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At least 1,261 records · Page 70Linked to original sources
PubMed1997

Methods for microscopic characterization of oral biofilms: analysis of colonization, microstructure, and molecular transport phenomena.

Assessment of the role of biofilm microstructure in biofilm-specific activities requires non-destructive measurement techniques for parameterization of structural characteristics in parallel with relevant biochemical and physiological data. This paper briefly reviews some current methods for biofilm structural analysis, with emphasis on new developments in optical imaging and mathematical modeling methods. Fluorescence imaging studies of bacterial colonization events occurring on exposed model tooth surfaces indicated that bacterial adhesion to sessile organisms was of central importance to the early colonization process and that this occurred in a non-random manner. Structural studies of mature biofilms by confocal microscopy demonstrated the spatial distribution of individual species using fluorescent antibodies. Biofilms grown under different physiological conditions exhibited differences in structure, and methods were developed for parameterizing the spatial orientations of the bacteria. Diffusive processes within biofilm microstructures were studied using a random walk model in both 2-D and 3-D. Modeling of convective flow within biofilm microstructures was achieved by application of lattice Boltzmann methodology.

Bacteriological Techniques↗
PubMed2006

Cell_motility: a cross-platform, open source application for the study of cell motion paths.

BACKGROUND: Migration is an important aspect of cellular behaviour and is therefore widely studied in cell biology. Numerous components are known to participate in this process in a highly dynamic manner. In order to obtain a better insight in cell migration, mutants or drugs are used and their motive phenotype is then linked with the disturbing factors. One of the typical approaches to study motion paths of individual cells relies on fitting mean square displacements to a persistent random walk function. Since the numerous calculations involved often rely on diverse commercial software packages, the analysis can be expensive, labour-intensive and error-prone work. Additionally, due to the nature of algorithms employed the calculations involved are not readily reproducible without access to the exact software package(s) used. RESULTS: We here present the cell_motility software, an open source Java application under the GNU-GPL license that provides a clear and concise analysis workbench for large amounts of cell motion data. Apart from performing the necessary calculations, the software also visualizes the original motion paths as well as the results of the calculations to help the user interpret the data. The application features an intuitive graphical user interface as well as full user and developer documentation and both source and binary files can be freely downloaded from the project website at http://genesis.UGent.be/cell_motility . CONCLUSION: In providing a free, open source software solution for the automated processing of cell motion data, we aim to achieve two important goals: labs can greatly simplify their data analysis pipeline as switching between different computational software packages becomes obsolete (thus reducing the chances for human error during data manipulation and transfer) and secondly, to provide scientists in the field with a freely available common platform to perform their analyses, enabling more efficient data quality control through peer reviewing.

Animals↗
PubMed2006

CGHScan: finding variable regions using high-density microarray comparative genomic hybridization data.

BACKGROUND: Comparative genomic hybridization can rapidly identify chromosomal regions that vary between organisms and tissues. This technique has been applied to detecting differences between normal and cancerous tissues in eukaryotes as well as genomic variability in microbial strains and species. The density of oligonucleotide probes available on current microarray platforms is particularly well-suited for comparisons of organisms with smaller genomes like bacteria and yeast where an entire genome can be assayed on a single microarray with high resolution. Available methods for analyzing these experiments typically confine analyses to data from pre-defined annotated genome features, such as entire genes. Many of these methods are ill suited for datasets with the number of measurements typical of high-density microarrays. RESULTS: We present an algorithm for analyzing microarray hybridization data to aid identification of regions that vary between an unsequenced genome and a sequenced reference genome. The program, CGHScan, uses an iterative random walk approach integrating multi-layered significance testing to detect these regions from comparative genomic hybridization data. The algorithm tolerates a high level of noise in measurements of individual probe intensities and is relatively insensitive to the choice of method for normalizing probe intensity values and identifying probes that differ between samples. When applied to comparative genomic hybridization data from a published experiment, CGHScan identified eight of nine known deletions in a Brucella ovis strain as compared to Brucella melitensis. The same result was obtained using two different normalization methods and two different scores to classify data for individual probes as representing conserved or variable genomic regions. The undetected region is a small (58 base pair) deletion that is below the resolution of CGHScan given the array design employed in the study. CONCLUSION: CGHScan is an effective tool for analyzing comparative genomic hybridization data from high-density microarrays. The algorithm is capable of accurately identifying known variable regions and is tolerant of high noise and varying methods of data preprocessing. Statistical analysis is used to define each variable region providing a robust and reliable method for rapid identification of genomic differences independent of annotated gene boundaries.

