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A new method to predict the evolution of the power spectral density for a finite-amplitude sound wave.

A method to predict the effect of nonlinearity on the power spectral density of a plane wave traveling in a thermoviscous fluid is presented. As opposed to time-domain methods, the method presented here is based directly on the power spectral density of the signal, not the signal itself. The Burgers equation is employed for the mathematical description of the combined effects of nonlinearity and dissipation. The Burgers equation is transformed into an infinite set of linear equations that describe the evolution of the joint moments of the signal. A method for solving this system of equations is presented. Only a finite number of equations is appropriately selected and solved by numerical means. For the method to be applied all appropriate joint moments must be known at the source. If the source condition has Gaussian characteristics (it is a Gaussian noise signal or a Gaussian stationary and ergodic stochastic process), then all the joint moments can be computed from the power spectral density of the signal at the source. Numerical results from the presented method are shown to be in good agreement with known analytical solutions in the preshock region for two benchmark cases: (i) sinusoidal source signal and (ii) a Gaussian stochastic process as the source condition.

Journal Article↗

Dimerization kinetics of the IgE-class antibodies by divalent haptens. II. The interactions between intact IgE and haptens.

Interactions between a monoclonal, DNP-specific IgE molecules (hybridoma A2) and divalent DNP-haptens in solution cause aggregation of the former predominantly into closed rings of two IgE and two divalent haptens (Schweitzer-Stenner, R., A. Licht, I. Lüscher, and I. Pecht. 1987. Biochemistry. 26:3602-3612). The time course of this process was now investigated by titrating the A2-IgE with divalent DNP-haptens having long and rigid oligoproline spacers (di(N epsilon-2,4-dinitrophenyl)-6-amino-hexanoate-aspartyl-(prolyl)n-L-ly- syl; n = 24, 27, 33). Binding was expressed in quenching of the IgE intrinsic tryptophan emission. As shown in the preceding paper, hapten addition to the IgE-A2 at rates faster than a distinct threshold value led to nonequilibrium titrations (NETs) from which kinetic processes slower than 2 s-1 can be resolved. Analysis of these titrations shows that the dimeric rings open at rates of approximately 10(-2) s-1, independent of the divalent hapten's spacer length. The ring closure rate, however, decreases with spacer length. The latter observation was qualitatively rationalized in terms of the diffusion process of a Gaussian chain which relates the ring closure rate constant to the expectation value for the distance between the free ends of the respective open chain.

Animals↗

Modulation ratio in comprehensive two-dimensional gas chromatography.

Comprehensive two-dimensional chromatography employs a serially coupled two-column arrangement where effluent from the first column is collected or sampled and then introduced to the second column according to a chosen modulation period. This is effected by use of a modulator at or near the column junction. One of the considerations in applying the technique is the period of the modulator, which determines the sampling duration of the first column effluent. Here, we propose that the sampling rate can be most effectively described by a new term, called the modulation ratio (MR). This is defined as the ratio of 4 times the first column peak standard deviation (4sigma) divided by the modulation period (PM) or 1.6985 times the half-height width of the peak (wh): MR = 4sigma/PM = wb/PM = (wh x 1.6985)/PM. The 4sigma value is more commonly recognized as the peak base width (wb). The use of 4sigma as the numerator is preferred to simply sigma because when the PM value used for an experiment is equal to sigma, then the MR value is calculated to be 4, implying that the primary peak will be modulated approximately 4 times as is normally recommended for a comprehensive multidimensional separation. The less well-defined term of modulation number (NM) has been previously used and proposed as the number of modulations per peak and, therefore, is intended to convey the manner in which the primary column peak is sampled; this is a subjective and not well-characterized value. The use of MR should provide users with a meaningful and strictly defined value when reporting experimental conditions. The utility of MR is demonstrated through a mathematical model of the modulation process for both Gaussian and tailing peaks, supported by an experimental study of the modulation ratio. It is shown that for the analysis of trace compounds where precise quantitative measurements are being made, the experiment should be conducted with an MR of at least 3. Conversely, for semiquantitative methods or the analysis of major components, an MR of approximately 1.5 should suffice.

