependent interaction of melanosomes with F-actin in the periphery prevents these organelles from returning on microtubules to the cell center, causing their distal accumulation. This "capture" model is supported by the demonstration that (a) expression of the myosin Va tail domain within wild-type cells creates a dilute-like phenotype via a process involving initial colocalization of tail domains with melanosomes in the periphery, followed by an approximately 120-min, microtubule-based redistribution of melanosomes to the cell center; (b) microtubule-dependent melanosome movement appears to be damped by myosin Va; (c) intermittent, microtubule-independent, approximately 0.14 microm/s melanosome movements are seen only in wild-type melanocytes; and (d) these movements do not drive obvious spreading of melanosomes over 90 min. We conclude that long-range, bidirectional, microtubule-dependent melanosome movements, coupled with actomyosin Va-dependent capture of melanosomes in the periphery, is the predominant mechanism responsible for the centrifugal transport and peripheral accumulation of melanosomes in mouse melanocytes. This mechanism represents an alternative to straightforward transport models when interpreting other myosin V mutant phenotypes.

Actin Cytoskeleton↗
PubMed1983

Lymphocyte migration into three-dimensional collagen matrices: a quantitative study.

Lymphocytes have been plated onto the surface of three-dimensional gels of native collagen fibers, and their distribution throughout the three-dimensional collagen matrix has been determined in a quantitative fashion at various times thereafter. Information regarding the total number of applied cells may be obtained by this means. Lymphocyte penetration into the collagen gel does not appear to involve the expression of collagenolytic activity, nor does it require the presence of serum. Analysis of the kinetics of lymphocyte penetration into the gel matrix indicates that lymphocytes are migrating in a "random-walk" fashion. Our objective has been to establish a model system for studying the cell-matrix and cell-cell interactions which influence the pattern of lymphocyte recirculation in vivo and the results presented here are discussed in this context.

Cell Adhesion↗
PubMed2000

Interplanetary Magnetic Field Line Mixing Deduced from Impulsive Solar Flare Particles.

We have studied fine-scale temporal variations in the arrival profiles of approximately 20 keV nucleon-1 to approximately 2 MeV nucleon-1 ions from impulsive solar flares using instrumentation on board the Advanced Composition Explorer spacecraft at 1 AU between 1997 November and 1999 July. The particle events often had short-timescale ( approximately 3 hr) variations in their intensity that occurred simultaneously across all energies and were generally not in coincidence with any local magnetic field or plasma signature. These features appear to be caused by the convection of magnetic flux tubes past the observer that are alternately filled and devoid of flare ions even though they had a common flare source at the Sun. Thus, we have used the particles to study the mixing of the interplanetary magnetic field that is due to random walk. We deduce an average timescale of 3.2 hr for these features, which corresponds to a length of approximately 0.03 AU.

Journal Article↗
PubMed2003

A diffusion-based theory of organism dispersal in heterogeneous populations.

We develop a general theory of organism movement in heterogeneous populations that can explain the leptokurtic movement distributions commonly measured in nature. We describe population heterogeneity in a state-structured framework, employing advection-diffusion as the fundamental movement process of individuals occupying different movement states. Our general analysis shows that population heterogeneity in movement behavior can be defined as the existence of different movement states and among-individual variability in the time individuals spend in these states. A presentation of moment-based metrics of movement illustrates the role of these attributes in general dispersal processes. We also present a special case of the general theory: a model population composed of individuals occupying one of two movement states with linear transitions, or exchange, between the two states. This two-state "exchange model" can be viewed as a correlated random walk and provides a generalization of the telegraph equation. By exploiting the main result of our general analysis, we characterize the exchange model by deriving moment-based metrics of its movement process and identifying an analytical representation of the model's time-dependent solution. Our results provide general and specific theoretical explanations for empirical patterns in organism movement; the results also provide conceptual and analytical bases for extending diffusion-based dispersal theory in several directions, thereby facilitating mechanistic links between individual behavior and spatial population dynamics.

Animal Migration↗
PubMed2004

From individual behavior to metapopulation dynamics: unifying the patchy population and classic metapopulation models.

