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PubMed2004

Fractal modeling of human isochronous serial interval production.

The Hurst exponent (H) was estimated for series of 256 time intervals produced by human participants, collected in 5 sessions performed on different days. Each series was obtained during the continuation phase following synchronization with 25 isochronous intervals generated by a computer and presented through headphones. Dispersional analysis yielded estimates of H > 0.5. These were sufficiently stable to yield statistically significant differences between participants and between each target interval duration (0.5, 0.8, 1.1, and 1.5 s). The results indicate that variability in isochronous serial interval production (ISIP) can be modeled as fractional Gaussian noise, which corroborates and qualifies previous research indicating positive serial dependency or long memory in ISIP data in terms of drift and 1/ f noise characteristics. It is concluded that ISIP is a more complex process than is assumed by influential timing models and theories, and that realistic modeling of human timing must account for nonlinear variability patterns.

Analysis of Variance↗

PubMed1993

Transition modes in Ising networks: an approximate theory for macromolecular recognition.

For a statistical lattice, or Ising network, composed of N identical units existing in two possible states, 0 and 1, and interacting according to a given geometry, a set of values can be found for the mean free energy of the 0-->1 transition of a single unit. Each value defines a transition mode in an ensemble of nu N = 3N - 2N possible values and reflects the role played by intermediate states in shaping the energetics of the system as a whole. The distribution of transition modes has a number of intriguing properties. Some of them apply quite generally to any Ising network, regardless of its dimension, while others are specific for each interaction geometry and dimensional embedding and bear on fundamental aspects of analytical number theory. The landscape of transition modes encapsulates all of the important thermodynamic properties of the network. The free energy terms defining the partition function of the system can be derived from the modes by simple transformations. Classical mean-field expressions can be obtained from consideration of the properties of transition modes in a rather straightforward way. The results obtained in the analysis of the transition mode distributions have been used to develop an approximate treatment of the problem of macromolecular recognition. This phenomenon is modeled as a cooperative process that involves a number of recognition subsites across an interface generated by the binding of two macromolecular components. The distribution of allowed binding free energies for the system is shown to be a superposition of Gaussian terms with mean and variance determined a priori by the theory. Application to the analysis of the biologically interaction of thrombin with hirudin has provided some useful information on basic aspects of the interaction, such as the number of recognition subsites involved and the energy balance for binding and cooperative coupling among them. Our results agree quite well with information derived independently from analysis of the crystal structure of the thrombin-hirudin complex.

Binding Sites↗

PubMed1989

Compensation of spatial system response in SPECT with conjugate gradient reconstruction technique.

A procedure for the determination of the system matrix in single photon emission tomography (SPECT) is described which uses the conjugate gradient reconstruction technique in order to take into account the variable system resolution of a camera equipped with parallel-hole collimators. The procedure involves the acquisition of the system line spread functions (LSF) in the region occupied by the object to be studied. Those data are used to generate a set of weighting factors based on the assumption that the LSFs of the collimated camera are of Gaussian shape with the full width at half maximum (FWHM) linearly dependent on the source depth in the span of image space. The factors are stored on a disc file for subsequent use in the reconstruction process. Afterwards the reconstruction is performed using the conjugate gradient method with the system matrix modified by the incorporation of these precalculated factors in order to take into account the variable geometrical system response. The set of weighting factors is regenerated whenever the acquisition conditions are changed (collimator, radius of rotation). In the case of an ultra high resolution (UHR) collimator 2000 weighting factors need to be calculated. The modification of the system matrix for the geometrical response allows the number of iterations to increase, considerably improving image definition without the appearance of noise artifacts. Moreover, phantom studies show that the number of iterations is less critical because of improved stability in the convergence to the solution. For brain studies of patients 10-15 iterations are usually performed. Studies with a single line source give a value between 7 and 8 mm for the FWHM of the point spread function (PSF) when the conjugate gradient method with modified system matrix is used on data acquired with a UHR collimator, whereas without the modification of the system matrix the result is 9 mm FWHM, if filtered backprojection (FBP) is used with the same filter as in the clinical studies the result is 15 mm FWHM. The results of this work show that proper definition of the system matrix using conjugate gradients influences the quality of the reconstruction remarkably. Nevertheless, further work has to be done in order to assess to what extent the system matrix is ill-conditioned and, eventually, to define a suitable regularization technique.

