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At least 1,423 records · Page 79Linked to original sources
PubMed1998

Cortical granule exocytosis is triggered by different thresholds of calcium during fertilisation in sea urchin eggs.

In sea urchin eggs, fertilisation is followed by a calcium wave, cortical granule exocytosis and fertilisation envelope elevation. Both the calcium wave and cortical granule exocytosis sweep across the egg in a wave initiated at the point of sperm entry. Using differential interference contrast (DIC) microscopy combined with laser scanning confocal microscopy, populations of cortical granules undergoing calcium-induced exocytosis were observed in living urchin eggs. Calcium imaging using the indicator Calcium Green-dextran was combined with an image subtraction technique for visual isolation of individual exocytotic events. Relative fluorescence levels of the calcium indicator during the fertilisation wave were compared with cortical fusion events. In localised regions of the egg, there is a 6s delay between the detection of calcium release and fusion of cortical granules. The rate of calcium accumulation was altered experimentally to ask whether this delay was necessary to achieve a threshold concentration of calcium to trigger fusion, or was a time-dependent activation of the cortical granule fusion apparatus after the 'triggering' event. Calcium release rate was attenuated by blocking inositol 1,4,5-triphospate (InsP3)-gated channels with heparin. Heparin extended the time necessary to achieve a minimum concentration of calcium at the sites of cortical granule exocytosis. The data are consistent with the conclusion that much of the delay observed normally is necessary to reach threshold concentration of calcium. Cortical granules then fuse with the plasma membrane. Further, once the minimum threshold calcium concentration is reached, cortical granule fusion with the plasma membrane occurs in a pattern suggesting that cortical granules are non-uniform in their calcium sensitivity threshold.

Animals↗
PubMed1998

Robust parameter estimation of intensity distributions for brain magnetic resonance images.

This paper presents two new methods for robust parameter estimation of mixtures in the context of magnetic resonance (MR) data segmentation. The head is constituted of different types of tissue that can be modeled by a finite mixture of multivariate Gaussian distributions. Our goal is to estimate accurately the statistics of desired tissues in presence of other ones of lesser interest. These latter can be considered as outliers and can severely bias the estimates of the former. For this purpose, we introduce a first method, which is an extension of the expectation-maximization (EM) algorithm, that estimates parameters of Gaussian mixtures but incorporates an outlier rejection scheme which allows to compute the properties of the desired tissues in presence of atypical data. The second method is based on genetic algorithms and is well suited for estimating the parameters of mixtures of different kind of distributions. We use this property by adding a uniform distribution to the Gaussian mixture for modeling the outliers. The proposed genetic algorithm can efficiently estimate the parameters of this extended mixture for various initial settings. Also, by changing the minimization criterion, estimates of the parameters can be obtained by histogram fitting which considerably reduces the computational cost. Experiments on synthetic and real MR data show that accurate estimates of the gray and white matters parameters are computed.

Adolescent↗
PubMed2005

Noisy text categorization.

This work presents categorization experiments performed over noisy texts. By noisy, we mean any text obtained through an extraction process (affected by errors) from media other than digital texts (e.g., transcriptions of speech recordings extracted with a recognition system). The performance of a categorization system over the clean and noisy (Word Error Rate between approximately 10 and approximately 50 percent) versions of the same documents is compared. The noisy texts are obtained through handwriting recognition and simulation of optical character recognition. The results show that the performance loss is acceptable for Recall values up to 60-70 percent depending on the noise sources. New measures of the extraction process performance, allowing a better explanation of the categorization results, are proposed.

Algorithms↗
PubMed2002

Analytical study on bioheat transfer problems with spatial or transient heating on skin surface or inside biological bodies.

Several closed form analytical solutions to the bioheat transfer problems with space or transient heating on skin surface or inside biological bodies were obtained using Green's function method. The solutions were applied to study several selected typical bioheat transfer processes, which are often encountered in cancer hyperthermia, laser surgery, thermal comfort analysis, and tissue thermal parameter estimation. Thus a straightforward way to quantitatively interpret the temperature behavior of living tissues subject to constant, sinusoidal, step, point or stochastic heatings etc. both in volume and on boundary were established. Further solution to the three-dimensional bioheat transfer problems was also given to illustrate the versatility of the present method. Implementations of this study to the practical problems were addressed.

