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Noise reduction in brain evoked potentials based on third-order correlations.

In this paper, we use third-order correlations (TOC) in developing a filtering technique for the recovery of brain evoked potentials (EPs). The main idea behind the presented technique is to pass the noisy signal through a finite impulse response filter whose impulse response is matched with the shape of the noise-free signal. It is shown that it is possible to estimate the filter impulse response on basis of a selected third-order correlation slice (TOCS) of the input noisy signal. This is justified by two facts. The first one is that the noise-free EPs can be modeled as a sum of damped sinusoidal signals and the selected TOCS preserve the signal structure. The second fact is that the TOCS is insensitive to both Gaussian noise and other symmetrically distributed non-Gaussian noise, (white or colored). Furthermore, the approach can be applied to either nonaveraged or averaged EP observation data. In the nonaveraged data case, the approach therefore preserves information about amplitude and latency changes. Both fixed and adaptive versions of the proposed filtering technique are described. Extensive simulation results are provided to show the validity and effectiveness of the proposed cumulant-based filtering technique in comparison with the conventional correlation-based counterpart.

Evoked Potentials, Somatosensory↗

Deformable boundary detection of stents in angiographic images.

In this paper, a procedure is described for deformable boundary detection of medical tools, called stents, in angiographic images. A stent is a surgical stainless steel coil that is placed in the artery in order to improve blood circulation in regions where a stenosis has appeared. Assuming initially a set of three-dimensional (3-D) models of stents and using perspective projection of various deformations of the 3-D model of the stent, a large set of synthetic two-dimensional (2-D) images of stents is constructed. These synthetic images are then used as a training set for deriving a multivariate Gaussian density estimate based on eigenspace decomposition and formulating a maximum-likelihood estimation framework in order to reach an initial rough estimate for automatic object recognition. The silhouette of the detected stent is then refined by using a 2-D active contour (snake) algorithm integrated with a novel iterative initialization technique, which takes into consideration the geometry of the stent. The algorithm is experimentally evaluated using real angiographic images containing stents.

Algorithms↗

Forensic analysis of nonlinear collusion attacks for multimedia fingerprinting.

Digital fingerprinting is a technology for tracing the distribution of multimedia content and protecting them from unauthorized redistribution. Unique identification information is embedded into each distributed copy of multimedia signal and serves as a digital fingerprint. Collusion attack is a cost-effective attack against digital fingerprinting, where colluders combine several copies with the same content but different fingerprints to remove or attenuate the original fingerprints. In this paper, we investigate the average collusion attack and several basic nonlinear collusions on independent Gaussian fingerprints, and study their effectiveness and the impact on the perceptual quality. With unbounded Gaussian fingerprints, perceivable distortion may exist in the fingerprinted copies as well as the copies after the collusion attacks. In order to remove this perceptual distortion, we introduce bounded Gaussian-like fingerprints and study their performance under collusion attacks. We also study several commonly used detection statistics and analyze their performance under collusion attacks. We further propose a preprocessing technique of the extracted fingerprints specifically for collusion scenarios to improve the detection performance.

Algorithms↗

Inverse plan optimization accounting for random geometric uncertainties with a multiple instance geometry approximation (MIGA).

Radiotherapy treatment plans that are optimized to be highly conformal based on a static patient geometry can be degraded by setup errors and/or intratreatment motion, particularly for IMRT plans. To achieve improved plans in the face of geometrical uncertainties, direct simulation of multiple instances of the patient anatomy (to account for setup and/or motion uncertainties) is used within the inverse planning process. This multiple instance geometry approximation (MIGA) method uses two or more instances of the patient anatomy and optimizes a single beam arrangement for all instances concurrently. Each anatomical instance can represent expected extremes or a weighted distribution of geometries. The current implementation supports mapping between instances that include distortions, but this report is limited to the use of rigid body translations/ rotations. For inverse planning, the method uses beamlet dose calculations for each instance, with the resulting doses combined using a weighted sum of the results for the multiple instances. Beamlet intensities are then optimized using the inverse planning system based on the cost for the composite dose distribution. MIGA can simulate various types of geometrical uncertainties, including random setup error and intratreatment motion. A limited number of instances are necessary to simulate Gaussian-distributed errors. IMRT plans optimized using MIGA show significantly less degradation in the face of geometrical errors, and are robust to the expected (simulated) motions. Results for a complex head/neck plan involving multiple target volumes and numerous normal structures are significantly improved when the MIGA method of inverse planning is used. Inverse planning using MIGA can lead to significant improvements over the use of simple PTV volume expansions for inclusion of geometrical uncertainties into inverse planning, since it can account for the correlated motions of the entire anatomical representation. The optimized plan results reflect the differing patient geometry situations which can be important near the surface or heterogeneities. For certain clinical situations, the MIGA optimization approach can correct for a significant part of the degradation of the plan caused by the setup uncertainties.

Artifacts↗

Ectopic development of skeletal muscle induced by subcutaneous transplant of rat satellite cells.

