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PubMed2004

Preprocessing of two-dimensional gel electrophoresis images.

Proteomics produces a huge amount of two-dimensional gel electrophoresis images. Their analysis can yield a lot of information concerning proteins responsible for different diseases or new unidentified proteins. However, an automatic analysis of such images requires an efficient tool for reducing noise in images. This allows proper detection of the spots' borders, which is important in protein quantification (as the spots' areas are used to determine the amounts of protein present in an analyzed mixture). Also in the feature-based matching methods the detected features (spots) can be described by additional attributes, such as area or shape. In our study, a comparison of different methods of noise reduction is performed in order to find out a method best suited for reducing noise in gel images. Among the compared methods there are the classical methods of linear filtering, e.g., the mean and Gaussian filtering, the nonlinear method, i.e., median filtering, and also the methods better suited for processing of nonstationary signals, such as spatially adaptive linear filtering and filtering in the wavelet domain. The best results are obtained by filtering of gel images in the wavelet domain, using the BayesThresh method of threshold value determination.

Electrophoresis, Gel, Two-Dimensional↗

PubMed2006

Amphetamine affects the start of responding in the peak interval timing task.

In this paper we investigate how amphetamine affects performance in a PI task by comparing two analyses of responding during peak trials. After training on 24 s fixed interval (FI-24) with 96 s peak trials, rats were given amphetamine for 4 consecutive days at doses of .5 and 1.0 mg/kg. Responses during peak trials were fitted with a Gaussian distribution to estimate the expected time of reinforcement from the peak time. A single trials analysis was also performed to determine the start time and stop time of the transition into and out of a high rate of responding on each peak trial. Amphetamine significantly decreased peak times as measured with the Gaussian curve fitting. However, in the single trials analysis, animals initiated responding significantly earlier, but did not stop responding earlier. Thus, fitting a Gaussian to the average performance across trials sometimes provides a different characterization of the timing process than does analyzing the start and stop of responding on individual trials. In the current experiment, the latter approach provided a more precise characterization of the effects of amphetamine on response timing.

Amphetamine↗

PubMed1991

Protein dynamics. Comparative investigation on heme-proteins with different physiological roles.

We report the low temperature carbon monoxide recombination kinetics after photolysis and the temperature dependence of the visible absorption spectra of the isolated alpha SH-CO and beta SH-CO subunits from human hemoglobin A in ethylene glycol/water and in glycerol/water mixtures. Kinetic measurements on sperm whale (Physeter catodon) myoglobin and previously published optical spectroscopy data on the latter protein and on human hemoglobin A, in both solvents, (Cordone, L., A. Cupane, M. Leone, E. Vitrano, and D. Bulone. 1988. J. Mol. Biol. 199:312-218) are taken as reference. Low temperature flash photolysis data are analyzed within the multiple substates model proposed by Frauenfelder and co-workers (Austin, R. H., K. W. Beeson, L. Eisenstein, H. Frauenfelder, and I. C. Gunsalus. 1975. Biochemistry. 14:5355-5373). Within this model a distribution of activation enthalpies for ligand binding accounts for the structural heterogeneity of the protein, while the preexponential factor, containing also the entropic contribution to the free energy of the process, is considered to be constant for all conformational substates. Optical spectra are deconvoluted in gaussian components and the temperature dependence of the moments of the resulting bands is analyzed, within the harmonic Frank-Condon approximation, to obtain information on the stereodynamic properties of the heme pocket. The kinetic and spectral parameters thus obtained are found to be protein dependent also with respect to their sensitivity to changes in the composition of the external medium. A close correlation between the kinetic and spectral features is observed for the proteins examined under all experimental conditions studied. The results reported are discussed in terms of differences in the heme pocket structure and in the conformational heterogeneity among the various proteins, as related to their different capability to accommodate constraints imposed by the external medium.

Animals↗

PubMed1999

An alternative method for the estimation of the terminal slope when a few data points are available.

