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At least 811 records · Page 45Linked to original sources
PubMed2004

Adaptive denoising of event-related functional magnetic resonance imaging data using spectral subtraction.

A new adaptive signal-preserving technique for noise suppression in event-related functional magnetic resonance imaging (fMRI) data is proposed based on spectral subtraction. The proposed technique estimates a parametric model for the power spectrum of random noise from the acquired data based on the characteristics of the Rician statistical model. This model is subsequently used to estimate a noise-suppressed power spectrum for any given pixel time course by simple subtraction of power spectra. The new technique is tested using computer simulations and real data from event-related fMRI experiments. The results show the potential of the new technique in suppressing noise while preserving the other deterministic components in the signal. Moreover, we demonstrate that further analysis using principal component analysis and independent component analysis shows a significant improvement in both convergence and clarity of results when the new technique is used. Given its simple form, the new method does not change the statistical characteristics of the signal or cause correlated noise to be present in the processed signal. This suggests the value of the new technique as a useful preprocessing step for fMRI data analysis.

Algorithms↗
PubMed2000

Stochastic variation in food availability influences weight and age at maturity.

Variation in mean food availability, and in the variance around the mean, affects the growth rate during development. Previous theoretical work on the influence of environmental quality or growth rates on the phenotypic traits age and size at maturation assumed that there is no variation in growth rate or food availability within a generation. We develop a stochastic dynamic programming (SDP) model of the foraging behaviour of aphidophagous syrphids, and use this model to predict when syrphids should pupate (mature) when average food availability changes, or varies stochastically, during development. The optimal strategy takes into account not only the availability of food, but also the timing of its availability. Food availability, when small, influences developmental time, but not weight at pupation. Food availability, when large, influences weight at pupation, but not developmental time. When the food supply is low, the optimal strategy adjusts the size at pupation downwards for stochastic as opposed to deterministic availability of food. The conclusions reinforce the need for life-history studies to consider state dependence and short-term variability in growth rates.

Animals↗
PubMed1999

Some state space models of HIV pathogenesis under treatment by anti-viral drugs in HIV-infected individuals.

In this paper we have extended the model of HIV pathogenesis under treatment by anti-viral drugs given by Perelson et al. [A.S. Perelson et al., Science 271 (1999) 1582] to a stochastic model. By using this stochastic model as the stochastic system model, we have developed a state space model for the HIV pathogenesis under treatment by anti-viral drugs. In this state space model, the observation model is a statistical model based on the observed numbers of RNA virus copies over different times. For this model we have developed procedures for estimating and predicting the numbers of infectious free HIV and non-infectious free HIV as well as the numbers of different types of T cells through extended Kalman filter method. As an illustration, we have applied the method of this paper to the data of patient Nos. 104, 105 and 107 given by Perelson et al. [A.S. Perelson et al., Science 271 (1999) 1582] under treatment by Ritonavir. For these individuals, it is shown that within two weeks since treatment, most of the free HIV are non-infectious, indicating the usefulness of the treatment. Furthermore, the Kalman filter method revealed a much stronger effect of the treatment within the first 10 to 20 h than that predicted by the deterministic model.

CD4 Lymphocyte Count↗
PubMed2003

Modeling biological systems using Dynetica--a simulator of dynamic networks.

UNLABELLED: We present Dynetica, a user-friendly simulator of dynamic networks for constructing, visualizing, and analyzing kinetic models of biological systems. In addition to generic reaction networks, Dynetica facilitates construction of models of genetic networks, where many reactions are gene expression and interactions among gene products. Further, it integrates the capability of conducting both deterministic and stochastic simulations. AVAILABILITY AND SUPPLEMENTARY INFORMATION: Dynetica 1.0, example models, and the user's guide are available at http://www.its.caltech.edu/~you/Dynetica/Dynetica_page.htm

Algorithms↗
PubMed2002

A method for determinism in short time series, and its application to stationary EEG.

A novel method for detecting determinism in short time series is developed and applied to investigate determinism in stationary electroencephalogram (EEG) recordings. This method is based on the observation that the trajectory of a time series generated from a differentiable dynamical system behaves smoothly in an embedded state space. The angles between two successive tangent vectors in the trajectory reconstructed from the time series is calculated as a function of time. The irregularity of the angle variations obtained from the time series is estimated using second-order difference plots, and compared with that of the corresponding surrogate data. Using this method, we demonstrate that scalp EEG recordings from normal subjects do not exhibit a low-dimensional deterministic structure. This method can be useful for analyzing determinism in short time series, such as those from physiological recordings.

