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At least 487 records · Page 27Linked to original sources

PubMed2006

Hydrophobic collapse in (in silico) protein folding.

A model of hydrophobic collapse, which is treated as the driving force for protein folding, is presented. This model is the superposition of three models commonly used in protein structure prediction: (1) 'oil-drop' model introduced by Kauzmann, (2) a lattice model introduced to decrease the number of degrees of freedom for structural changes and (3) a model of the formation of hydrophobic core as a key feature in driving the folding of proteins. These three models together helped to develop the idea of a fuzzy-oil-drop as a model for an external force field of hydrophobic character mimicking the hydrophobicity-differentiated environment for hydrophobic collapse. All amino acids in the polypeptide interact pair-wise during the folding process (energy minimization procedure) and interact with the external hydrophobic force field defined by a three-dimensional Gaussian function. The value of the Gaussian function usually interpreted as a probability distribution is treated as a normalized hydrophobicity distribution, with its maximum in the center of the ellipsoid and decreasing proportionally with the distance versus the center. The fuzzy-oil-drop is elastic and changes its shape and size during the simulated folding procedure.

Amino Acids↗

PubMed2006

Spike sorting: Bayesian clustering of non-stationary data.

Spike sorting involves clustering spikes recorded by a micro-electrode according to the source neurons. It is a complicated task, which requires much human labor, in part due to the non-stationary nature of the data. We propose to automate the clustering process in a Bayesian framework, with the source neurons modeled as a non-stationary mixture-of-Gaussians. At a first search stage, the data are divided into short time frames, and candidate descriptions of the data as mixtures-of-Gaussians are computed for each frame separately. At a second stage, transition probabilities between candidate mixtures are computed, and a globally optimal clustering solution is found as the maximum-a-posteriori solution of the resulting probabilistic model. The transition probabilities are computed using local stationarity assumptions, and are based on a Gaussian version of the Jensen-Shannon divergence. We employ synthetically generated spike data to illustrate the method and show that it outperforms other spike sorting methods in a non-stationary scenario. We then use real spike data and find high agreement of the method with expert human sorters in two modes of operation: a fully unsupervised and a semi-supervised mode. Thus, this method differs from other methods in two aspects: its ability to account for non-stationary data, and its close to human performance.

Algorithms↗

PubMed2004

An inverse system for incorporation of conditioning to pressure and streamline-based calibration.

A streamline-based history matching technique is employed to perform fast and efficient permeability identification and to integrate tracer data into an inverse model. To incorporate tracer data into the inverse model, a given tracer breakthrough curve is interpreted as cumulative breakthrough along independent streamlines. Permeabilities are modified along each streamline to match the tracer breakthrough curve. In this way, there is no explicit computation of sensitivity coefficients, nor any matrix inversion. However, this approach is incomplete by itself. Since the modifications occur along the streamlines, the identified permeability distribution is often incompatible with the actual permeability distribution. Thus, streamlines should be positioned correctly before the streamline-based method is applied. To accomplish this, geostatistical methods such as kriging and sequential Gaussian simulation (SGS) are implemented to provide an appropriate disposition of streamlines at the beginning of the inverse process. Then, permeabilities are iteratively calibrated in a conventional grid system to satisfy pressure and permeability observation data, and simultaneously modified along streamlines to match tracer data. The two independent optimization processes assist mutually and lead to stable convergence to a minimum. By applying the proposed inverse system to synthetic reference fields, it is observed that identified fields satisfactorily reproduce the permeability distribution of the reference fields. In addition, the pressure distributions of the identified and the reference fields are fairly alike, and the identified tracer breakthrough curves are well fitted to those of the reference fields. With regard to spatial patterns of transport behaviors, the streamlines of the identified fields show similar trajectories to those of the reference fields, and the time of flight distributions of the inversed fields are also analogous to those of the reference fields. The proposed inverse system is capable of estimating the future performance of a two-dimensional aquifer from a constrained number of permeability and pressure observation data accompanied by tracer data.

