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PubMed2004

Dynamical suppression of 1/f noise processes in qubit systems.

We investigate the capability of dynamical decoupling techniques to reduce decoherence from a realistic environment generating 1/f noise. The predominance of low frequency modes in the noise profile allows for decoherence scenarios where relatively slow control rates suffice for a drastic improvement. However, the actual figure of merit is very sensitive to the details of the dynamics, with decoupling performance which may deteriorate for non-Gaussian noise and/or high frequency working points. Our results are promising for robust solid-state qubits and beyond.

Models, Theoretical↗

PubMed2007

Aging, focus switching, and task switching in a continuous calculation task: evidence toward a new working memory control process.

This study examined switching of the focus of attention in working memory in relation to global task switching in a continuous calculation task using two rules (midpoint and up-and-down) in a group of 25 younger adults and a group of 23 older adults. Age differences emerged in accuracy when participants worked on two strings simultaneously (necessitating a focus switch); focus switching did not interact with age in the response time domain. No age differences were obtained for global task switching. Ex-Gaussian decomposition showed a shift due to focus switching in all parameters, but a shift in leading edge only for task switching. The results suggest that task switching and focus switching rely on different processes, and that there is a specific age-related deficit in focus switching.

Adolescent↗

PubMed2006

Excluded volume effect on confined polymer translocation through a short nanochannel.

We simulated the translocation process of a polymer chain from a source container to a drain container through a short nanochannel. We utilized the bond fluctuation model coupled with Monte Carlo dynamics in our simulations. The calculation results show that the excluded volume effect significantly affects the polymer's translocation time tau. This time depends nonmonotonically on the polymer length N. For a fixed nanochannel length, tau decreases when the polymer length increases. tau, however, increases when the polymer length exceeds a certain threshold. This observation differs from those predicated for a Gaussian chain. In this paper, we will further present our findings to explain this phenomenon. The knowledge we gain from this research can enhance the understanding of complex transport processes in many biological systems.

Journal Article↗

PubMed2005

Evaluation of a generalized regression artificial neural network for extending cadmium's working calibration range in graphite furnace atomic absorption spectrometry.

A generalized regression artificial neural network (GRANN) was developed and evaluated for modeling cadmium's nonlinear calibration curve in order to extend its upper concentration limit from 4.0 microg L-1 up to 22.0 microg L-1. This type of neural network presents important advantages over the more popular backpropagation counterpart which are worth exploiting in analytical applications, namely, (1) a smaller number of variables have to be optimized, with the subsequent reduction in "development hassle"; and, (2) shorter development times, thanks to the fact that the adjustment of the weights (the artificial synapses) is a non-iterative, one-pass process. A backpropagation artificial neural network (BPANN), a second-order polynomial, and some less frequently employed polynomial and exponential functions (e.g., Gaussian, Lorentzian, and Boltzmann), were also evaluated for comparison purposes. The quality of the fit of the various models, assessed by calculating the root mean square of the percentage deviations, was as follows: GRANN>Boltzmann>second-order polynomial>BPANN>Gauss>Lorentz. The accuracy and precision of the models were further estimated through the determination of cadmium in the certified reference material "Trace Metals in Drinking Water" (High Purity Standards, Lot No. 490915), which has a cadmium certified concentration (12.00+/-0.06 microg L-1) that lies in the nonlinear regime of the calibration curve. Only the models generated by the GRANN and BPANN accurately predicted the concentrations of a series of solutions, prepared by serial dilution of the CRM, with cadmium concentrations below and above the maximum linear calibration limit (4.0 microg L-1). Extension of the working range by using the proposed methodology represents an attractive alternative from the analytical point of view, since it results in less specimen manipulation and consequently reduced contamination risks without compromising either the accuracy or the precision of the analyses. The implementation of artificial neural networks also helps to reduce the trial-and-error task of looking for the right mathematical model from among the many possibilities currently available in the various scientific and statistic software packages.

Journal Article↗

PubMed2005

Differential scanning calorimetric studies of a Bacillus halodurans alpha-amylase.