Adult↗
PubMed2002

Adult patient doses in interventional neuroradiology.

We investigated radiation doses to 149 adult patients who underwent interventional neuroradiologic procedures, consisting of 132 patients who had diagnostic imaging examinations and 17 patients who had therapeutic procedures. The interventional procedures were carried out on a biplane system capable of performing fluoroscopy and digital subtraction angiography (DSA). The x-ray imaging system was interfaced to a patient dosimetry system, which computed surface (skin) doses based on the selected radiographic technique factors in each of the radiographic and fluoroscopic imaging modes. For each patient, an assessment was made of the maximum surface dose received during the procedure, which predicts the possibility of inducing deterministic effects. Knowledge of the surface doses, beam quality and x-ray cross sectional area permitted the computation of the total energy imparted to each patient. Energy imparted values were converted to effective dose, which provides an estimate of the stochastic radiation risk to the patient. The median surface dose for the frontal plane during diagnostic imaging examinations was 1.3 Gy, with a maximum surface dose of 5.1 Gy. The median surface dose for the frontal plane during therapeutic procedures was 2.8 Gy with a maximum surface dose of 5.0 Gy. Ratios of the lateral to frontal median surface doses were 0.47 for diagnostic examinations and 0.68 for interventional procedures. The median energy imparted was 1.8 J during fluoroscopy, and 4.3 J during radiography, showing that on average, 66% of the patient exposure comes from radiographic imaging (DSA). For diagnostic examinations, the median patient effective dose was 33 mSv, with a maximum of 152 mSv. For therapeutic procedures, the median patient effective dose was 74 mSv, with a maximum of 156 mSv. In interventional neuroradiology, surface doses could induce deterministic effects, and the corresponding effective doses are noticeably higher than those normally encountered in diagnostic radiology.

Adult↗
PubMed1986

[Case studies of the use of the locally adjusted polynomial regression].

Firstly the operation mode of the procedures of local adjusted polynomial regression is explained by an artificial example of data. After that, the properties of these nonparametric estimation procedures of unknown continuous functions from measured data are demonstrated by some examples arising in experimental examinations. Especially the aspect is discussed how far the main task of separating the deterministic component from the random one in the course of measured values may be fulfilled by using different degrees of polynomials in connection with different values of the smoothing parameter.

Biometry↗
PubMed2005

A deterministic model of growth factor-induced angiogenesis.

Understanding the formation and structure of a capillary network is critical for any reparative strategy since the capillary network dictates tissue survival, hemodynamics, and mass transport. Vascular assembly and patterning has largely been studied using a reductionist approach where a particular endothelial cell molecular pathway or cellular mechanism is investigated as a relatively closed system. This trend of research has yielded a staggering wealth of genes, proteins, and cells that play critical roles in angiogenesis and some have resulted in successful targeted angiogenic therapies. However, these genes, proteins, and cells do not exist in discrete closed systems, rather they are intimately coupled across spatial and temporal dimensions. Designing experiments to study a single or group of perturbations is fraught with confounding complications. An integrative tool is required that incorporates gene, protein, and cell information and appropriately describes the complex systems behavior of vascular assembly and patterning. In this paper, we propose a new deterministic mathematical formulation to model growth factor-induced angiogenesis. Conductivity of the extracellular matrix for the movement/extension of capillary sprouts is a new concept introduced to account for the heterogeneity and anisotropy of the extracellular matrix. The replacement of traditional endothelial cell density by the capillary indicator function enhances the capabilities of capturing the capillary network sharply in a fine scale (i.e., tracking the dynamics of the tip in uni-cellular scale). Major mechanisms including cell proliferation, sprout branching, and anastomosis are incorporated directly into this continuous mathematical model and model parameters are perturbed to determine the strength of their effect on angiogenesis. The model is fully deterministic and generates the overall dendritic structure of the capillary network morphologically similar to those observed in vivo. The simulations "capture" significant vascular patterning, such as vascular loops and backward growth. Moreover, the simulations provide a deeper understanding of the influence of extracellular matrix on angiogenesis and vascular patterning. An advantage of this model is that the complex physical, chemical and biological processes in angiogenesis can be described and consequently analyzed by a mathematical system with self-contained information.

Animals↗
PubMed2006

Links between annual, Milankovitch and continuum temperature variability.