Calibration↗

PubMed1996

Effective source size, yield and beam profile from multi-layered bremsstrahlung targets.

Modern conformal radiotherapy benefits from heterogeneous dose delivery using scanned narrow bremsstrahlung beams of high energy in combination with dynamic double focused multi-leaf collimation and purging magnets. When using a purging magnet to remove electrons and positrons the target space is limited and unorthodox thin multi-layered targets are needed. A computational technique has therefore been developed to determine the forward yield and the angular distributions of the bremsstrahlung beam as well as the size and location of the effective and the virtual photon point source for arbitrary multi-layer bremsstrahlung targets. The Gaussian approximation of the diffusion equation for the electrons has been used and convolved with the bremsstrahlung production process. For electrons with arbitrary emittance impinging on targets of any multi-layer and atomic number combination, the model is well applicable, at least for energies in the range 1-100 MeV. The intrinsic bremsstrahlung photon profile has been determined accurately by deconvolving the electron multiple scattering process from thin experimental beryllium target profiles. For electron pencil beams incident on a target of high density and atomic number such as tungsten, the size of the effective photon source stays at around a tenth of a millimetre. The effective photon source for low-Z materials such as Be, C and Al is located at depths from 3-7 mm in the target, decreasing with increasing atomic number. The effective photon source at off-axis positions then moves out considerably from the central axis, which should be considered when aligning collimators. For high-Z materials such as tungsten, the location of the effective photon source is at a few tenths of a millimetre deep. The virtual photon point source is located only a few tenths of a millimetre upstream of the effective photon source both for high- and low-Z materials. For 50 MeV electrons incident on multi-layered full range targets the radial energy fluence distributions will have a full width at half maximum (FWHM) of 80 to 100 mm at 1 m from the target. The best target composition made of two layers when the space is limited to 15 mm was found to be 9 mm-Be followed by 6 mm W. A thin beryllium target (approximately 3 mm) results in a high-intensity bremsstrahlung lobe with a FWHM of about 35 mm at the isocentre. Interestingly, the forward dose rate in such a beam is as high as 62% of the maximum achievable with an optimal target design, even if on average only 1 MeV is lost by the electrons.

Biophysical Phenomena↗

PubMed2004

Enhancement by noise in parallel arrays of sensors with power-law characteristics.

An optimally tuned power-law sensor is shown capable of amplifying the signal-to-noise ratio of a sine wave in Gaussian white noise. When associated in parallel arrays, further improvement can be obtained with independent noises injected on these sensors. This form of stochastic resonance in arrays, obtained here with smooth threshold-free nonlinearities, yields signal-to-noise ratio gains above unity in a true regime of added noise for a sine wave in Gaussian white noise, along with a class of nonlinear devices with useful potentialities for noise-aided information processing.

Journal Article↗

PubMed2006

Dynamics of a tracer granular particle as a nonequilibrium Markov process.

The dynamics of a tracer particle in a stationary driven granular gas is investigated. We show how to transform the linear Boltzmann equation, describing the dynamics of the tracer into a master equation for a continuous Markov process. The transition rates depend on the stationary velocity distribution of the gas. When the gas has a Gaussian velocity probability distribution function (PDF), the stationary velocity PDF of the tracer is Gaussian with a lower temperature and satisfies detailed balance for any value of the restitution coefficient alpha. As soon as the velocity PDF of the gas departs from the Gaussian form, detailed balance is violated. This nonequilibrium state can be characterized in terms of a Lebowitz-Spohn action functional W(tau) defined over trajectories of time duration tau. We discuss the properties of this functional and of a similar functional W(tau), which differs from the first for a term that is nonextensive in time. On the one hand, we show that in numerical experiments (i.e., at finite times tau), the two functionals have different fluctuations and W always satisfies an Evans-Searles-like symmetry. On the other hand, we cannot observe the verification of the Lebowitz-Spohn-Gallavotti-Cohen (LS-GC) relation, which is expected for W(tau) at very large times tau. We give an argument for the possible failure of the LS-GC relation in this situation. We also suggest practical recipes for measuring W(tau) and W(tau) in experiments.