Humans↗

PubMed2006

Spherical harmonics microwave algorithm for shape and location reconstruction of breast cancer tumor.

A reconstruction algorithm to simultaneously estimate the shape and location of three-dimensional breast cancer tumor is presented and its utility is analyzed. The approach is based on a spherical harmonic decomposition to capture the shape of the tumor. We combine a gradient descent optimization method with a direct electromagnetic solver to determine the coefficients in the harmonic expansion as well as the coordinates of the center of the tumor. The results demonstrate the potential advantage of collecting data using a multiple-view/tomographic-type strategy. We show how the order of the harmonic expansion must be increased to capture increasingly "irregularly" shaped tumors and explore the resulting increase in the central processing unit (CPU) time required by the algorithm. Our approach shows accurate reconstruction of the tumor image regardless of the source polarization. This work demonstrates the promise of the algorithm when used on data corrupted with Gaussian noise and when perfect knowledge of the tumor electrical properties is not available.

Algorithms↗

PubMedDate not supplied

A simplified approach for modulation transfer function determinations in computed tomography.

In order to determine the modulation transfer functions (MTF's) for x-ray computed tomography (CT) scanners, a measurement must be performed to obtain either the point spread function (PSF) or the line spread function (LSF). Thereafter, the usual procedure is to interpolate between the measured points and to determine the Fourier transforms numerically in order to obtain the MTF. Since this must usually be done many times to evaluate various reconstruction kernels and scan modalities, the process is tedious. Fortunately, it can be greatly simplified by utilizing a mathematical function to describe the PSF or LSF. Measured data for five CT scanners indicates that the PSF can usually be described by a Gaussian function. Hence, the MTF can be written in a generalized form eliminating the necessity of performing Fourier transformations each time. The MTF is determined directly from a single performance characteristic related to the full width at half maximum. The accuracy of the approach is compared with detailed MTF calculations for five CT scanners and it is shown to agree favorably with this data.

Fourier Analysis↗

PubMed2002

Effects of incoherent and coherent source spectral information in geoacoustic inversion.

This paper examines the effect on matched-field geoacoustic inversion of including source spectral information, as can be available in controlled-source acoustic surveys. Source information can consist of relative or absolute knowledge of the source amplitude and/or phase spectra, and can allow frequency-coherent processing of spatial acoustic-field data. A number of multi-frequency acoustic processors, appropriate for specific types of source information, are defined based on the likelihood function for complex acoustic-field data with Gaussian noise. The information content of the various processors is quantified in terms of marginal probability distributions and highest-probability density intervals for the unknown geoacoustic and geometric parameters, which define the accuracy expected in inversion. Marginal distributions are estimated using a fast Gibbs sampler approach to Bayesian inversion, which provides an efficient, unbiased sampling of the multi-dimensional posterior probability density. The analysis is illustrated for incoherent and coherent processors corresponding to several types of source knowledge ranging from complete information to no information, and the results are considered as a function of the spatial and frequency sampling of the acoustic fields.

Acoustics↗

PubMed1987

On the detection of signals in non-white noise.

We have studied the detection, by human observers, of suprathreshold bandlimited signals embedded at various locations in non-white, Gaussian filtered noise. Detection models based upon the direct cross-correlation between the signal and the noise image (matched filtering) cannot account for the results of our experiments. Our findings point instead at a detection process occurring at the level of signal decomposition, and jointly determined by: (a) the differential outputs of discrete, bandlimited spatial analyzers selectively responsive to different components of the signal; and (b) variable detection rules adaptively related to such outputs and to the type of signal information available to the observer.