Journal Article↗

Indications of nonlinear deterministic and finite-dimensional structures in time series of brain electrical activity: dependence on recording region and brain state.

We compare dynamical properties of brain electrical activity from different recording regions and from different physiological and pathological brain states. Using the nonlinear prediction error and an estimate of an effective correlation dimension in combination with the method of iterative amplitude adjusted surrogate data, we analyze sets of electroencephalographic (EEG) time series: surface EEG recordings from healthy volunteers with eyes closed and eyes open, and intracranial EEG recordings from epilepsy patients during the seizure free interval from within and from outside the seizure generating area as well as intracranial EEG recordings of epileptic seizures. As a preanalysis step an inclusion criterion of weak stationarity was applied. Surface EEG recordings with eyes open were compatible with the surrogates' null hypothesis of a Gaussian linear stochastic process. Strongest indications of nonlinear deterministic dynamics were found for seizure activity. Results of the other sets were found to be inbetween these two extremes.

Brain↗

Usefulness of an intraoperative electrophysiological navigator system for subthalamic nucleus surgery in Parkinson's disease.

OBJECTS: The characteristics and benefits are presented of an intraoperative neurophysiological navigator computerized system developed in our center (Columbus-Track 1.0) that helps the surgical team in neuronal identification and in strategy processes in subthalamic nucleus surgery for Parkinson's disease (PD). METHODS: The navigator consists of three assembled parts: (1) neuronal identification, based on wavelet processing, filtering and gaussian characteristics of the signal; (2) track identification, based on anatomical coincidence, somatomotor response and microstimulation quotient, and (3) strategy, coordinating correction for the next track. A retrospective comparative study was performed with 15 consecutive PD patients (30 targets) operated without the system and the next 15 consecutive patients operated with the aid of the system. With the aid of the computerized navigation system, a significant reduction in the number of tracks was observed (t = -2.503, p = 0.0015), with a mean difference of 1.2 tracks per hemisphere. A non-significant reduction in the total intervention time was also observed, with a mean difference of 20 min per hemisphere (t = -1.418, p = 0.161). CONCLUSIONS: The intraoperative computerized navigation system can aid the surgical team in better identifying the neuronal signal and in defining the optimal track to achieve the target.

Humans↗

On the distribution and convergence of feature space in self-organizing maps.

In this paper an analysis of the statistical and the convergence properties of Kohonen's self-organizing map of any dimension is presented. Every feature in the map is considered as a sum of a number of random variables. We extend the Central Limit Theorem to a particular case, which is then applied to prove that the feature space during learning tends to multiple gaussian distributed stochastic processes, which will eventually converge in the mean-square sense to the probabilistic centers of input subsets to form a quantization mapping with a minimum mean squared distortion either globally or locally. The diminishing effect, as training progresses, of the initial states on the value of the feature map is also shown.

Algorithms↗

Including long-range dependence in integrate-and-fire models of the high interspike-interval variability of cortical neurons.