Journal Article↗

PubMed2004

Current fluctuations in nonequilibrium diffusive systems: an additivity principle.

We formulate a simple additivity principle allowing one to calculate the whole distribution of current fluctuations through a large one dimensional system in contact with two reservoirs at unequal densities from the knowledge of its first two cumulants. This distribution (which in general is non-Gaussian) satisfies the Gallavotti-Cohen symmetry and generalizes the one predicted recently for the symmetric simple exclusion process. The additivity principle can be used to study more complex diffusive networks including loops.

Journal Article↗

PubMed2000

Foliage echoes: a probe into the ecological acoustics of bat echolocation.

The research reported here aims at understanding the biosonar system of bats based on the properties of its natural inputs (ecological acoustics). Echoes from foliages are studied as examples of ubiquitous, natural targets. The echo properties and their qualitative relationship to plant architecture are described. The echoes were found to be profoundly stochastic and in general neither Gaussian nor stationary. Consequently, features useful for discrimination of such target classes will be confined to estimated random process parameters. Several such statistical signal features which are sufficiently invariant to allow a classification of the used example plants were identified: the characteristic exponent and the dispersion of an alpha-stable model for the amplitude distribution, a crest factor defined as the ratio of maximum squared amplitude and signal energy, the dispersion of the first threshold passage distribution, the structure of the correlation matrix, and a nonstationarity in sound channel gain. Discrimination error probability could be reduced by combining features pairwise. The best combination was the crest factor and the correlation coefficient of a log-linear model of the time-variant sound channel gain; it yielded an estimated Bayes risk of 6.9% for data pooled from different views.

Acoustics↗

PubMedDate not supplied

EM-REML estimation of covariance parameters in Gaussian mixed models for longitudinal data analysis.

This paper presents procedures for implementing the EM algorithm to compute REML estimates of variance covariance components in Gaussian mixed models for longitudinal data analysis. The class of models considered includes random coefficient factors, stationary time processes and measurement errors. The EM algorithm allows separation of the computations pertaining to parameters involved in the random coefficient factors from those pertaining to the time processes and errors. The procedures are illustrated with Pothoff and Roy's data example on growth measurements taken on 11 girls and 16 boys at four ages. Several variants and extensions are discussed.

Journal Article↗

PubMed2006

Optical integrator for optical dark-soliton detection and pulse shaping.

The design and analysis of an Nth-order optical integrator using the digital filter technique is presented. The optical integrator is synthesized using planar-waveguide technology. It is shown that a first-order optical integrator can be used as an optical dark-soliton detector by converting an optical dark-soliton pulse into an optical bell-shaped pulse for ease of detection. The optical integrators can generate an optical step function, staircase function, and paraboliclike functions from input optical Gaussian pulses. The optical integrators may be potentially used as basic building blocks of all-optical signal processing systems because the time integrals of signals may sometimes be required for further use or analysis. Furthermore, an optical integrator may be used for the shaping of optical pulses or in an optical feedback control system.

Journal Article↗

PubMed1998

Myoelectric signal classification using neural networks.

A feed-forward neural network is used for diagnosis of spastic paralysis. It is a two-layer perceptron and it is able to classify two kinds of myoelectric signal recorded in surface electromyography: the normal EMG and the EMG in the case of spastic paralysis. The myoelectric signal was recorded with a surface electrode pair and sampled at 10 kHz. The EMG activity is stochastic and the instantaneous amplitude distribution for a fixed level of contraction is Gaussian. The signal variance is considered a measure of muscle force. We can describe any kind of this process by the AR model. For a precisely modeling of EMG there are necessary many AR model parameters. In the classification problem we have it is not necessary to use a high order AR model. We find a 4-th order AR model is good enough for this study. The Hopfield algorithm is used to calculate the parameters of the autoregressive model.