Spatially structured populations in patchy habitats show much variation in migration rate, from patchy populations in which individuals move repeatedly among habitat patches to classic metapopulations with infrequent migration among discrete populations. To establish a common framework for population dynamics in patchy habitats, we describe an individual-based model (IBM) involving a diffusion approximation of correlated random walk of individual movements. As an example, we apply the model to the Glanville fritillary butterfly (Melitaea cinxia) inhabiting a highly fragmented landscape. We derive stochastic patch occupancy model (SPOM) approximations for the IBMs assuming pure demographic stochasticity, uncorrelated environmental stochasticity, or completely correlated environmental stochasticity in local dynamics. Using realistic parameter values for the Glanville fritillary, we show that the SPOMs mimic the behavior of the IBMs well. The SPOMs derived from IBMs have parameters that relate directly to the life history and behavior of individuals, which is an advantage for model interpretation and parameter estimation. The modeling approach that we describe here provides a unified framework for patchy populations with much movements among habitat patches and classic metapopulations with infrequent movements.

Animal Migration↗
PubMed2004

Intrinsic scaling complexity in animal dispersion and abundance.

Ecological theory related to animal distribution and abundance is at present incomplete and to some extent naive. We suggest that this may partly be due to a long tradition in the field of model development for choosing mathematical and statistical tools for convenience rather than applicability. Real population dynamics are influenced by nonlinear interactions, nonequilibrium conditions, and scaling complexity from system openness. Thus, a coherent theory for individual-, population-, and community-level processes should rest on mathematical and statistical methods that explicitly confront these issues in a manner that satisfies principles from statistical mechanics for complex systems. Instead, ecological theory is traditionally based on premises from simpler statistical mechanical theory for memory-free, scale-specific, random-walk, and diffusion processes, while animals from many taxa generally express strategic homing, site fidelity, and conspecific attraction in direct violation of primary model assumptions. Thus, the main challenge is to generalize the theory for memory-free physical, many-body systems to include a more realistic memory-influenced framework that better satisfies ecological realism. We describe, simulate, and discuss three testable aspects of a model for multiscaled habitat use at the individual level: (1) scale-free distribution of movement steps under influence of self-reinforcing site fidelity, (2) fractal spatial dispersion of intra-home range relocations, and (3) nonasymptotic expansion of observed intra-home range patch use with increasing set of relocations. Examples of literature data apparently supporting the conjecture that multiscaled, strategic space use is widespread among many animal taxa are also described. We suggest that the present approach, which provides a protocol to test for influence from scale-free, memory-dependent habitat use at the individual level, may also point toward a guideline for development of a generalized theoretical framework for complex population kinetics and spatiotemporal population dynamics.

Animal Migration↗
PubMed2005

A null model of morphospace occupation.

Progress in understanding the relationship between lineage diversity, morphological diversity, and morphospace dynamics has been hampered by the lack of an appropriate null model of morphospace occupation. In this article, we introduce a simple class of models based on branching random walks (BRWs) for continuous traits. We show that many of the observed patterns of morphospace occupation might be simply a consequence of the dynamics of BRWs and therefore might not require special explanations. We also provide expected patterns of morphospace occupation according to a number of different conditions. In particular, we model BRWs on neutral landscapes and demonstrate that clumping in morphospace is possible even in the absence of adaptive landscapes with well-defined peaks and valleys. The quantitative definition of the BRW provides a means to analyze, both computationally and analytically, patterns of morphospace occupation according to different hypotheses.

Ecosystem↗
PubMed1997

Optical imaging in medicine: II. Modelling and reconstruction.

The desire for a diagnostic optical imaging modality has motivated the development of image reconstruction procedures involving solution of the inverse problem. This approach is based on the assumption that, given a set of measurements of transmitted light between pairs of points on the surface of an object, there exists a unique three-dimensional distribution of internal scatterers and absorbers which would yield that set. Thus imaging becomes a task of solving an inverse problem using an appropriate model of photon transport. In this paper we examine the models that have been developed for this task, and review current approaches to image reconstruction. Specifically, we consider models based on radiative transfer theory and its derivatives, which are either stochastic in nature (random walk, Monte Carlo, and Markov processes) or deterministic (partial differential equation models and their solutions). Image reconstruction algorithms are discussed which are based on either direct backprojection, perturbation methods, nonlinear optimization, or Jacobian calculation. Finally we discuss some of the fundamental problems that must be addressed before optical tomography can be considered to be an understood problem, and before its full potential can be realized.