Phase plane plots are graphical expressions for differential equations plotting the state derivative dc/dt versus the state c. Using these plots, we developed a novel method for the estimation of the terminal slope from time-concentration data. The values of the derivatives used for the construction of the phase plane plots were calculated by two different methods of numerical differentiation. The first method (D1) is based on the classical calculation of slope of the line connecting two successive data points. The alternative method (D2) relies on an initial second-order polynomial interpolation utilizing three successive data points followed by the calculation of the derivative at each one of the concentration values. A forced-through-zero linear regression of the phase plane plot data is used to derive an estimate for the slope. For comparative purposes, the standard approach based on the semilogarithmic plot was also applied. For a hypothetical drug absorbed by first-order process into a one-compartment model, simulated time-concentration data disturbed by a Gaussian zero mean random error with various coefficients of variation were generated. Various sampling schedules, with two, three, four, or five data points, were utilized for the estimation of the terminal slope. Performances of the proposed methods on simulated data were expressed by means of root-mean-squared error, bias, and standard deviation. In all cases, D2 was superior to D1. The D2 method outperforms the standard method in that it furnishes estimates closer to the real values in all cases when two data points and in most cases when three data points were used. All methods behave similarly when four or five data points were used.

Pharmacokinetics↗

PubMed2000

Symbolic approach for measuring temporal "irreversibility"

We describe a symbolic approach for measuring temporal "irreversibility" in time-series measurements. Temporal irreversibility is important because it excludes Gaussian linear dynamics and static transformations of such dynamics from the set of possible generating processes. A symbolic method for measuring temporal irreversibility is attractive because it is computationally efficient, robust to noise, and simplifies statistical analysis of confidence limits. We propose a specific algorithm, called "false flipped symbols," for establishing the presence of temporal irreversibility without the need for generating surrogate data. Besides characterizing experimental data, our results are relevant to the question of selecting alternative models. We illustrate our points with numerical model output and experimental measurements.

Journal Article↗

PubMed2006

Cooperative information maximization with Gaussian activation functions for self-organizing maps.

In this paper, we propose a new information-theoretic method to produce explicit self-organizing maps (SOMs). Competition is realized by maximizing mutual information between input patterns and competitive units. Competitive unit outputs are computed by the Gaussian function of distance between input patterns and competitive units. A property of this Gaussian function is that, as distance becomes smaller, a neuron tends to fire strongly. Cooperation processes are realized by taking into account the firing rates of neighboring neurons. We applied our method to uniform distribution learning, chemical compound classification and road classification. Experimental results confirmed that cooperation processes could significantly increase information content in input patterns. When cooperative operations are not effective in increasing information, mutual information as well as entropy maximization is used to increase information. Experimental results showed that entropy maximization could be used to increase information and to obtain clearer SOMs, because competitive units are forced to be equally used on average.

Cluster Analysis↗

PubMed2000

[Electroencephalography inverse problem by subspace decomposition of the fourth-order cumulant matrix].

It is an important topic in electroencephalography (EEG) research to localize the EEG activity sources from the scalp recordings. In this paper, based on the fourth-order cumulant matrix, a new sub-space decomposition algorithm is proposed for the EEG inverse problem. As the second-order moments (cumulants) has the drawback of being sensitive to the noise covariance. Using the fourth-order cumulants we need not know the noise covariances, as long as the noise is Gaussian. Computer simulation study on a three-layer concentric sphere head model shows its better performance than the two-order cumulate method in depressing the spatial coherent Gaussian noise.

Algorithms↗

PubMed1997

A directional clustering technique for random data classification.

This paper introduces a new clustering technique for random data classification based on an enhanced version of the Voronoi diagram. This technique is optimized to deal in the best way possible with data distributions which in their spatial representations experience overlap. A mathematical framework is given in view of this enhanced analysis and provides insight to key issues involving (a) the use of a correction process to complement the traditional Voronoi diagram and (b) the introduction of directional vectors in Gaussian and elliptical data distributions for enhanced data clustering. The computational requirements of the proposed approach are provided, and the computer results involving both randomly generated and real-world data prove the soundness of this clustering technique.