The thermal unfolding of Amy 34, a recombinant alpha-amylase from Bacillus halodurans, has been investigated using differential scanning calorimetry (DSC). The denaturation of Amy 34 involves irreversible processes with an apparent denaturation temperature (T(m)) of 70.8 degrees C at pH 9.0, with four transitions, as determined using multiple Gaussian curves. The T(m) increased by 5 degrees C in the presence of 100-fold molar excess of CaCl2 while the aggregation of Amy 34 was observed in the presence of 1000-fold molar excess of CaCl2. Increase in the calcium ion concentration from 1- to 5-fold molar excess resulted in an increase in calorimetric enthalpy (DeltaH(cal)), however, at higher concentrations of CaCl2 (up to 100-fold), DeltaH(cal) was found to decrease, accompanied by a decrease in entropy change (DeltaS), while the T(m) steadily increased. The presence of 100-fold excess of metal chelator, EDTA, resulted in a decrease in T(m) by 10.4 degrees C. T(m) was also decreased to 61.1 degrees C and 65.9 degrees C at pH 6.0 and pH 11.0, respectively.

Bacillus↗

PubMed2005

Detection, discrimination and integration of second-order orientation information in strabismic and anisometropic amblyopia.

To better understand the nature of the cortical deficit in amblyopia we undertook a systematic investigation of second-order processing in 8 amblyopic and 8 normal observers. We investigated local detection, discrimination and global integration. Our local stimulus consisted of a Gaussian patch of fractal noise multiplied by a 1-d sinusoidal modulator. Our global stimulus consisted of an array of such elements. We revealed second-order detection deficits for stimuli with equi-visible carriers. Orientation discrimination for an isolated second-order patch was comparable in normal and amblyopic eyes. We showed that pure integration of second-order patterns can be normal in amblyopia.

Adult↗

PubMed1992

Conformational substates in azurin.

Azurin is a small blue copper protein in the electron transfer chain of denitrifying bacteria. It forms a photolabile complex with nitric oxide (NO) at low temperatures. We studied the temperature dependence of the ligand binding equilibrium and the kinetics of the association reaction after photodissociation over a wide range of temperature (80-280 K) and time (10(-6)-10(2) s). The nonexponential rebinding below 200 K is independent of the NO concentration and is interpreted as internal recombination. The rebinding can be modeled with the Arrhenius law by using a single preexponential factor of 6.3 x 10(8) s-1 and a Gaussian distribution of enthalpy barriers centered at 23 kJ/mol with a width of 11 kJ/mol. Above 200 K, a slower, exponential rebinding process appears. The dependence of the kinetics on the NO concentration characterizes this reaction as bimolecular rebinding. The binding kinetics of NO to azurin show impressive analogies to the binding of carbon monoxide to myoglobin. We conclude that conformational substates occur not only in heme proteins but also in proteins with different active sites and secondary structures.

Azurin↗

PubMed2001

Quantum state reconstruction of the single-photon Fock state.

We have reconstructed the quantum state of optical pulses containing single photons using the method of phase-randomized pulsed optical homodyne tomography. The single-photon Fock state 1> was prepared using conditional measurements on photon pairs born in the process of parametric down-conversion. A probability distribution of the phase-averaged electric field amplitudes with a strongly non-Gaussian shape is obtained with the total detection efficiency of (55+/-1)%. The angle-averaged Wigner function reconstructed from this distribution shows a strong dip reaching classically impossible negative values around the origin of the phase space.

Journal Article↗

PubMed1993

Effect of spectral envelope smearing on speech reception. II.

This paper describes two experiments on the effect of reduced spectral contrast on the speech-reception threshold (SRT) for sentences in a background of interfering sound. Signal processing is performed by smoothing the envelope of the squared short-time fast Fourier transform by a convolution with a Gaussian-shaped filter, and overlapping additions to reconstruct a continuous signal. In the first experiment the effect of reduced spectral contrast on the SRT for male speech is investigated and compared with previously obtained results for female speech [ter Keurs et al., J. Acoust. Soc. Am. 91, 2872-2880 (1992)]. Spectral energy is smeared over bandwidths of 1/8, 1/4, 1/3, 1/2, 1, 2, and 4 oct. The results show that, despite the differences in spectral pattern between male and female voices, the SRT in noise increases similarly for both voices for smearing bandwidths over 1/3 oct. In terms of the ripple density of the spectral envelope the results indicate that the range of lower spectral modulations, up to a limit of about 1.5 periods/oct, is sufficient for the intelligibility of speech in interfering sounds. In the second experiment the extent of the threshold difference between a speech masker and a noise masker is investigated for spectral smearing bandwidths of 1/2, 1, and 2 oct. The release from masking found for the speech masker relative to the (steady-state) noise masker decreases with spectral envelope smearing.