Humans↗

PubMed2005

Persistence length of titin from rabbit skeletal muscles measured with scattering and microrheology techniques.

The persistence length of titin from rabbit skeletal muscles was measured using a combination of static and dynamic light scattering, and neutron small angle scattering. Values of persistence length in the range 9-16 nm were found for titin-II, which corresponds to mainly physiologically inelastic A-band part of the protein, and for a proteolytic fragment with 100-nm contour length from the physiologically elastic I-band part. The ratio of the hydrodynamic radius to the static radius of gyration indicates that the proteins obey Gaussian statistics typical of a flexible polymer in a -solvent. Furthermore, measurements of the flexibility as a function of temperature demonstrate that titin-II and the I-band titin fragment experience a similar denaturation process; unfolding begins at 318 K and proceeds in two stages: an initial gradual 50% change in persistence length is followed by a sharp unwinding transition at 338 K. Complementary microrheology (video particle tracking) measurements indicate that the viscoelasticity in dilute solution behaves according to the Flory/Fox model, providing a value of the radius of gyration for titin-II (63 +/- 1 nm) in agreement with static light scattering and small angle neutron scattering results.

Animals↗

PubMed1997

Higher-order statistics: a robust vehicle for diagnostic assessment and characterisation of lung sounds.

The use of higher-order statistics for diagnostic assessment and characterisation of lung sounds is presented in this article. The parametric approach of bispectrum estimation, which is a third-order spectrum, based on a non-Gaussian white noise driven autoregressive (AR) model, reveals information about lung sounds that is not contained in the ordinary power spectrum, such as the degree of nonlinearity and deviations from normality. Characterisation of source and transmission of lung sounds is achieved using an AR model based on third-order statistics. Furthermore, harmonic analysis of lung sounds is combined with the bicoherence index in order to obtain information regarding possible quadratic phase coupling among harmonic components of musical lung sounds. Experiments have shown that higher-order statistics can offer reliable evaluation of lung sounds characteristics, since their general properties and robustness in noiseless or noisy environments (lung sounds contaminated with additive symmetrical noise, e.g., Gaussian) proved to have superior advantages in objective analysis of pulmonary dysfunction.

Humans↗

PubMed2006

Chromatography as Lévy stochastic process.

The Stochastic Theory of Chromatography has been revised in light of some of the most relevant Lévy's findings in Theory of Probability, including the so-called Lévy's distance, the characteristic function and the theory of infinitesimally divisible distributions. These concepts represent the key to exploit and understand, at a molecular basis, phenomena typical of chromatographic separations under linear conditions, such as peak tailing and splitting. In particular, Lévy's distance has been used to quantify the degree of convergence of real peaks towards an ideal Gaussian shape; the characteristic function properties, introduced by Lévy to deal with the problem of the addition of independent random variables, have been employed to solve a wide variety of chromatographic models (including adsorption on heterogeneous surfaces) and to interpret mobile phase dispersion from a probabilistic point of view. Finally, Lévy's studies concerning infinitesimally divisible distributions have allowed to introduce in the stochastic description of chromatography, effects associated to dispersion in mobile phase. It has been demonstrated that, according to Lévy's canonical representation of stochastic processes, the basis of chromatography is a mobile phase Poisson Process. Represented as a Lévy's process, the microscopic-probabilistic model of chromatography permits the establishment of a connection between single-molecule properties and their statistical fluctuations and shapes of real chromatographic peaks allowing, at the same time, for the constitution of a link between different branches of physical sciences.

Chromatography↗

PubMed2005

Density functional theory study of the geometry, energetics, and reconstruction process of Si111 surfaces.