Electrodes↗

PubMed2005

Enhanced temporal response properties of anteroventral cochlear nucleus neurons to broadband noise.

Compared with auditory nerve (AN) fibers, trapezoid body (TB) fibers of the cat show enhanced synchronization to low-frequency tones. This phenomenon probably contributes to the high temporal resolution of binaural processing. We examined whether enhanced synchronization also occurs to sustained broadband noise. We recorded responses to a reference Gaussian noise and its polarity-inverted version in the TB of barbiturate-anesthetized cats. From these we constructed shuffled autocorrelograms (SACs) and quantified spike timing by measuring the amplitude and width of their central peak. Many TB fibers with low characteristic frequency (CF) showed SACs with higher and narrower central peaks than ever observed in the AN, indicating better consistency and precision of temporal coding. Larger peaks were also observed in TB fibers with high CF, but this was mostly caused by higher average firing rates, resulting in a larger number of coincident spikes across stimulus repetitions. The results document monaural preprocessing of the temporal information delivered to binaural nuclei in the olivary complex, which likely contributes to the high sensitivity to interaural time differences.

Acoustic Stimulation↗

PubMedDate not supplied

Endosulfan transport: II. Modeling airborne dispersal and deposition by spray and vapor.

Endosulfan (C9H6O3Cl6S; 6,7,8,9,10,10-hexachloro-1,5,5a,6,9,9a-hexahydro-6,9-methano-2,4,3-benzodioxathiepin 3-oxide) and other agricultural chemicals can be transported from farms to rivers by several airborne pathways including spray drift and vapor transport. This paper describes a modeling framework for quantifying both of these airborne pathways, consisting of components describing the source, dispersion, and deposition phases of each pathway. Throughout, the framework uses economical descriptions consistent with the need to capture the major physical processes. The dispersion of spray and vapor is described by similarity and mass-conservation principles approximated by Gaussian solutions. Deposition of particles to vegetation is described by a single-layer model incorporating contributions from settling, impaction, and Brownian diffusion. Vapor deposition to water surfaces is described by a simple kinetic formulation dependent on an exchange velocity. All model components are tested against available field and laboratory data. The models, and the measurements used for comparisons, both demonstrate that spray drift and vapor transport are significant pathways. The broader context, described in another paper, is an integrative assessment of all transport pathways (both airborne and waterborne) contributing to endosulfan transport from farms to rivers.

Agriculture↗

PubMed2003

A neuro-fuzzy approach to classification of ECG signals for ischemic heart disease diagnosis.

The paper focuses on the neuro-fuzzy classifier called Fuzzy-Gaussian Neural Network (FGNN) to recognize the ECG signals for Ischemic Heart Disease (IHD) diagnosis. The proposed ECG processing cascade has two main stages: (a) Feature extraction from the QRST zone of ECG signals using either the Principal Component Analysis (PCA) or the Discrete Cosine Transform (DCT); (b) Pattern classification for IHD diagnosis using the FGNN. We have performed the software implementation and have experimented the proposed neuro-fuzzy model for IHD diagnosis. We have used an ECG database of 40 subjects, where 20 subjects are IHD patients and the other 20 are normal ones. The best performance has been of 100% IHD recognition score. The result is exciting as much as we have used only one lead (V5) of ECG records as input data, while the current diagnosis approaches require the set of 12 lead ECG signals!

Databases, Factual↗

PubMed1992

Effect of spectral envelope smearing on speech reception. I.