Body Temperature↗
PubMed2000

A self-consistent cell flux expression for simultaneous chemotaxis and contact guidance in tissues.

During wound healing, both chemotaxis and contact guidance can contribute to the migration of blood and tissue cells to the wound. In order to understand the wound healing process, we must thus understand how cells respond to both these simultaneous directional cues, which are not necessarily coaligned. Although chemotaxis and contact guidance have been studied individually, the interaction between them has not been addressed. We extend a stochastic cell movement model, developed by Dickinson and Tranquillo (1995) [6] for individual cues, for simultaneous chemotaxis and contact guidance by a two-parameter perturbation analysis in terms of the two associated cues, a chemotactic factor gradient and aligned tissue fibers. We present results from analysis of the first-order perturbation, which includes the cell flux expression heuristically proposed by others, but reveals paradoxical results for other indices of cell movement, such as the mean-squared displacement. We then present second-order perturbation results that resolve these paradoxical results. Finally, we relate these results to a continuum mechanical model developed by Barocas and Tranquillo (1997) [3] that predicts fiber alignment due to cell traction induced tissue contraction.

Animals↗
PubMed1991

Thymic selection in CD8 transgenic mice supports an instructive model for commitment to a CD4 or CD8 lineage.

Immature thymocytes, which coexpress CD4 and CD8, give rise to mature CD4+CD8- and CD4-CD8+ T cells. Only those T cells that recognize self-MHC are selected to mature, a process known as positive selection. The specificity of the T cell antigen receptor (TCR) for class I or class II MHC influences the commitment to a CD4 or CD8 lineage. This may occur by a directed mechanism or by stochastic commitment followed by a selection step that allows only CD8+, class I-specific and CD4+, class II-specific cells to survive. We have generated a mouse line expressing a CD8 transgene under the control of the T cell-specific CD2 regulatory sequences. Although constitutive CD8 expression does not affect thymic selection of CD4+ cells, selection of a class I-specific TCR in the CD8 subset is substantially improved. This outcome is consistent with a model for positive selection in which selection occurs at a developmental stage in which both CD4 and CD8 are expressed, and positive selection by class I MHC generates an instructive signal that directs differentiation to a CD8 lineage.

Animals↗
PubMed1996

Statistical properties of breath-to-breath variations in ventilation at constant PETCO2 and PETO2 in humans.

The purpose of this study was to provide a statistical description of the breath-to-breath variations in ventilation during steady breathing in both rest and during light exercise, with the end-tidal gases controlled by using an end-tidal forcing system. Sixty data sets were studied, only one of which was white (i.e., did not show autocorrelation). Three simple autoregressive moving average (ARMA) models, i.e., AR1, AR2, and AR1MA1, and one simple state-space model were fitted to the data and resulted in white residuals in 15, 31, 46, and 48 out of 60 occasions, respectively. Evolutionary spectral analysis revealed that only 13 data sets had a constant power spectrum, although 50 were uniformly modulated. An autoregressive estimate of variance could be used to "demodulate" the data in most cases, but the results were not significantly affected by fitting the model to the demodulated data. The results indicate that 1) both simple ARMA models and a simple state-space model can describe the autocorrelation present; 2) variations in spectral power were present in the data that cannot be described by these models; and 3) these variations were often due to a uniform modulation and did not significantly affect the coefficients for the models. For these kinds of data, a heteroscedastic form of state-space model provides an attractive theoretical structure for the noise processes.

Air Pressure↗
PubMed2001

Looking beyond selection probabilities: adaptation of the chi(2) measure for the performance analysis of selection methods in GAs.

Viewing the selection process in a genetic algorithm as a two-step procedure consisting of the assignment of selection probabilities and the sampling according to this distribution, we employ the chi(2) measure as a tool for the analysis of the stochastic properties of the sampling. We are thereby able to compare different selection schemes even in the case that their probability distributions coincide. Introducing a new sampling algorithm with adjustable accuracy and employing two-level test designs enables us to further reveal the intrinsic correlation structures of well-known sampling algorithms. Our methods apply well to integral methods like tournament selection and can be automated.

Algorithms↗
PubMed1997

A quantum accounting and detective quantum efficiency analysis for video-based portal imaging.