Diagnostic Imaging↗
PubMed2005

Monte Carlo simulations of increased/decreased scattering inclusions inside a turbid slab.

We analyse the effect on scattered photons of anomalous optical inclusions in a turbid slab with otherwise uniform properties. Our motivation for doing so is that inclusions affect scattering contrast used to quantify optical properties found from transmitted light intensity measured in transillumination experiments. The analysis is based on a lattice random walk formalism which takes into account effects of both positive and negative deviations of the scattering coefficient from that of the bulk. Our simulations indicate the existence of a qualitative difference between the effects of these two types of perturbations. In the case of positive perturbations the time delay is found to be proportional to the square of the size of the inclusion while for negative perturbations the time delay is a linear function of its volume.

Algorithms↗
PubMed2006

Mean time-of-flight of photons in transillumination measurements of optically anisotropic tissue with an inclusion.

We study the effect of optical anisotropy on the mean time-of-flight of photons in a slab of turbid medium containing an inclusion whose optical properties differ from those of the bulk. For this analysis the difference in the mean time for a photon introduced into the slab to reach a specified target point with and without the inclusion is calculated. This difference is defined to be a measure of the contrast. The theoretical model is based on a continuous-time random walk on a lattice, which can be solved exactly and furnishes an exact expression for the contrast. Qualitative and quantitative characteristics of the contrast are analysed as functions of the geometric configuration of the system components (locations of the source, the inclusion and the detector), parameters that specify the optical anisotropy of the medium, and either the scattering properties of the inclusion or the lifetime of the small fluorophore in the case of the time-resolved fluorescence experimental configuration.

Algorithms↗
PubMed2006

Absorption and scattering coefficient dependence of laser-Doppler flowmetry models for large tissue volumes.

Based on quasi-elastic scattering theory (and random walk on a lattice approach), a model of laser-Doppler flowmetry (LDF) has been derived which can be applied to measurements in large tissue volumes (e.g. when the interoptode distance is >30 mm). The model holds for a semi-infinite medium and takes into account the transport-corrected scattering coefficient and the absorption coefficient of the tissue, and the scattering coefficient of the red blood cells. The model holds for anisotropic scattering and for multiple scattering of the photons by the moving scatterers of finite size. In particular, it has also been possible to take into account the simultaneous presence of both Brownian and pure translational movements. An analytical and simplified version of the model has also been derived and its validity investigated, for the case of measurements in human skeletal muscle tissue. It is shown that at large optode spacing it is possible to use the simplified model, taking into account only a 'mean' light pathlength, to predict the blood flow related parameters. It is also demonstrated that the 'classical' blood volume parameter, derived from LDF instruments, may not represent the actual blood volume variations when the investigated tissue volume is large. The simplified model does not need knowledge of the tissue optical parameters and thus should allow the development of very simple and cost-effective LDF hardware.

Absorption↗
PubMed2001

Empirical estimators of gamma fits to tracer-dilution curves and their technical basis and practical scope.

A gamma fit facilitates smoothing and extrapolation of distorted tracer-dilution curves in blood flow studies. Theoretically based empirical estimators were developed as simple alternatives to direct regression approaches from simulated gamma distributions with a wide range of shape asymmetry. Key curve features of peak height p, full width w at half peak height, rising and falling limb inflection tangents and asymmetry of the peak time with respect to the p/2 height occurrences were related to the parameters of the distribution by multiple linear regression after suitable transformations. The product pw was simply related to the total area A under the curve, pw/A being 0.93 +/- 0.01 in 70 cardiac output determinations from ten surgical patients. Shape and scale parameters were closely related to the standard deviation, inflection point properties and w for the curves. Mensuration devices suitable for cardiac output computers were developed that calculated total areas from incomplete portions under gamma curves and by-passed the need for parameter estimation. There was limited point in estimating the distribution parameters just to derive particle transit times, because of the ad hoc nature of the fitting form, which did not allow for the back-dispersion by Brownian motion of tracer molecules diluting in blood flow. Nonetheless, the accuracy of area prediction using a gamma fit was adequate for most clinical purposes and comparable to that via the random walk function, giving good insight to established results and computing procedures.