We report the structures and energies from first principles density functional calculations of 12 different reconstructed (111) surfaces of silicon, including the 3x3 to 9x9 dimer-adatom-stacking fault (DAS) structures. These calculations used the Perdew-Burke-Ernzerhof generalized gradient approximation of density functional theory and Gaussian basis functions. We considered fully periodic slabs of various thicknesses. We find that the most stable surface is the DAS 7x7 structure, with a surface energy of 1.044 eV/1x1 cell (1310 dyn/cm). To analyze the origins of the stability of these systems and to predict energetics for more complex, less-ordered systems, we develop a model in which the surface energy is partitioned into contributions from seven different types of atom environments. This analysis is used to predict the surface energy of larger DAS structures (including their asymptotic behavior for very large unit cells) and to study the energetics of the sequential size change (SSC) model proposed by Shimada and Tochihara for the observed dynamical reconstruction of the Si(111) 1x1 structure. We obtain an energy barrier at the 2x2 cell size and confirm that the 7x7 regular stage of the SSC model (corresponding to the DAS 7x7 reconstruction) provides the highest energy reduction per unit cell with respect to the unreconstructed Si111 1x1 surface.

Journal Article↗

PubMed2004

Parametric design and correlational analyses help integrating fMRI and electrophysiological data during face processing.

Face perception is typically associated with activation in the inferior occipital, superior temporal (STG), and fusiform gyri (FG) and with an occipitotemporal electrophysiological component peaking around 170 ms on the scalp, the N170. However, the relationship between the N170 and the multiple face-sensitive activations observed in neuroimaging is unclear. It has been recently shown that the amplitude of the N170 component monotonically decreases as gaussian noise is added to a picture of a face [Jemel et al., 2003]. To help clarify the sources of the N170 without a priori assumptions regarding their number and locations, ERPs and fMRI were recorded in five subjects in the same experiment, in separate sessions. We used a parametric paradigm in which the amplitude of the N170 was modulated by varying the level of noise in a picture, and identified regions where the percent signal change in fMRI correlated with the ERP data. N170 signals were observed for pictures of both cars and faces but were stronger for faces. A monotonic decrease with added noise was observed for the N170 at right hemisphere sites but was less clear on the left and occipital central sites. Correlations between fMRI signal and N170 amplitudes for faces were highly significant (P < 0.001) in bilateral fusiform gyrus and superior temporal gyrus. For cars, the strongest correlations were observed in the parahippocampal region and in the STG (P < 0.005). Besides contributing to clarify the spatiotemporal course of face processing, this study illustrates how ERP information may be used synergistically in fMRI analyses. Parametric designs may be developed further to provide some timing information on fMRI activity and help identify the generators of ERP signals.

Adult↗

PubMed2003

Network visualization system for computational chemistry.

Network Visualization System for Computational Chemistry (NVSCC) is a molecular graphics program designed for the visualization of molecular assemblies. NVSCC accepts the output files from the most popular ab initio quantum chemical programs, GAUSSIAN and GAMESS, and provides visualization of molecular structures based on atomic coordinates. The main differences between NVSCC and other programs are: Network support due to built-in FTP and telnet clients, which allows for the processing of output from and the sending of input to different computer systems and operating systems. The possibility of working with output files in real time mode. The possibility of animation from an output file during all steps of optimization. The quick processing of huge volumes of data. The development of custom interfaces.

Journal Article↗

PubMed1979

Radiative and nonradiative transitions in subchloroplast particles highly enriched in P-700.

Radiative and nonradiative processes were investigated in subchloroplast particles highly enriched in P-700 (1 P-700 to 10 chlorophyll molecules) according to the method of classical fluorescence and of photoacoustical spectroscopy. The envelope of fluorescence spectrum divided into three Gaussian bands and their quantum yields of fluorescence were calculated. Indpendently the quantum yield of fluorescence was determined from the spectral course of the photoacoustical signal. Finally, the estimate of the photochemical activity of P-700, based upon the measured fluorescence quantum yield and upon the measured nonradiative losses of excitation energy, was done.

Chlorophyll↗

PubMed2002

Comparison of the capability of peak functions in describing real chromatographic peaks.