The effect of reduced spectral contrast on the speech-reception threshold (SRT) for sentences in noise and on phoneme identification, was investigated with 16 normal-hearing subjects. Signal processing was performed by smoothing the envelope of the squared short-time fast Fourier transform (FFT) by convolving it with a Gaussian-shaped filter, and overlapping additions to reconstruct a continuous signal. Spectral energy in the frequency region from 100 to 8000 Hz was smeared over bandwidths of 1/8, 1/4, 1/3, 1/2, 1, 2, and 4 oct for the SRT experiment. Vowel and consonant identification was studied for smearing bandwidths of 1/8, 1/2, and 2 oct. Results showed the SRT in noise to increase as the spectral energy was smeared over bandwidths exceeding the ear's critical bandwidth. Vowel identification suffered more from this type of processing than consonant identification. Vowels were primarily confused with the back vowels /c,u/, and consonants were confused where place of articulation is concerned.

Acoustic Stimulation↗

PubMed2006

Automated tool for the detection of cell nuclei in digital microscopic images: application to retinal images.

PURPOSE: To develop an automated tool that provides reliable, consistent, and accurate results for counting cell nuclei in tissue sections. METHODS: We propose a novel method based on an image processing algorithm to analyze large sets of digital micrographs. The nucleus detector design is based on a Laplacian of Gaussian filter. We use the leave-one-out cross validation method for estimating the generalization error, which is then used to choose the model and parameters of the proposed nucleus detector with both fluorescent and dye stained images. We also evaluate the performance of a nucleus detector by comparing the results with manual counts. RESULTS: When our nucleus detector is applied to previously unanalyzed images of feline retina, it correctly counts nuclei within the outer nuclear layer (ONL) with an average error of 3.67% ranging from 0 to 6.07%, and nuclei within the inner nuclear layer (INL) with an average error of 8.55% ranging from 0 to 13.76%. Our approach accurately identifies the location of cell bodies. Even though we have a relatively large error in the INL due to the large intra-observer variation, both manual counting and nucleus detector result in the same conclusion. This is the first time that cell death in the INL in response to retinal detachment is analyzed quantitatively. We also test the proposed tool with various images and show that it is applicable to a wide range of image types with nuclei varying in size and staining intensity. CONCLUSIONS: The proposed method is simple and reliable. It also has widespread applicability to a variety of sample preparation and imaging methods. Our approach will be immediately useful in quantifying cell number in large sets of digital micrographs and from high-throughput imaging. The tool is available as a plug-in for Image J.

Algorithms↗

PubMed2006

The development of temporal resolution: between-channel gap detection in infants and adults.

PURPOSE: Infants have a good ability to detect brief silent gaps between 2 short identical sound markers (within-channel gap detection), with thresholds between 2 and 11 ms. The present experiment traces the development of temporal resolution for between-channel gaps (i.e., gaps delineated by spectrally disparate markers). This ability appears crucial for the perception of complex stimuli such as speech and is thought to reflect more central auditory processing. METHOD: Infants age 6-7.5 months and adults were tested in a between-channel gap detection task using a conditioned head-turn procedure. Gaps were marked by 1- and 4-kHz Gaussian-enveloped sine-tone markers. RESULTS: Infant gap thresholds were between 30 and 40 ms under conditions in which adult thresholds were between 10 and 20 ms. CONCLUSIONS: Unlike within-channel gap detection, the central temporal processing required for between-channel gap detection is still immature at 6 months of age.

Acoustic Stimulation↗

PubMed2004

Production and characterization of spiral phase plates for optical wavelengths.

We describe the fabrication and characterization of a high-quality spiral phase plate as a device to generate optical vortices of low (3-5) specified charge at visible wavelengths. The manufacturing process is based on a molding technique and allows for the production of high-precision, smooth spiral phase plates as well as for their replication. An attractive feature of this process is that it permits the fabrication of nominally identical spiral phase plates made from different materials and thus yielding different vortex charges. When such a plate is inserted in the waist of a fundamental Gaussian beam, the resultant far-field intensity profile shows a rich vortex structure, in excellent agreement with diffraction calculations based on ideal spiral phase plates. Using a simple optical test, we show that the reproducibility of the manufacturing process is excellent.

Journal Article↗