Climate variability exists at all timescales-and climatic processes are intimately coupled, so that understanding variability at any one timescale requires some understanding of the whole. Records of the Earth's surface temperature illustrate this interdependence, having a continuum of variability following a power-law scaling. But although specific modes of interannual variability are relatively well understood, the general controls on continuum variability are uncertain and usually described as purely stochastic processes. Here we show that power-law relationships of surface temperature variability scale with annual and Milankovitch-period (23,000- and 41,000-year) cycles. The annual cycle corresponds to scaling at monthly to decadal periods, while millennial and longer periods are tied to the Milankovitch cycles. Thus the annual, Milankovitch and continuum temperature variability together represent the response to deterministic insolation forcing. The identification of a deterministic control on the continuum provides insight into the mechanisms governing interannual and longer-period climate variability.

Journal Article↗
PubMed1996

Poisson-distributed active fusion complexes underlie the control of the rate and extent of exocytosis by calcium.

We have investigated the consequences of having multiple fusion complexes on exocytotic granules, and have identified a new principle for interpreting the calcium dependence of calcium-triggered exocytosis. Strikingly different physiological responses to calcium are expected when active fusion complexes are distributed between granules in a deterministic or probabilistic manner. We have modeled these differences, and compared them with the calcium dependence of sea urchin egg cortical granule exocytosis. From the calcium dependence of cortical granule exocytosis, and from the exposure time and concentration dependence of N-ethylmaleimide inhibition, we determined that cortical granules do have spare active fusion complexes that are randomly distributed as a Poisson process among the population of granules. At high calcium concentrations, docking sites have on average nine active fusion complexes.

Animals↗
PubMed2003

Fingerprints of determinism in an apparently stochastic corrosion process.

We detect hints of determinism in an apparently stochastic corrosion problem. This experimental system has industrial relevance as it mimics the corrosion processes of pipelines transporting water, hydrocarbons, or other fuels to remote destinations. We subject this autonomous system to external periodic perturbations. Keeping the amplitude of the superimposed perturbations constant and varying the frequency, the system's response is analyzed. It reveals the presence of an optimal forcing frequency for which maximal response is achieved. These results are consistent with those for a deterministic system and indicate a classical resonance between the forcing signal and the autonomous dynamics. Numerical studies using a generic corrosion model are carried out to complement the experimental findings.

Journal Article↗
PubMed1999

From the contraceptive to the anthropocentric revolution (Gregory Pincus in memoriam).

The author has seen more progress in science and technology than all scientists of all preceding periods together since the dawn of history and has witnessed a number of powerful revolutions (e.g. scientific, information, postindustrial, globalization, environmental, contraceptive, reproductive health, gender equity and demographic) that have profoundly changed the world and our perception of it. The contraceptive revolution started off this irreversible process with spectacular results. By 1990, contraception had become a global lifestyle for more than 900 million couples. It also resulted in subsequent revolutions in reproductive health and gender equity in a new world with a dramatically changed population structure with fewer and fewer children and more and more elderly. These revolutions will assist humankind in the 21st century in deconstructing the deterministic world view of past centuries and replacing it with a science-driven anthropocentric world view.

Contraception↗
PubMed2003

On the role of stochastic channel behavior in intracellular Ca2+ dynamics.

I present a stochastic model for intracellular Ca(2+) oscillations. The model starts from stochastic binding and dissociation of Ca(2+) to binding sites on a single subunit of the IP(3)-receptor channel but is capable of simulating large numbers of clusters for many oscillation periods too. I find oscillations with variable periods ranging from 17 s to 120 s and a standard deviation well in the experimentally observed range. Long period oscillations can be perceived as nucleation phenomenon and can be observed for a large variety of single channel dynamics. Their period depends on the geometric characteristics of the cluster array. Short periods are in the range of the time scale of channel dynamics. Both long and short period oscillations occur for parameters with a nonoscillatory deterministic regime.

Buffers↗
PubMed1994

Stochastic versus deterministic variability in simple neuronal circuits: I. Monosynaptic spinal cord reflexes.

Long time series of monosynaptic Ia-afferent to alpha-motoneuron reflexes were recorded in the L7 or S1 ventral roots in the cat. Time series were collected before and after spinalization at T13 during constant amplitude stimulations of group Ia muscle afferents in the triceps surae muscle nerves. Using autocorrelation to analyze the linear correlation in the time series demonstrated oscillations in the decerebrate state (4/4) that were eliminated after spinalization (5/5). Three tests for determinism were applied to these series: 1) local flow, 2) local dispersion, and 3) nonlinear prediction. These algorithms were validated with time series generated from known deterministic equations. For each experimental and theoretical time series used, matched time-series of stochastic surrogate data were generated to serve as mathematical and statistical controls. Two of the time series collected in the decerebrate state (2/4) demonstrated evidence for deterministic structure. This structure could not be accounted for by the autocorrelation in the data, and was abolished following spinalization. None of the time series collected in the spinalized state (0/5) demonstrated evidence of determinism. Although monosynaptic reflex variability is generally stochastic in the spinalized state, this simple driven system may display deterministic behavior in the decerebrate state.