This paper describes the results of a comparison of four peak functions in describing real chromatographic peaks. They are the empirically transformed Gaussian, polynomial modified Gaussian, generalized exponentially modified Gaussian and hybrid function of Gaussian and truncated exponential functions. Real chromatographic peaks of different shapes (fronting. symmetric, and tailing) are obtained by various separation conditions of reversed-phase liquid chromatography. They are then fitted to the peak functions via the Marquardt-Levenberg algorithm, a nonlinear least-squares curve-fitting procedure, by Microsoft Solver. The qualities of the fits are evaluated by the sum of the squares of the residuals. It is concluded in the study that the empirically transformed Gaussian function offers the highest flexibility (best fits) to all shapes of chromatographic peaks, including extremely asymmetric tailing peaks with a peak asymmetry of up to 8. The flexibility of this function should improve our ability to process chromatographic peaks such as deconvolution of overlapped peaks and smoothing noisy peaks for the determination of statistical moments.

Chromatography, Liquid↗

PubMed2005

Role of the direct reaction H2S + SO2 in the homogeneous Claus reaction.

Quantum chemical methods at the Gaussian-2 and -3 levels of theory have been used to investigate the reactions between H(2)S, SO(2), and S(2)O such as might occur in the front-end furnace of the Claus process. The direct reaction between H(2)S and SO(2) occurs via a 5-centered transition state with an initial barrier of approximately 135 kJ mol(-1) and an overall barrier of approximately 153 kJ mol(-1) to produce S(2)O and H(2)O. We indicate approximate values here because there are a number of isomers in the reaction pathway that have barriers slightly different from those quoted. The presence of a water molecule lowers this by approximately 60 kJ mol(-1), but the van der Waals complex required for catalysis by water is thermodynamically unfavorable under the conditions in the Claus reactor. The direct reaction between H(2)S and S(2)O can occur via two possible pathways; the analogous reaction to H(2)S + SO(2) has an initial barrier of approximately 117 kJ mol(-1) and an overall barrier of approximately 126 kJ mol(-1) producing S(3) and H(2)O, and a pathway with a 6-centred transition state has a barrier of approximately 111 kJ mol(-1), producing HSSSOH. Rate constants, including a QRRK analysis of intermediate stabilization, are reported for the kinetic scheme proposed here.

Journal Article↗

PubMed1990

Temperature-derivative spectroscopy: a tool for protein dynamics.

A relaxation method that measures the derivative of a population with respect to temperature is introduced and used to study the recombination of CO to sperm whale myoglobin after a photolyzing flash. Measurement of the geminate process in the infrared CO-stretch bands shows distributed activation enthalpies with different distributions for each band, transitions between two bands that correspond to photolyzed ligands, and kinetic hole burning. The data are well described by gaussian enthalpy distributions; the results match and complement those of isothermal methods. The temperature-derivative technique is further used to explore the recombination of CO from outside the heme pocket.

Kinetics↗

PubMed2002

Local frequency representations for robust multimodal image registration.

Automatic registration of multimodal images involves algorithmically estimating the coordinate transformation required to align the data sets. Most existing methods in the literature are unable to cope with registration of image pairs with large nonoverlapping field of view (FOV). We propose a robust algorithm, based on matching dominant local frequency image representations, which can cope with image pairs with large nonoverlapping FOV. The local frequency representation naturally allows for processing the data at different scales/resolutions, a very desirable property from a computational efficiency view point. Our algorithm involves minimizing-over all rigid/affine transformations--the integral of the squared error (ISE or L2 E) between a Gaussian model of the residual and its true density function. The residual here refers to the difference between the local frequency representations of the transformed (by an unknown transformation) source and target data. We present implementation results for image data sets, which are misaligned magnetic resonance (MR) brain scans obtained using different image acquisition protocols as well as misaligned MR-computed tomography scans. We experimently show that our L2E-based scheme yields better accuracy over the normalized mutual information.

Brain↗