The quality of images generated with radiographic imaging systems can be degraded if an inadequate number of secondary quanta are used at any stage before production of the final image. A theoretical technique known as a "quantum accounting diagram" (QAD) analysis has been developed recently to predict the detective quantum efficiency (DQE) of an imaging system as a function of spatial frequency based on an analysis of the propagation of quanta. It is used to determine the "quantum sink" stage(s) (stages which degrade the DQE of an imaging system due to quantum noise caused by a finite number of quanta), and to suggest design improvements to maximize image quality. We have used this QAD analysis to evaluate a video-based portal imaging system to determine where changes in design will have the most benefit. The system consists of a thick phosphor layer bonded to a 1 mm thick copper plate which is viewed by a T.V. camera. The imaging system has been modeled as ten cascaded stages, including: (i) conversion of x-ray quanta to light quanta; (ii) collection of light by a lens; (iii) detection of light quanta by a T.V. camera; (iv) the various blurring processes involved with each component of the imaging system; and, (v) addition of noise from the T.V. camera. The theoretical DQE obtained with the QAD analysis is in excellent agreement with the experimental DQE determined from previously published data. It is shown that the DQE is degraded at low spatial frequencies (< 0.25 cycles/mm) by quantum sinks both in the number of detected x rays and the number of detected optical quanta. At higher spatial frequencies, the optical quantum sink becomes the limiting factor in image quality. The secondary quantum sinks can be prevented, up to a spatial frequency of 0.5 cycles/mm, by increasing the overall system gain by a factor of 9 or more, or by improving the modulation transfer function (MTF) of components in the optical chain.

Biophysical Phenomena↗
PubMed1976

Analysis of intercellular distributions of chromatid aberrations.

59 intercellular distributions of chemically induced and spontaneous chromatid aberrations were analyzed for goodness of fit in respect of the Poisson (PD), the geometrical (GD), and the negative binomial distributions (NBD). The data are excellently described by the NBD. This distribution can be deduced from a model out of the queueing theory and is based on the hypothesis of restitution. Estimators are obtained for the ratio of restitution and induction processes involved in the origin of chromosomal aberrations.

Alkylating Agents↗
PubMed1992

Forecasting health: data needs and implications for model structure.

An agenda for analysing data on the health and functioning of the elderly must indicate new types of data to be collected, innovations in data collection strategies and new methods for analysis and forecasting. The required research agenda is broad and will require inputs from investigators in a number of disciplines. The data and methods required will need to be developed in order to reflect national, regional and local variations in the health phenomena under study; they will also have to be responsive to these variations. In the end, however, if the investment is to be most useful, it must be integrated into simulation and forecasting models, the mechanics of which are based on individual-level processes and not on the elements of the service system.

Breast Neoplasms↗
PubMed1998

Estimating the transmission rate for a highly infectious disease.

It is pointed out that estimates of disease transmission parameters based on the final size of an epidemic are unsatisfactory when all susceptibles are infected and that this is an event with a substantial probability for communities of practical interest. We propose a method for estimating the transmission rate for such highly infectious diseases under the assumptions that the removal process of the disease is fully observed and that the mean duration of the infectious period is known. The method uses smoothed differentiation of the removal process. A simulation study shows that the method performs satisfactorily.

Communicable Diseases↗
PubMed1995

Dynamics of fibroblast spreading.

A new technique of microinterferometry permits cellular growth and motile dynamics to be studied simultaneously in living cells. In isolated chick heart fibroblasts, we have found that the non-aqueous mass of each cell tends to increase steadily, with minor fluctuations, throughout the cell cycle. The spread area of each cell also tends to increase during interphase but fluctuates between wide limits. These limits are dependent on the cell's mass and the upper limit is particularly sharp and directly proportional to mass. From a dynamical point of view, the spread area of a cell is determined by the balance between the rates of two antagonistic processes: protrusion of cellular material into new territory and retraction of material from previously occupied territory. The spatial asymmetry of these processes determines the translocation of the cell. We have found with the chick fibroblasts that the rates of the two processes are generally closely matched to each other and appear to be dependent on the cell's area of spreading. Both continue incessantly in well spread cells, even when there is no net translocation of the cell, and the lower limit of each activity is directly proportional to spread area. The two processes show different behaviour, however, during changes in the spread area of the cell. Both increases and decreases in area appear to be brought about by changes in the rate of retraction, the rate of protrusion remaining relatively constant. A simple stochastic model based on a limited supply of adhesion molecules can simulate all our observations including the mass-limited spreading, the strong correlation between protrusion and retraction and the retraction-dominated changes in area. We conclude that the spread area of the cell is actively regulated, possibly by a simple automatic mechanism that adjusts the area of spreading in relation to the mass of the cell and controls the rate of protrusion to compensate rapidly for spontaneous fluctuations in retraction.