Acoustic Stimulation↗

PubMed1996

Is growth saltatory? The usefulness and limitations of frequency distributions in analyzing pulsatile data.

Several investigators have proposed that descriptive statistics can be employed to identify and discriminate growth patterns. These studies assumed that the shape of the frequency distribution of daily growth velocities (FDGVs) is diagnostic in differentiating between a pattern of growth characterized by smooth, continuous daily acquisition and a pattern of growth characterized by a discontinuous, i.e. pulsatile process. The FDGV from a saltation and stasis, i.e. episodic or pulsatile, growth pattern was assumed to be bimodal or significantly skewed to the right, whereas a continuous growth function was assumed to be approximately Gaussian. The use of FDGV characteristics is an unprecedented approach to the analysis of longitudinal growth data and was not previously validated for this use. The present study investigates the performance characteristics of the FDGV method by Monte-Carlo simulations of known saltatory, i.e. pulsatile, growth patterns. These analyses show that the FDGV for a saltation and stasis growth process can be either unimodal or bimodal and either skewed to the right or to the left. Data collection frequency, measurement error, and total study duration all determine the shape of the FDGV and the statistical significance of the results. If the FDGV is highly skewed, then it is consistent with saltatory growth. However, if the FDGV is not highly skewed, then it is consistent with both the saltatory model and a smooth, continuous growth model, and thus, the results are ambiguous. We conclude that FDGV analysis is not a valid method to exclude saltation and stasis growth processes in longitudinal growth studies.

Child Development↗

PubMed1988

Pattern and motion vision without Laplacian zero crossings.

The zero crossings of band-limited signals are known to be rich in information. Recent models of information processing in biological visual systems have proposed that image structure is represented initially by such zero crossings, after the image has been bandpass filtered at multiple scales by neural receptive fields whose two-dimensional profiles resemble the Laplacian of a Gaussian. Because the resulting zero crossings generally correspond to physically meaningful structures such as edges and occlusion boundaries, and indeed under some conditions can exhaustively specify the original image, such representations have proven useful and efficient in a variety of machine vision problems. However, some simple information-processing operations that are apparent in human pattern and motion vision can be shown to be impossible in such representations, because the zero crossings in the bandpassed signals do not capture the necessary information (at any scale of analysis), because the information that they provide is misleading, or because there are no such crossings in the signals after delta 2 G sigma filtering at any scale. Examples are provided of simple visual signal-processing tasks (texture discrimination, motion perception, pattern detection) that human beings can perform effortlessly but that cannot be performed in the proposed multiscale delta 2 G sigma zero-crossings schemes. These perceptual capabilities offer evidence against this model of early image representation in human vision.

Animals↗

PubMed1981

Serial ordering in spike trains: what's it "trying to tell us"?

Summarized herein is the evidence that supports the hypothesis that neuronal action potentials (spike trains) are coded not only in terms of simple discharge rate but also can be serially coded by certain patterns of spike intervals. Based on the relative interval description method of Sherry and Marczynski (1972), our analyses of single-unit activity from cerebellar cortex neurons of rats seem to support three principal categories of conclusions; (1) Serial dependence of intervals does exist. This has been demonstrated with a variety of conventional statistical tests. These serial dependencies have also been shown to be independent of the (nonsequential) interval distribution variability. (2) Information theory is appropriate for evaluating spike trains. We have developed and tested methods for computing a fractional entropy for a given number of adjacent intervals, for assessing the relative fractional entropy of any one interval in a set of intervals, for computing for a group of neurons the mean and standard deviation of fractional entropy for specified clusters or intervals, and for transforming these values so that interval clusters of differing number can all be compared on the same numerical entropy scale (percentage maximum fractional entropy). In addition to the descriptive and quantitative value of such measures, we have also demonstrated their utility in testing hypotheses and in making empirical correlations. (3) The nervous system seems to process spike train intervals in "bytes", not "hits", of adjacent, serially ordered intervals. Among the several lines of evidence for this conclusion is the demonstration that drug-induced (ethanol) changes in fractional entropy of specific interval clusters seem to involve a "linked" combination of certain interval clusters, some which increase and others which decrease in incidence. Also, by using n-dimensional Chi-Square methodology, we have demonstrated that the relationships of adjacent intervals represent a Markovian process in which the duration of a given interval is partially determined by the duration of as many as four immediately preceding intervals. Finally, we showed that the relative fractional entropy (% maximum) of interval clusters of different numbers does not have a Gaussian distribution but rather is distributed in surprising ways by the specific number and relative durations of adjacent intervals. So just what is the serial ordering and information content of spike train intervals trying to tell us?. Perhaps it is trying to say that the nervous system processes information on a moment-by-moment basis in terms of "bytes" of short sequences of spikes with specific patterns of relative interspike durations. If so, we should be able to identify and characterize those "bytes". Much further testing must be done before we can claim that "neural codes" operate on the principles described herein. Nonetheless, we have made the issues explicit, and in our opinion have provided enough evidence to warrant further investigation.