Data Interpretation, Statistical↗

PubMed2004

Elephants can always remember: exact long-range memory effects in a non-Markovian random walk.

We consider a discrete-time random walk where the random increment at time step t depends on the full history of the process. We calculate exactly the mean and variance of the position and discuss its dependence on the initial condition and on the memory parameter p . At a critical value p((1) )(c ) =1/2 where memory effects vanish there is a transition from a weakly localized regime [where the walker (elephant) returns to its starting point] to an escape regime. Inside the escape regime there is a second critical value where the random walk becomes superdiffusive. The probability distribution is shown to be governed by a non-Markovian Fokker-Planck equation with hopping rates that depend both on time and on the starting position of the walk. On large scales the memory organizes itself into an effective harmonic oscillator potential for the random walker with a time-dependent spring constant k=(2p-1)/t . The solution of this problem is a Gaussian distribution with time-dependent mean and variance which both depend on the initiation of the process.

Journal Article↗

PubMedDate not supplied

Fractal character of the electrocardiogram: distinguishing heart-failure and normal patients.

Statistical analysis of the sequence of heartbeats can provide information about the state of health of the heart. We used a variety of statistical measures to identify the form of the point process that describes the human heartbeat. These measures are based on both interevent intervals and counts, and include the interevent-interval histogram, interval-based periodogram, rescaled range analysis, the event-number histogram, Fano-factor, Allan Factor, and generalized-rate-based periodogram. All of these measures have been applied to data from both normal and heart-failure patients, and various surrogate versions thereof. The results show that almost all of the interevent-interval and the long-term counting statistics differ in statistically significant ways for the two classes of data. Several measures reveal 1/f-type fluctuations (long-duration power-law correlation). The analysis that we have conducted suggests the use of a conveniently calculated, quantitative index, based on the Allan factor, that indicates whether a particular patient does or does not suffer from heart failure. The Allan factor turns out to be particularly useful because it is easily calculated and is jointly responsive to both short-term and long-term characteristics of the heartbeat time series. A phase-space reconstruction based on the generalized heart rate is used to obtain a putative attractor's capacity dimension. Though the dependence of this dimension on the embedding dimension is consistent with that of a low-dimensional dynamical system (with a larger apparent dimension for normal subjects), surrogate-data analysis shows that identical behavior emerges from temporal correlation in a stochastic process. We present simulated results for a purely stochastic integrate-and-fire model, comprising a fractal-Gaussian-noise kernel, in which the sequence of heartbeats is determined by level crossings of fractional Brownian motion. This model characterizes the statistical behavior of the human electrocardiogram remarkably well, properly accounting for the behavior of all of the measures studied, over all time scales.

Electrocardiography↗

PubMed2005

A principle of fractal-stochastic dualism and Gompertzian dynamics of growth and self-organization.

The emergence of Gompertzian dynamics at the macroscopic, tissue level during growth and self-organization is determined by the existence of fractal-stochastic dualism at the microscopic level of supramolecular, cellular system. On one hand, Gompertzian dynamics results from the complex coupling of at least two antagonistic, stochastic processes at the molecular cellular level. It is shown that the Gompertz function is a probability function, its derivative is a probability density function, and the Gompertzian distribution of probability is of non-Gaussian type. On the other hand, the Gompertz function is a contraction mapping and defines fractal dynamics in time-space; a prerequisite condition for the coupling of processes. Furthermore, the Gompertz function is a solution of the operator differential equation with the Morse-like anharmonic potential. This relationship indicates that distribution of intrasystemic forces is both non-linear and asymmetric. The anharmonic potential is a measure of the intrasystemic interactions. It attains a point of the minimum (U(0), t(0)) along with a change of both complexity and connectivity during growth and self-organization. It can also be modified by certain factors, such as retinoids.