Algorithms↗
PubMed2006

Effect of gravity on the dynamics of nonequilibrium fluctuations in a free-diffusion experiment.

Diffusion is commonly believed to be a homogeneous process at the mesoscopic scale, being driven only by the random walk of fluid molecules. On the contrary, very large amplitude, long wavelength fluctuations always accompany diffusive processes. In the presence of gravity, fluctuations in a fluid containing a stabilizing gradient are affected by two different processes: diffusion, which relaxes them, and the buoyancy force, which quenches them. These phenomena affect both the overall amplitude of fluctuations and their time dependence. For the case of free diffusion, the time-correlation function of the concentration fluctuations is predicted to exhibit an exponential decay with correlation time depending on the wave vector q. For large wave vector fluctuations, diffusion dominates, and the correlation time is predicted to be 1 / (Dq2). For small wave vector fluctuations, gravitational forces have time to play a significant role, and the correlation time is predicted to be proportional to q2. The effects of gravity and diffusion are comparable for a critical wave vector q(c) determined by fluid properties and gravity. We have utilized a quantitative dynamic shadowgraph technique to obtain the temporal correlation function of a mixture of LUDOX(R) TMA and water undergoing free diffusion. This technique allows one to simultaneously measure correlation functions achieving good statistics for a number of different wave vectors in a single measurement. Wave vectors as small as 70 cm(-1) have been investigated, which is very difficult to achieve with ordinary dynamic light-scattering techniques. We present results on the transition from the diffusive decay of fluctuations to the regime in which gravity is dominant.

Journal Article↗
PubMed1997

Cytoplasmic assembly of microtubules in cultured cells.

The origin of non-centrosomal microtubules was investigated in a variety of animal cells in culture by means of time-lapse digital fluorescence microscopy. A previous study (Keating et al. (1997) Proc. Nat. Acad. Sci. USA 94, 5078-5083) demonstrated a pathway for formation of non-centrosomal microtubules by release from the centrosome. Here we show a parallel pathway not dependent upon the centrosome. Correlative immunostaining with anti-tubulin antibodies and electron microscopy established that apparent free microtubules observed in vivo were not growing ends of long stable microtubules. Free microtubules appeared spontaneously in the cytoplasm and occasionally by breakage of long microtubules. Estimates of the frequencies of free microtubule formation suggest that it can be a relatively common rather than exceptional event in PtK1 cells and may represent a significant source of non-centrosomal microtubules. The observation of free microtubules permitted analysis of the microtubule minus end. Unlike the plus end which showed dynamic instability, the minus end was stable or depolymerized. Breakage of long microtubules generated nascent plus and minus ends; the nascent minus end was generally stable while the plus end was always dynamic. The stability of microtubule minus ends in vivo apparently provides the necessary condition for free microtubule formation in the cytoplasm. Parameters of the dynamic instability of plus ends of free microtubules were similar to those for the distal ends of long microtubules, indicating that the free microtubules were not exceptional in their dynamic behavior. Random walk analysis of microtubule end dynamics gave apparent diffusion coefficients for free and long microtubules which permitted an estimate of turnover half-times. The results support the concept that, in PtK1 cells, a pathway other than plus end dynamics is needed to account for the rapidity of microtubule turnover.

Animals↗
PubMed2003

In vivo quantitative three-dimensional localization of tumor labeled with exogenous specific fluorescence markers.