Animals↗

PubMed2004

Advantages in using multi-frequency driving ultrasound for optimizing echo particle image velocimetry techniques.

We have recently developed an ultrasound based velocimetry technique, termed echo particle image velocimetry (echo PIV). This method takes advantage of the non-linear backscatter characteristics of ultrasound contrast microbubbles when exposed to certain ultrasonic field. Preliminary in vitro, animal and clinical studies have shown significant promise of this method for measuring multiple velocity components with good temporal and spatial resolution. However, there is still difficulty in maximizing the non-linearity of bubble backscatter using conventional Gaussian-pulse excitation techniques because significant harmonic components may not be produced at modest pressure amplitudes and the higher incident pressure amplitudes required to induce non-linear behavior may cause bubble destruction. We present here a potential solution to this problem through the use of multi-frequency excitation. A rectangular pulse with multiple harmonics is used to drive the bubble. The backscatter process is studied through a modified Rayleigh-Plesset equation. Results show that the rectangular wave is effective in improving the visibility of microbubbles with ultrasound backscattered efficiency significantly higher than the widely used Gaussian waveform. Use of rectangular pulses with 4 and 2 harmonics showed no significant difference in bubble backscatter behavior, indicating that a two-frequency excitation may be sufficient to induce non-linear behavior of the microbubbles practically at modest incident pressures.

Algorithms↗

PubMed1998

Stochastic modeling of the dynamics of CD4+ T-cell infection by HIV and some Monte Carlo studies.

In this paper, we develop a stochastic model for the interaction between CD4+ T cells and the human immunodeficiency virus (HIV) virus by taking into account the basic biological mechanism as described in [1-4]. We studied this stochastic model through extensive Monte Carlo simulations. Our results show that, in some cases, there is a positive probability that the virus will be eliminated by the process. We have also shown that, at the earlier stage of the infection, the probability distributions of the CD4+ T cells and free HIV are skewed; however, these distributions will eventually converge to the Gaussian distributions after several years. A real-data example is given to illustrate the application of our model.

CD4-Positive T-Lymphocytes↗

PubMed2001

Direct reconstruction of non-Cartesian k-space data using a nonuniform fast Fourier transform.

An algorithm of Dutt and Rokhlin (SIAM J Sci Comput 1993;14:1368-1383) for the computation of a fast Fourier transform (FFT) of nonuniformly-spaced data samples has been extended to two dimensions for application to MRI image reconstruction. The 2D nonuniform or generalized FFT (GFFT) was applied to the reconstruction of simulated MRI data collected on radially oriented sinusoidal excursions in k-space (ROSE) and spiral k-space trajectories. The GFFT was compared to conventional Kaiser-Bessel kernel convolution regridding reconstruction in terms of image reconstruction quality and speed of computation. Images reconstructed with the GFFT were similar in quality to the Kaiser-Bessel kernel reconstructions for 256(2) pixel image reconstructions, and were more accurate for smaller 64(2) pixel image reconstructions. Close inspection of the GFFT reveals it to be equivalent to a convolution regridding method with a Gaussian kernel. The Gaussian kernel had been dismissed in earlier literature as nonoptimal compared to the Kaiser-Bessel kernel, but a theorem for the GFFT, bounding the approximation error, and the results of the numerical experiments presented here show that this dismissal was based on a nonoptimal selection of Gaussian function.