Algorithms↗

PubMed1998

Eye movement control during reading: a simulation of some word-targeting strategies.

McConkie, Kerr, Reddix, & Zola [(1988). Vision Research, 28, 1107-1118] demonstrated that the distributions of landing sites on a word tended to be gaussian in shape. They provided a detailed account of the behaviour of the eye once a target had been selected and a saccade initiated, but said little about the process of target selection itself. The purpose of this study was to take as a starting point the landing site distributions of McConkie et al., in particular the residuals derived from fitting the gaussians to the empirical data, and to explore by computer simulation a number of saccade targeting strategies in order to discover candidates that best accounted for the residual data. Our results indicate that the strategy that gives the best fit involves targeting the longest word in a right parafoveal window extending 20 characters to the right of the currently fixated word. The implications of this finding for models of reading are discussed.

Attention↗

PubMed1990

[Accuracy of detecting stenotic changes on coronary cineangiograms using computer image processing].

To accurately interpret stenotic changes on coronary cineangiograms, an automatic method of detecting stenotic lesions using computer image processing was developed. First, tracing of artery was performed. The vessel edges were then determined by unilateral Gaussian fitting. The stenotic change was detected on the basis of the reference diameter estimated by Hough transformation. This method was evaluated in 132 segments of 27 arteries in 18 patients. Three observers carried out visual interpretation and computer-aided interpretation. The rate of detection by visual interpretation was 6.1, 28.8 and 20.5%, and by computer-aided interpretation, 39.4, 39.4 and 45.5%. With computer-aided interpretation, the agreement between any two observers on lesions and non-lesions was 40.2% and 59.8%, respectively. Therefore, visual interpretation tended to underestimate the stenotic changes on coronary cineangiograms. We think that computer-aided interpretation increases the reliability of diagnosis on coronary cineangiograms.

Cineangiography↗

PubMed2003

[Application of a modified method of wavelet noise removing to noisy ICP-AES spectra].

A new method for noise removal from signal by the wavelet transform was developed. Compared with analytical signal, noise has higher frequency and smaller amplitude. By the new wavelet filtering method, the high frequency components were first removed, and then the small ones in the remaining transformed vectors were discarded. The proposed approach was evaluated by the processing of simulated and experimental noisy ICP-AES spectra. Different amounts of noise were added to a Gaussian peak to obtain a series of noisy ICP spectra. The simulated noisy spectra with R (signal to noise ratio) = 6 and N (data number) = 51, and with R = 6 and N = 17 were used to illustrate the feasibility of the proposed method. The performances of noise removal by the wavelet smoothing, the wavelet denoising and the proposed technique were compared. It was found that using the new approach, the relative errors of peak height would be no more than 5% for spectra with normal sampling points and R > or = 2. Moreover, the baseline could be easily defined, which was helpful to the accurate measurement of peak height. Experimental spectra of Al and V at low concentrations were processed by the proposed method. Intense noises were efficiently removed and the spectra became smoother without underestimating the analytical signal. The distortion of V 303.310 nm line was substantially rectified. The linear correlation coefficients between the peak heights in the reconstructed spectra and the concentrations were found to be 0.9953 for Al and 0.9836 for V, respectively.

Algorithms↗

PubMed2003

Conditional analysis of mixed Poisson processes with baseline counts: implications for trial design and analysis.

The design of clinical trials is typically based on marginal comparisons of a primary response under two or more treatments. The considerable gains in efficiency afforded by models conditional on one or more baseline responses has been extensively studied for Gaussian models. The purpose of this article is to present methods for the design and analysis of clinical trials in which the response is a count or a point process, and a corresponding baseline count is available prior to randomization. The methods are based on a conditional negative binomial model for the response given the baseline count and can be used to examine the effect of introducing selection criteria on power and sample size requirements. We show that designs based on this approach are more efficient than those proposed by McMahon et al. (1994).