We introduce a diffused optical detection system based on the administration of a fluorophore-antibody conjugate to diseased tissue. The conjugate interacts with the antigens expressed by the diseased tissue, resulting in fluorescent labeling of the antigen. By combining an optical detection system with a reconstruction algorithm developed on the basis of the random-walk model, we were able to determine the position of the fluorophore (and, thus, of the diseased cells) in the tissue. We present three-dimensional reconstructions of the location of a fluorophore (FITC-fluorescein isothiocyanate) in the tongues of mice. Measurements were performed with the fluorophore embedded at various simulated depths. The simulations were performed with agarose-based gel slabs applied to the tongue as tissuelike phantoms. Reconstructed fluorophore locations agree well with the actual values.

Algorithms↗
PubMed2005

Influence of fluorescence reabsorption and trapping on solid-state optical cooling.

We analyze the random process of fluorescence reabsorption and trapping in solid-state optical materials in general and its influence on the efficiency of optical cooling of solids by anti-Stokes fluorescence in particular. Using the absorption and fluorescence spectra of Yb3+:ZrF4-BaF2-LaF3-AlF3-NaF (ZBLAN) as input data, we employ a random-walk model to test analytical approximations of the fluorescence escape efficiency and cooling efficiency, including reflections at the boundary.

Journal Article↗
PubMed2006

Modeling low-coherence enhanced backscattering using Monte Carlo simulation.

Constructive interference between coherent waves traveling time-reversed paths in a random medium gives rise to the enhancement of light scattering observed in directions close to backscattering. This phenomenon is known as enhanced backscattering (EBS). According to diffusion theory, the angular width of an EBS cone is proportional to the ratio of the wavelength of light lambda to the transport mean-free-path length l(s)* of a random medium. In biological media a large l(s)* approximately 0.5-2 mm >> lambda results in an extremely small (approximately 0.001 degrees ) angular width of the EBS cone, making the experimental observation of such narrow peaks difficult. Recently, the feasibility of observing EBS under low spatial coherence illumination (spatial coherence length Lsc << l(s)*) was demonstrated. Low spatial coherence behaves as a spatial filter rejecting longer path lengths and thus resulting in an increase of more than 100 times in the angular width of low coherence EBS (LEBS) cones. However, a conventional diffusion approximation-based model of EBS has not been able to explain such a dramatic increase in LEBS width. We present a photon random walk model of LEBS by using Monte Carlo simulation to elucidate the mechanism accounting for the unprecedented broadening of the LEBS peaks. Typically, the exit angles of the scattered photons are not considered in modeling EBS in the diffusion regime. We show that small exit angles are highly sensitive to low-order scattering, which is crucial for accurate modeling of LEBS. Our results show that the predictions of the model are in excellent agreement with the experimental data.

Animals↗
PubMed2001

Analytical solutions for time-resolved fluorescence lifetime imaging in a turbid medium such as tissue.

An analytical solution is developed to quantify a site-specific fluorophore lifetime perturbation that occurs, for example, when the local metabolic status is different from that of surrounding tissue. This solution may be used when fluorophores are distributed throughout a highly turbid media and the site of interest is embedded many mean scattering distances from the source and the detector. The perturbation in lifetime is differentiated from photon transit delays by random walk theory. This analytical solution requires a priori knowledge of the tissue-scattering and absorption properties at the excitation and emission wavelengths that may be obtained from concurrent time-resolved reflection measurements. Additionally, the solution has been compared with the exact, numerically solved solution. Thus the presented solution forms the basis for practical lifetime imaging in turbid media such as tissue.

Biological Phenomena↗
PubMed2006

Photon diffusion coefficient in scattering and absorbing media.

We present a unified derivation of the photon diffusion coefficient for both steady-state and time-dependent transport in disordered absorbing media. The derivation is based on a modal analysis of the time-dependent radiative transfer equation. This approach confirms that the dynamic diffusion coefficient is given by the random-walk result D = cl(*)/3, where l(*) is the transport mean free path and c is the energy velocity, independent of the level of absorption. It also shows that the diffusion coefficient for steady-state transport, often used in biomedical optics, depends on absorption, in agreement with recent theoretical and experimental works. These two results resolve a recurrent controversy in light propagation and imaging in scattering media.