Afferent Pathways↗
PubMed2000

Adaptative effects of loss of vision on upright undisturbed stance.

In order to evaluate the long term effect of blindness on an undisturbed postural task, seven blind individuals (BLI) were compared to twelve healthy individuals (REF) who were required to close their eyes. To this aim, centre of pressure (CP) trajectories were recorded through a force platform on which the subjects remained upright. Through a low-pass filter, the vertical projection of the centre of gravity (CG(v)) and consequently the difference CP-CG(v) were estimated. The former represents the controlled variable whilst the latter is assumed to express the resultant joint stiffness. A first analysis consisted in studying the frequency distribution of these motions. Increased mean amplitudes in both elementary motions and no difference between frequency distributions were observed for the BLI when compared to the REF group. These trajectories were then modelled as a fractional Brownian motion process in order to gain insight about the nature of the control mechanisms called into play and their spatio-temporal organisation. Moreover, the main characteristic observed in the BLI group is a decreased in CP-CG(v) motions, which, according to Winter's model, may be related to joint stiffness. In addition, reduced spatial transition point co-ordinates and more deterministic control mechanisms aimed at returning the estimated CG to an equilibrium point during the longest Deltat were observed. This phenomenon is more pronounced in the antero-posterior direction and also allows the blind subject to significantly diminish their CG sways. Finally, these features are discussed in relation to other similarly analysed investigations.

Adult↗
PubMed2003

[Deterministic and stochastic models for circadian rhythms].

Circadian rhythms, characterized by a period of about 24h, are generated in nearly all living organisms by the negative autoregulation of clock gene expression. Deterministic models based on this genetic regulation account for circadian oscillations in constant environmental conditions (e.g., in constant darkness) and for entrainment of these rhythms by light-dark cycles. When the number of clock mRNA and protein molecules is low, it is necessary to resort to stochastic simulations to assess the influence of molecular noise on circadian oscillations. Indeed, it is possible that the autoregulatory mechanism of gene expression might not produce stable rhythms due to fluctuations if the number of molecules involved in the clock mechanism remains too low. We have compared the deterministic and stochastic approaches for a model based on the negative autoregulation of a clock gene. We show by means of stochastic simulations that robust circadian oscillations can already occur when the maximum number of mRNA and protein molecules is of the order of a few tens or hundreds, respectively. Furthermore, the results indicate that the cooperativity characterizing the repression of the transcription process strenghtens the robustness of circadian rhythms and that entrainment by light-dark cycles stabilizes the phase of the oscillations.

Circadian Rhythm↗
PubMed1998

A deterministic model for the economic evaluation of broiler production systems.

A deterministic model for the economic evaluation of broiler production and the derivation of economic values in broiler breeding was developed and tested. The model distinguishes four production stages: multiplier breeder, hatchery, commercial grower, and processor. The processor is included to determine relationships for the price per kilogram of live weight and the quality of the carcass, either on a "whole sale" or "further processed" base. Quantity of product output for the system is fixed by a predetermined amount of kilogram carcass of final product broilers finished by the commercial grower. Profitability of production and cost prices per unit product for subsequent stages can be calculated. Exogenous parameters are easily changeable in order to calculate profitability and cost prices for different production levels or production circumstances. Economic values can be derived considering influences of changes in genetic merit for performance traits on profitability or cost price, for integrated and nonintegrated production systems. By changing exogenous parameters, the model can also be used to analyze profitability or derive economic values for other meat-type poultry, such as turkey.

Agriculture↗
PubMed2003

Self-organization in evolution: a mathematical perspective.

The neo-Darwinian view of evolution centres upon the role of the gene. Here there seems to be little scope for self-organization. This conclusion is reinforced by traditional models of polymorphism in terms of allele frequencies in a mean-field gene-pool. However, models based on phenotypes, and including nonlinear and collective effects, suggest that evolution can indeed be viewed as a process whereby the ecosystem self-organizes. Here we focus on the phenomenon of speciation, and discuss a series of phenotypic models which together illuminate some of the issues surrounding the role of self-organization, including new approaches to fitness landscapes and species selection. All of these models represent speciation as a symmetry-breaking bifurcation, but in different mathematical contexts including deterministic dynamical systems, stochastic dynamical systems, and iterated function schemes. The main conclusions are surprisingly robust, despite the diversity of the models.

Adaptation, Physiological↗