Algorithms↗

PubMed2007

Gaussianization-based quasi-imputation and expansion strategies for incomplete correlated binary responses.

New quasi-imputation and expansion strategies for correlated binary responses are proposed by borrowing ideas from random number generation. The core idea is to convert correlated binary outcomes to multivariate normal outcomes in a sensible way so that re-conversion to the binary scale, after performing multiple imputation, yields the original specified marginal expectations and correlations. This conversion process ensures that the correlations are transformed reasonably which in turn allows us to take advantage of well-developed imputation techniques for Gaussian outcomes. We use the phrase 'quasi' because the original observations are not guaranteed to be preserved. We argue that if the inferential goals are well-defined, it is not necessary to strictly adhere to the established definition of multiple imputation. Our expansion scheme employs a similar strategy where imputation is used as an intermediate step. It leads to proportionally inflated observed patterns, forcing the data set to a complete rectangular format. The plausibility of the proposed methodology is examined by applying it to a wide range of simulated data sets that reflect alternative assumptions on complete data populations and missing-data mechanisms. We also present an application using a data set from obesity research. We conclude that the proposed method is a promising tool for handling incomplete longitudinal or clustered binary outcomes under ignorable non-response mechanisms.

Adolescent↗

PubMed1992

[Assessment of the severity of interstitial lung diseases in chest radiographs using a computer-aided analysis system. A comparison with X-ray CT].

A new computer-aided system to assess the severity of interstitial lung diseases in chest radiographs using proposed parameters, radiographic indices, was developed. The radiographic index is the normalized percent area of shadows in a ROI selected in the lung fields of chest radiographs. In the right lungs of 82 patients, 164 ROIs were processed by computerized methods such as filtering, binarization, determination and subtraction of linear shadows. In subtraction method, the image processed with determination of linear shadows is subtracted from the image filtered by 4-directional Laplacian-Gaussian filters. Then, the radiographic indices, Dbin (binarization), Dlin (linear shadow determination) and Dsub (subtraction), were obtained for the corresponding images. The combined radiographic index "Dcom" was calculated from "Dlin" and "Dsub". Values of these indices of the ROIs were compared with the grade (0-4) of the severity of interstitial involvement evaluated by CT. The results were obtained as follows: 1) Dbin, Dlin and Dcom provided good correlation with the severity throughout 5 grades, while Dsub did not. 2) As a parameter for detection of interstitial lung diseases, Dcom was significantly superior to the other indices (p less than .05). 3) As a parameter for assessment of severity of the diseases, Dlin showed the best performance and Dcom was the second best. Dlin and Dcom were superior to Dbin, and Dsub was inferior to Dbin. These results indicate that a new system is useful for assessment of the severity of interstitial lung diseases in chest radiographs.

Adult↗

PubMed1983

Quantitative characterisation procedure for auditory neurons based on the spectro-temporal receptive field.

Studies dealing with auditory information processing often present the dynamic spectrum of the sound stimulus (sonogram) in addition to the stimulus waveform. The sonogram, presenting the spectral and temporal properties of the sound in a combined way, reflects properties that are assumed relevant in central information processing. For 12 neurons recorded from the midbrain of the grass frog the sonogram of a Gaussian wide-band noise stimulus was correlated with the output of the neuron to that noise. From this input-output correlogram the spectro-temporal receptive field (STRF) was calculated. The STRF reflects those spectral and temporal properties of the stimulus that influence the firing probability of the neuron. A quantitative procedure was developed to calculate the neuron's response as far as it could be derived from the STRF. This procedure basically consisted of a convolution between STRF and the sonogram of the stimulus followed by a summation over the various frequency bands. In this way it proved possible to estimate to what extent the STRF characterised the neuron's firing behaviour. Heuristic approaches, in which the neuron was modelled to a parallel series of band-pass filters, a summator and a static nonlinearity, representing a spike-generating mechanism, resulted in a considerable improvement of the characterisation.

Animals↗