Absorption↗
PubMed2004

Quantitative optical imaging of the pharmacokinetics of fluorescent-specific antibodies to tumor markers through tissuelike turbid media.

Fluorescent optical imaging of tumors deep within tissue depends on specific binding of antibodies to the tumors' surface markers. These fluorescent antibodies propagating in the vicinity of the tumor can be attached to and (or) diffused away from it. We illustrate application of a new tool, based on the random-walk theory in turbid media, for extracting the pharmacokinetics of these fluorescent antibodies by data deconvolution, excluding the effect of upper turbid tissue layers.

Animals↗
PubMed2004

Experimental evaluation of an anisotropic scattering model of a slab geometry.

A model has been developed based on random walk theory that allows the diffusion of light along a principal axis to differ from that in orthogonal directions. We present expressions that describe the time-resolved intensity measured across a slab and on the surface of a semi-infinite medium for a principal axis oriented parallel or perpendicular to the surface. The model of time-resolved transmittance is compared with experimental data acquired by use of a phantom consisting of wax fibers arranged within a solid cube of resin. It is shown that a single set of optical parameters is sufficient to model the experimental measurements acquired across all three orientations of the cube.

Algorithms↗
PubMed2006

Noise-induced linewidth in frequency combs.

Frequency combs generated by trains of pulses emitted from mode-locked lasers are analyzed when the center time and phase of the pulses undergo noise-induced random walk, which broadens the comb lines. Asymptotic analysis and computation reveal that, when the standard deviation of the center-time jitter of the nth pulse scales as n(p/2) where p is a jitter exponent, the linewidth of the kth comb line scales as k(2/p). The linear-dispersionless (p=1) and pure-soliton (p=3) dynamics in lasers are derived as special cases of this time-frequency duality relation. In addition, the linewidth induced by phase jitter decreases with power P(out), as (P(out))(-1/p).

Journal Article↗
PubMed2005

Parsing a cognitive task: a characterization of the mind's bottleneck.

Parsing a mental operation into components, characterizing the parallel or serial nature of this flow, and understanding what each process ultimately contributes to response time are fundamental questions in cognitive neuroscience. Here we show how a simple theoretical model leads to an extended set of predictions concerning the distribution of response time and its alteration by simultaneous performance of another task. The model provides a synthesis of psychological refractory period and random-walk models of response time. It merely assumes that a task consists of three consecutive stages-perception, decision based on noisy integration of evidence, and response-and that the perceptual and motor stages can operate simultaneously with stages of another task, while the central decision process constitutes a bottleneck. We designed a number-comparison task that provided a thorough test of the model by allowing independent variations in number notation, numerical distance, response complexity, and temporal asynchrony relative to an interfering probe task of tone discrimination. The results revealed a parsing of the comparison task in which each variable affects only one stage. Numerical distance affects the integration process, which is the only step that cannot proceed in parallel and has a major contribution to response time variability. The other stages, mapping the numeral to an internal quantity and executing the motor response, can be carried out in parallel with another task. Changing the duration of these processes has no significant effect on the variance.

Acoustic Stimulation↗
PubMed2005

Directed migration of positively selected thymocytes visualized in real time.

Development of many vertebrate tissues involves long-range cell migrations. In most cases, these migrations have been inferred from analysis of single time points and the migration process has not been directly observed and quantitated in real time. In the mammalian adult thymus, immature CD4+ CD8+ double-positive (DP) thymocytes are found in the outer cortex, whereas after T cell antigen receptor (TCR) repertoire selection, CD4+ CD8- and CD4- CD8+ single-positive (SP) thymocytes are found in the central medulla. Here we have used two-photon laser-scanning microscopy and quantitative analysis of four-dimensional cell migration data to investigate the movement of thymocytes through the cortex in real time within intact thymic lobes. We show that prior to positive selection, cortical thymocytes exhibit random walk migration. In contrast, positive selection is correlated with the appearance of a thymocyte population displaying rapid, directed migration toward the medulla. These studies provide our first glimpse into the dynamics of developmentally programmed, long-range cell migration in the mammalian thymus.

Animals↗
PubMed2000

Regulation of quantal size by presynaptic mechanisms.