Many different types of integrate-and-fire models have been designed in order to explain how it is possible for a cortical neuron to integrate over many independent inputs while still producing highly variable spike trains. Within this context, the variability of spike trains has been almost exclusively measured using the coefficient of variation of interspike intervals. However, another important statistical property that has been found in cortical spike trains and is closely associated with their high firing variability is long-range dependence. We investigate the conditions, if any, under which such models produce output spike trains with both interspike-interval variability and long-range dependence similar to those that have previously been measured from actual cortical neurons. We first show analytically that a large class of high-variability integrate-and-fire models is incapable of producing such outputs based on the fact that their output spike trains are always mathematically equivalent to renewal processes. This class of models subsumes a majority of previously published models, including those that use excitation-inhibition balance, correlated inputs, partial reset, or nonlinear leakage to produce outputs with high variability. Next, we study integrate-and-fire models that have (nonPoissonian) renewal point process inputs instead of the Poisson point process inputs used in the preceding class of models. The confluence of our analytical and simulation results implies that the renewal-input model is capable of producing high variability and long-range dependence comparable to that seen in spike trains recorded from cortical neurons, but only if the interspike intervals of the inputs have infinite variance, a physiologically unrealistic condition. Finally, we suggest a new integrate-and-fire model that does not suffer any of the previously mentioned shortcomings. By analyzing simulation results for this model, we show that it is capable of producing output spike trains with interspike-interval variability and long-range dependence that match empirical data from cortical spike trains. This model is similar to the other models in this study, except that its inputs are fractional-gaussian-noise-driven Poisson processes rather than renewal point processes. In addition to this model's success in producing realistic output spike trains, its inputs have long-range dependence similar to that found in most subcortical neurons in sensory pathways, including the inputs to cortex. Analysis of output spike trains from simulations of this model also shows that a tight balance between the amounts of excitation and inhibition at the inputs to cortical neurons is not necessary for high interspike-interval variability at their outputs. Furthermore, in our analysis of this model, we show that the superposition of many fractional-gaussian-noise-driven Poisson processes does not approximate a Poisson process, which challenges the common assumption that the total effect of a large number of inputs on a neuron is well represented by a Poisson process.

Action Potentials↗

Crooks equation for steered molecular dynamics using a Nosé-Hoover thermostat.

The Crooks equation [Eq. (10) in J. Stat. Phys. 90, 1481 (1998)], originally derived for microscopically reversible Markovian systems, relates the work done on a system during an irreversible transformation to the free energy difference between the final and the initial state of the transformation. In the present work we provide a theoretical proof of the Crooks equation in the context of constant volume, constant temperature steered molecular dynamics simulations of systems thermostated by means of the Nosé-Hoover method (and its variant using a chain of thermostats). As a numerical test we use the folding and unfolding processes of decaalanine in vacuo at finite temperature. We show that the distribution of the irreversible work for the folding process is markedly non-Gaussian thereby implying, according to Crooks equation, that also the work distribution of the unfolding process must be inherently non-Gaussian. The clearly asymmetric behavior of the forward and backward irreversible work distributions is a signature of a non-Markovian regime for the folding/unfolding of decaalanine.

Journal Article↗

Volumetric bone marrow cellularity (VBMC) assessment from routinely processed trephines using three-dimensional x-ray histology and gaussian peak modelling.

Objective.Bone marrow cellularity is routinely estimated from a small number of two-dimensional histology sections, making assessment sensitive to section representativeness, processing artefacts and observer interpretation. Three-dimensional (3D) x-ray histology (XRH), using x-ray computed microtomography (µCT), enables non-destructive whole-block imaging of trephine biopsies. This study evaluated whether XRH combined with Gaussian peak modelling could provide a pragmatic whole-block volumetric bone marrow cellularity (VBMC) estimate from formalin-fixed paraffin-embedded (FFPE) trephine biopsy blocks.Approach.Six routinely processed FFPE bone marrow trephine blocks were imaged using µCT-based XRH at ∼15 µm spatial resolution. VBMC was defined as the red-marrow (RM) fraction of the marrow soft-tissue compartment, RM/(RM + intra-biopsy wax), with wax serving as the volumetric proxy for adipocyte/yellow marrow space. Whole-volume greyscale histograms were modelled using a three-peak Gaussian approach representing intra-biopsy wax, RM and demineralised trabecular matrix. Peak-height and area-under-the-curve metrics were compared with whole-volume 3D segmentation and clinical two-dimensional (2D) cellularity estimates.Main Results.Gaussian peak modelling successfully approximated the segmented tissue-phase distributions. The peak-height-derived VBMC metric showed the closest agreement with whole-volume 3D segmentation, with an average absolute percentage difference of 9.3%, compared with 18.6% for clinical expert 2D cellularity estimates. The area-under-the-curve metric followed similar trends but consistently overestimated VBMC. Clinical 2D cellularity broadly followed whole-biopsy trends but showed one discordant case not explained by slice-position sampling alone. XRH also enabled unrestricted virtual reslicing and visualisation of sectioning-associated artefacts prior to further microtomy.Significance.Pre-sectioning XRH combined with Gaussian peak modelling provides a rapid, segmentation-free route to volumetric cellularity estimation from intact clinical FFPE trephine blocks. The approach supports objective whole-biopsy assessment while remaining compatible with routine histopathology workflows, reflecting the expected limitations of section-based visual estimation despite its role as the current clinical standard. In the near term, it could provide a non-disruptive adjunct to conventional 2D cellularity reporting, pending larger validation studies.