Algorithms↗
PubMed2004

Role of streams in myxobacteria aggregate formation.

Cell contact, movement and directionality are important factors in biological development (morphogenesis), and myxobacteria are a model system for studying cell-cell interaction and cell organization preceding differentiation. When starved, thousands of myxobacteria cells align, stream and form aggregates which later develop into round, non-motile spores. Canonically, cell aggregation has been attributed to attractive chemotaxis, a long range interaction, but there is growing evidence that myxobacteria organization depends on contact-mediated cell-cell communication. We present a discrete stochastic model based on contact-mediated signaling that suggests an explanation for the initialization of early aggregates, aggregation dynamics and final aggregate distribution. Our model qualitatively reproduces the unique structures of myxobacteria aggregates and detailed stages which occur during myxobacteria aggregation: first, aggregates initialize in random positions and cells join aggregates by random walk; second, cells redistribute by moving within transient streams connecting aggregates. Streams play a critical role in final aggregate size distribution by redistributing cells among fewer, larger aggregates. The mechanism by which streams redistribute cells depends on aggregate sizes and is enhanced by noise. Our model predicts that with increased internal noise, more streams would form and streams would last longer. Simulation results suggest a series of new experiments.

Models, Molecular↗
PubMed2003

Analysis of Na+,K+-ATPase motion and incorporation into the plasma membrane in response to G protein-coupled receptor signals in living cells.

Dopamine (DA) increases Na(+),K(+)-ATPase activity in lung alveolar epithelial cells. This effect is associated with an increase in Na(+),K(+)-ATPase molecules within the plasma membrane (). Analysis of Na(+),K(+)-ATPase motion was performed in real-time in alveolar cells stably expressing Na(+),K(+)-ATPase molecules carrying a fluorescent tag (green fluorescent protein) in the alpha-subunit. The data demonstrate a distinct (random walk) pattern of basal movement of Na(+),K(+)-ATPase-containing vesicles in nontreated cells. DA increased the directional movement (by 3.5 fold) of the vesicles and an increase in their velocity (by 25%) that consequently promoted the incorporation of vesicles into the plasma membrane. The movement of Na(+),K(+)-ATPase-containing vesicles and incorporation into the plasma membrane were microtubule dependent, and disruption of this network perturbed vesicle motion toward the plasma membrane and prevented the increase in the Na(+),K(+)-ATPase activity induced by DA. Thus, recruitment of new Na(+),K(+)-ATPase molecules into the plasma membrane appears to be a major mechanism by which dopamine increases total cell Na(+),K(+)-ATPase activity.

Actins↗
PubMed2005

Infection in social networks: using network analysis to identify high-risk individuals.

Simulation studies using susceptible-infectious-recovered models were conducted to estimate individuals' risk of infection and time to infection in small-world and randomly mixing networks. Infection transmitted more rapidly but ultimately resulted in fewer infected individuals in the small-world, compared with the random, network. The ability of measures of network centrality to identify high-risk individuals was also assessed. "Centrality" describes an individual's position in a population; numerous parameters are available to assess this attribute. Here, the authors use the centrality measures degree (number of contacts), random-walk betweenness (a measure of the proportion of times an individual lies on the path between other individuals), shortest-path betweenness (the proportion of times an individual lies on the shortest path between other individuals), and farness (the sum of the number of steps between an individual and all other individuals). Each was associated with time to infection and risk of infection in the simulated outbreaks. In the networks examined, degree (which is the most readily measured) was at least as good as other network parameters in predicting risk of infection. Identification of more central individuals in populations may be used to inform surveillance and infection control strategies.

Community-Acquired Infections↗