Algorithms↗

PubMed2006

Dynamics of unfolded polypeptide chains in crowded environment studied by fluorescence correlation spectroscopy.

Proteins have evolved to fold and function within a cellular environment that is characterized by high macromolecular content. The earliest step of protein folding represents intrachain contact formation of amino acid residues within an unfolded polypeptide chain. It has been proposed that macromolecular crowding can have significant effects on rates and equilibria of biomolecular processes. However, the kinetic consequences on intrachain diffusion of polypeptides have not been tested experimentally, yet. Here, we demonstrate that selective fluorescence quenching of the oxazine fluorophore MR121 by the amino acid tryptophan (Trp) in combination with fast fluorescence correlation spectroscopy (FCS) can be used to monitor end-to-end contact formation rates of unfolded polypeptide chains. MR121 and Trp were incorporated at the terminal ends of polypeptides consisting of repetitive units of glycine (G) and serine (S) residues. End-to-end contact formation and dissociation result in "off" and "on" switching of MR121 fluorescence and underlying kinetics can be revealed in FCS experiments with nanosecond time resolution. We revisit previous experimental studies concerning the dependence of end-to-end contact formation rates on polypeptide chain length, showing that kinetics can be described by Gaussian chain theory. We further investigate effects of solvent viscosity and temperature on contact formation rates demonstrating that intrachain diffusion represents a purely diffusive, entropy-controlled process. Finally, we study the influence of macromolecular crowding on polypeptide chain dynamics. The data presented demonstrate that intrachain diffusion is fast in spite of hindered diffusion caused by repulsive interactions with macromolecules. Findings can be explained by effects of excluded volume reducing chain entropy and therefore accelerating the loop search process. Our results suggest that within a cellular environment the early formation of structural elements in unfolded proteins can still proceed quite efficiently in spite of hindered diffusion caused by high macromolecular content.

Diffusion↗

PubMed2005

The combined effect of spatial compounding and nonlinear filtering on the speckle reduction in ultrasound images.

Recently, a spatial compounding ultrasound imaging method was presented that utilizes a conventional 64-element phased array transducer with two unfocused pistons, each placed at one of the sides of the phased array transducer. This method is augmented here by inclusion of nonlinear filtering of the compounded images. The combined effects of the specific spatial compounding and nonlinear filtering on speckle reduction in the generated ultrasound images are studied and evaluated in two stages: First, the image quality is studied when nonlinear filtering is used as part of the spatial compounding. The study is performed by simulations using the Field II program, by processing several B-mode images of a kidney. The second stage compares the results obtained by the simulations to those obtained by in vitro laboratory experiments. Five different compounding strategies and two nonlinear filters, Gaussian and anisotropic diffusion, are investigated and evaluated in terms of image quality parameters-contrast and signal-to-noise ratio. It is shown that the combination of "averaging+nonlinear Gaussian filtering" produces the greatest improvement of image quality. When compared to a conventional phased array imaging system, the spatial compounding method that includes the conventional 64-element phased array transducer with two unfocused pistons, and employs the "averaging+nonlinear Gaussian filtering" strategy, obtains improvement in SNR that has reached 334%. Thus, though this method necessitates a somewhat wider probe, it produces significantly improved images.

Computer Simulation↗

PubMed2002

Simulation study for cloud detection with space lidars by use of analog detection photomultiplier tubes.

Output signal electrons from photomultiplier tubes (PMTs) have neither a Gaussian nor a Poisson distribution because of changes induced by multiplication when the number of input signal photons and dark electrons is fewer than approximately 100. Therefore the assumption of a Gaussian distribution of signal electrons cannot be used in simulations for space lidar observations with PMTs, for which the number of return signal photons is normally small. A theory is introduced for analog detection with PMTs that have Poisson-distributed secondary-electron emission at each dynode stage. The theory is validated by straightforward numerical simulations. It is shown that the multiplication in PMTs is a multiply stochastic Poisson process and that the distribution of output signal electrons can be interpreted basically as Neyman type A. Analysis by the threshold method of cloud detection with a space lidar shows considerable difference between a Gaussian approximation and the exact distribution. The result indicates that the threshold level must be optimized for the exact distribution. Return signals were simulated for a proposed space lidar, and cloud detection with the threshold method was demonstrated.

Journal Article↗