Imaging, Three-Dimensional↗

Minimal stochastic model for Fermi's acceleration.

We introduce a simple stochastic system able to generate anomalous diffusion for both position and velocity. The model represents a viable description of the Fermi's acceleration mechanism and it is amenable to analytical treatment through a linear Boltzmann equation. The asymptotic probability distribution functions for velocity and position are explicitly derived. The diffusion process is highly non-Gaussian and the time growth of moments is characterized by only two exponents nu(x) and nu(v). The diffusion process is anomalous (non-Gaussian) but with a defined scaling property, i.e., P(|r|,t)=1/t(nu(x))Fx(|r|/t(nu(x))) and similarly for velocity.

Journal Article↗

Image recognition in the presence of non-Gaussian noise with unknown statistics.

We design receivers to detect a known pattern or a reference signal in the presence of very general and non-Gaussian types of noise. Three sources of input-noise degradation are considered: additive, multiplicative, and disjoint background. The detection process involves two steps: (1) estimation of the relevant noise parameters within the framework of hypothesis testing and (2) maximizing a certain metric that measures the likelihood of the target being at a given location. The parameter estimation portion is carried out by moment-matching techniques. Because of the number of unknown parameters and the fact that various types of input-noise processes are non-Gaussian, the methods that are used to estimate these parameters differ from the standard methods of maximizing the likelihood function. To verify the existence of the target at a certain location, we use l(p)-norm metric for p > or = 0 to measure the likelihood of the target being present at the location of interest. Computer simulations are used to show that for the images tested here, the receivers designed herein perform better than some existing receivers.

Journal Article↗

Quantized rotation of atoms from photons with orbital angular momentum.

We demonstrate the coherent transfer of the orbital angular momentum of a photon to an atom in quantized units of variant Planck's over 2pi, using a 2-photon stimulated Raman process with Laguerre-Gaussian beams to generate an atomic vortex state in a Bose-Einstein condensate of sodium atoms. We show that the process is coherent by creating superpositions of different vortex states, where the relative phase between the states is determined by the relative phases of the optical fields. Furthermore, we create vortices of charge 2 by transferring to each atom the orbital angular momentum of two photons.

Journal Article↗

[Echodensitometry: a new echographic diagnostic possibility].

The determination and quantification of grey levels in the echography scale, designated by some authors Echodensitometry, is viewed as a new method for diagnosis using ultrasound techniques. This paper advances the results from a study conducted with an echographer equipped with an echographic density measuring device. This model analyzes the number of pixels in the image showing the most frequent level of grey. Normal and pathological parenchymatous urological organs (kidney, prostate and testicle) have been examined. Normal organs show a gaussian distribution of grey with a predominant level of typical grey for each of them. When affected by an acute inflammatory process the organs maintain their gaussian distribution but the predominant grey is lower (darker) due to the edema and the hyperaemia. When the inflammatory process becomes chronic, distribution, although somewhat irregular, is still gaussian but with higher predominance of grey (lighter) probably due to the fibrosis. The tumoral cases of our study also showed a gaussian curve even more irregular and with levels of variable grey. When specific areas of the tumour are analyzed the findings are very distinct depending on whether the areas are hypo or hyperechoic. Hyperechoic areas produce highly irregular maps. Research should be directed to provide more complex, although easy to perform systems of analysis which can correlate adequately with the histological study. It would be desirable that the equipment would be standardized to allow analysis of 'in vitro' images. If and when these objectives can be accomplished we would be able to venture into an echography histological diagnosis, something nowadays yet impossible.