Animals↗
PubMed2002

Quantitative analyses of anaerobic wastewater treatment processes: identifiability and parameter estimation.

We investigated the problem of identifying the parameters of a nonlinear fifth order model describing the population dynamics of two main bacterial groups in an anaerobic wastewater treatment process. In addition to addressing problems concerning structural and practical identifiability, we also analyzed how mathematical descriptions of bacterial population dynamics can model real data. Using three data sets recorded under different experimental conditions, we estimated important biochemical parameters and demonstrated that our model could describe the data successfully. Parameters, which are simultaneously determined using information from all three experiments, have more reliable estimates. We conclude that, after appropriate estimation, this model can be used for optimization and the control of continuous processes.

Anaerobiosis↗
PubMed1991

Synaptic noise in spike trains of normal and denervated electroreceptor organs.

The sequence of interspike intervals of the spontaneous activity in denervated electroreceptor organs of the catfish is analysed with several statistical techniques: visual inspection of dot displays, interval histograms, serial correlograms, tests for stationary and trends, and tests for renewal properties, based on the spectrum of intervals. The interspike interval train of primary afferents can usually be treated as a renewal process. Following denervation, a number of non-renewal properties emerge. The interval histogram of the renewal spike trains can be fitted well with a gamma probability density function; non-renewal cases need a more complex approach. We propose that the stochastic fluctuations in interval duration arise from randomly occurring quantal depolarizations (Stein's model of stochastic neuronal excitations. Two important properties with regard to synaptic transduction are: afferent firing results from capture of a limited number of depolarizing quanta; and the quantal input rate and the threshold for firing appear to be correlated.

Afferent Pathways↗
PubMed1999

The role of extreme events in the impacts of selective tropical forestry on erosion during harvesting and recovery phases at Danum Valley, Sabah.

Ten years' hydrological investigations at Danum have provided strong evidence of the effects of extremes of drought, as in the April 1992 El Niño southern oscillation event, and flood, as in January 1996. The 1.5 km2 undisturbed forest control catchment experienced a complete drying out of the stream for the whole 1.5 km of defined channel above the gauging station in 1992, but concentrated surface flow along every declivity from within a few metres of the catchment divide after the exceptional rains of 19 January 1996. Under these natural conditions, erosion is episodic. Sediment is discharged in pulses caused by storm events, collapse of debris dams and occasional landslips. Disturbance by logging accentuates this irregular regime. In the first few months following disturbance, a wave of sediment is moved by each storm, but over subsequent years, rare events scour sediment from bare areas, gullies and channel deposits. The spatial distribution of sediment sources changes with time after logging, as bare areas on slopes are revegetated and small gullies are filled with debris. Extreme storm events, as in January 1996, cause logging roads to collapse, with landslides leading to surges of sediment into channels, reactivating the pulsed sediment delivery by every storm that happened immediately after logging. These effects are not dampened out with increasing catchment scale. Even the 721 km2 Sungai Segama has a sediment yield regime dominated by extreme events, the sediment yield in that single day on 19 January 1996 exceeding the annual sediment load in several previous years. In a large disturbed catchment, such road failures and logging-activity-induced mass movements increase the mud and silt in floodwaters affecting settlements downstream. Management systems require long-term sediment reduction strategies. This implies careful road design and good water movement regulation and erosion control throughout the logging process.

Ecosystem↗
PubMed2005

Sampling rare switching events in biochemical networks.

Bistable biochemical switches are widely found in gene regulatory networks and signal transduction pathways. Their switching dynamics are difficult to study, however, because switching events are rare, and the systems are out of equilibrium. We present a simulation method for predicting the rate and mechanism of the flipping of these switches. We apply it to a genetic switch and find that it is highly efficient. The path ensembles for the forward and reverse processes do not coincide. The method is widely applicable to rare events and nonequilibrium processes.

Bacteriophage lambda↗