Quantal size is often modeled as invariant, although it is now well established that the number of transmitter molecules released per synaptic vesicle during exocytosis can be modulated in central and peripheral synapses. In this review, we suggest why presynaptically altered quantal size would be important at social synapses that provide extrasynaptic neurotransmitter. Current techniques used to measure quantal size are reviewed with particular attention to amperometry, the first approach to provide direct measurement of the number of molecules and kinetics of presynaptic quantal release, and to CNS dopamine neuronal terminals. The known interventions that alter quantal size at the presynaptic locus are reviewed and categorized as (1) alteration of transvesicular free energy gradients, (2) modulation of vesicle transmitter transporter activity, (3) modulation of fusion pore kinetics, (4) altered transmitter degranulation, and (5) changes in synaptic vesicle volume. Modulation of the number of molecules released per quantum underlies mechanisms of drug action of L-DOPA and the amphetamines, and seems likely to be involved in both normal synaptic modification and disease states. Statistical analysis for examining quantal size and data presentation is discussed. We include detailed information on performing nonparametric resampling statistical analysis, the Kolmogorov-Smirnov test for two populations, and random walk simulations using spreadsheet programs.

Animals↗
PubMedDate not supplied

Chemokinesis and necrotaxis of human granulocytes: the important cellular organelles.

The directed and non-directed locomotion of human polymorphonuclear leukocytes on a glass surface was compared to Brownian and drift motion. The average track velocity was measured under different conditions. The track velocity of colchicine treated cells was the same as control cells. However, cytochalasin B treated cells and cytokineplasts had a reduced track velocity compared with the control cells. The non-directed locomotion was investigated by measuring the mean square displacement as a function of time. The diffusion constant, D, which quantitates the random walk process, and the characteristic time, tau, which governs the migration of the cell, was calculated. The value of the diffusion constant depended on the cell treatment: For control cells 261 micron2/min, for colchicine treated cells 145 micron2/min, for cytochalasin B treated cells 55 micron2/min, and for cytokineplasts 47 micron2/min. The characteristic time was about 40 s. The measurement showed that the nondirected locomotion can be described by the Brownian motion. The directed locomotion was investigated by a necrotactic assay and quantitated by the McCutcheon index. This index was for control cells 0.85 +/- 0.07, for colchicine treated cells 0.8 +/- 0.07, and for cytokineplasts 0.75 +/- 0.1. The measurement showed that the directed locomotion can be described by a process which is called drift mode. From this method of analysis it was determined that the important organelles of the cell for the directed and the non-directed locomotion are: (i) A part of the plasma membrane, (ii) the microfilaments, and (iii) an unstructurated part of the cytoplasme. The microtubules of the cell are only of minor importance for the directed and the non-directed locomotion.

Cell Movement↗
PubMed2006

Non-Gaussian membrane potential dynamics imply sparse, synchronous activity in auditory cortex.

Many models of cortical dynamics have focused on the high-firing regime, in which neurons are driven near their maximal rate. Here we consider the responses of neurons in auditory cortex under typical low-firing rate conditions, when stimuli have not been optimized to drive neurons maximally. We used whole-cell patch-clamp recording in vivo to measure subthreshold membrane potential fluctuations in rat primary auditory cortex in both the anesthetized and awake preparations. By analyzing the subthreshold membrane potential dynamics on single trials, we made inferences about the underlying population activity. We found that, during both spontaneous and evoked responses, membrane potential was highly non-Gaussian, with dynamics consisting of occasional large excursions (sometimes tens of millivolts), much larger than the small fluctuations predicted by most random walk models that predict a Gaussian distribution of membrane potential. Thus, presynaptic inputs under these conditions are organized into quiescent periods punctuated by brief highly synchronous volleys, or "bumps." These bumps were typically so brief that they could not be well characterized as "up states" or "down states." We estimate that hundreds, perhaps thousands, of presynaptic neurons participate in the largest volleys. These dynamics suggest a computational scheme in which spike timing is controlled by concerted firing among input neurons rather than by small fluctuations in a sea of background activity.

Acoustic Stimulation↗