Densitometry↗

Modeling birthweight and gestational age distributions: additive vs. multiplicative processes.

Researchers have traditionally employed Gaussian distributions to model quantitative biological traits. Recently, mixtures of Gaussian distributions have begun to be used as well. However, there are many alternatives to the Gaussian distribution. From a theoretical perspective, the lognormal distribution is as applicable as the Gaussian (both are justified on the basis of the Central Limit Theorem). Here, the utility of mixtures of Gaussians and lognormals for describing birthweight and gestational age distributions are compared. This is carried out within the context of the hybrid-lognormal distribution, in which the Gaussian and lognormal are special cases. The data consists of African American births (1985-1988) and European American births (1988) in the state of New York. The results suggest that of the conventional distributions, a mixture of two Gaussians generally provides the best fit to birthweight and gestational age. However, in the case of birthweight a two-component hybrid-lognormal fits better than any of the simpler models. This may be due to a feature of the hybrid-lognormal distribution that can be interpreted as maternal constraints on fetal development.

Birth Weight↗

An image analyzing system for interstitial lung abnormalities in chest radiography. Detection and classification by Laplacian-Gaussian filtering and linear opacity judgment.

RATIONALE AND OBJECTIVES: The effectiveness of a computerized analysis system to detect and characterize interstitial lung abnormalities seen on chest radiographs was evaluated. This method included a process of four-directional Laplacian-Gaussian filtering and a process of linear opacity judgement. For quantitative analysis of interstitial opacities, the radiographic index, which is the percentage of opacity areas in a region of interest, was obtained and evaluated in the images. These opacities represented interstitial lung abnormalities. METHODS: Two regions of interest were selected in each right lung of 50 patients with normal lung parenchyma and 50 patients with diffuse interstitial lung abnormalities, confirmed with high-resolution computed tomography. These regions of interest were processed by our computerized analysis system. RESULTS: Abnormal lungs were well differentiated from normal lungs by the radiographic indices obtained from the images filtered by four-directional Laplacian-Gaussian filters and from those processed by linear opacity judgement. However, honeycomb lesions and other interstitial abnormalities (interstitial changes other than honeycombing) were differentiated from each other only by the radiographic indices obtained from the image processed by linear opacity judgment (P < .05). DISCUSSION: These results indicate that this system is useful for the detection and characterization of interstitial lung abnormalities.

Female↗

Non-Gaussian statistics of the vibrational fluctuations of myoglobin.

Experiments on the dynamics of vibrational fluctuations in myoglobin revealed an interesting behavioral cross-over occurring in the range 180-200 K. In this temperature range the mean square displacement of atomic positions versus temperature sharply increases its slope, indicating the dissociation of CO from the heme group. In this paper we develop a theoretical model that provides a framework for the quantitative description of this phenomenon. The basis of our calculations is an assumption of an effective potential with multiple local minima. In particular, we consider a quartic potential in place of the simple quadratic. We then use non-Gaussian statistics to obtain a relationship between the mean square displacement and model parameters. We compare our model to published experimental data and show that it can describe the data set using physically meaningful parameters which are fitted to the experimental data. In the process we verify the Gaussian approximation's applicability only to the low-temperature régime. In the high-temperature limit, however, deviations from the Gaussian approximation are due to the double-well nature of our effective potential. We find that the published datasets showing the thermal transition display the qualitative trends predicted by appropriate algebraic approximations to our predicted myoglobin behavior.

Computer Simulation↗

DNA microarray stochastic model.

A stochastic model of the DNA microarray image pixels is presented. The model includes spot pixel intensity distribution, interpixel correlations and the intensity distribution of background noise. The data is indicative of a small exponential additive noise process and a larger Gaussian fluctuation that scales with spot intensity. Correlations are observed among pixels in the spot and between test and control images. The correlated fluctuations may be attributed to variations across each spot in the amount of DNA placed on the spot during the array fabrication process. The model may be used in gene expression estimation algorithm development, both to test new algorithms through simulation and to develop optimum algorithms. The model should also be easily adapted to new array based technologies in proteomics.

Computer Simulation↗