The present study analyzes the ectopic development of the rat skeletal muscle originated from transplanted satellite cells. Satellite cells (10(6) cells) obtained from hindlimb muscles of newborn female 2BAW Wistar rats were injected subcutaneously into the dorsal area of adult male rats. After 3, 7, and 14 days, the transplanted tissues (N = 4-5) were processed for histochemical analysis of peripheral nerves, inactive X-chromosome and acetylcholinesterase. Nicotinic acetylcholine receptors (nAChRs) were also labeled with tetramethylrhodamine-labeled alpha-bungarotoxin. The development of ectopic muscles was successful in 86% of the implantation sites. By day 3, the transplanted cells were organized as multinucleated fibers containing multiple clusters of nAChRs (N = 2-4), resembling those from non-innervated cultured skeletal muscle fibers. After 7 days, the transplanted cells appeared as a highly vascularized tissue formed by bundles of fibers containing peripheral nuclei. The presence of X chromatin body indicated that subcutaneously developed fibers originated from female donor satellite cells. Differently from the extensor digitorum longus muscle of adult male rat (87.9 +/- 1.0 microm; N = 213), the diameter of ectopic fibers (59.1 microm; N = 213) did not obey a Gaussian distribution and had a higher coefficient of variation. After 7 and 14 days, the organization of the nAChR clusters was similar to that of clusters from adult innervated extensor digitorum longus muscle. These findings indicate the histocompatibility of rats from 2BAW colony and that satellite cells transplanted into the subcutaneous space of adult animals are able to develop and fuse to form differentiated skeletal muscle fibers.

Acetylcholinesterase↗

Design of computer-generated hologram with ring focus for nonmechanical corneal trephination with Er:YAG laser in penetrating keratoplasty.

PURPOSE: To calculate a beam-shaping optical element for homogeneous intensity distribution within a focal ring to be used in nonmechanical trephination with the Er:YAG laser in penetrating keratoplasty instead of a spot guiding device. METHODS: The phase distribution behind a holographic optical element (HOE) k psi(u) can be described by the addition of the hologram phase phiH(u) to the beam phase phiE(u): k psi(u) = phiH(u) + phiE(u), k = 2pi/lambda, where u denotes the coordinates inside the hologram aperture, k an integer, and lambda the laser wavelength. To avoid discontinuous wavefronts leading to speckle noise, a smooth phase function is necessary. After transforming the hologram aperture coordinates into the focal plane x in a focal distance f, psi can be retrieved from the slope equation: inverted delta psi(u) = x(u) - u/f. RESULTS: Creating a ring focus can be reduced to an essentially one-dimensional problem by separation of variables due to the symmetry condition. We calculated a computer-generated eight-level phase-only HOE with 4096 x 4096 pixels from a Gaussian-distributed 2.94 Er:YAG laser spot with a beam diameter of 10 mm and a focal distance of 100 mm. Thereby, a ring focus with an inner/outer radius of 7/8 mm can be created. To avoid Poisson's spo, the symmetry of the problem was broken by circular modulation of the phase leading to a spiral-like structure. The calculated efficiency of the HOE relating the energy within the ring to the total energy was 91%. CONCLUSION: With an HOE it is possible to redistribute the energy along the desired focal ring. The HOE design can be adapted to the intensity distribution of the impinging laser beam with its characteristic aperture shape. A circular homogeneous corneal trephination depth is possible, because the energy fluctuation from pulse to pulse does not locally affect the ablation process. A ring focus for the Er:YAG laser has the potential to render superfluous a manual beam control via micromanipulator and to allow a more rapid and more regular corneal trephination along aperture masks.

Cornea↗

Numerical and experimental study of critical roof collapse conditions in soft lithography.

One of the major issues during soft lithographic processes is that, if the pressing force on the stamp becomes too high, the stamp may erroneously come into contact with the substrate in zones where contact is not intended. This decreases the patterning accuracy and may lead to badly or nonperforming electronic devices and is therefore undesired. Design rules, available at an early stage in the design phase, are desired to speed-up the development of this technique. Ultimately, these rules should give an indication of the critical pressure that can safely be applied on the stamp thereby avoiding unwanted contact between the stamp and the substrate. To obtain these critical pressures, numerical analyses of the deformation behavior of two characteristic configurations in the microstructured surface pattern of the rubber stamp are performed. The deformation behavior of the rubber is modeled according to a Gaussian and a non-Gaussian approach, leading to a neo-Hookean and Arruda-Boyce constitutive model, respectively. Besides these material nonlinearities, geometrical nonlinearities are taken into account as well. The calculated pressure at which undesired contact takes place (the roof collapse pressure) is compared to experimentally obtained values for two particular types of structures, and the results are in agreement within the error margins of the experiments and those ensuing from the assumptions of the numerical simulations.

Journal Article↗

Predicted 1,3-dichloropropene air concentrations resulting from tree and vine applications in California.

The preplant soil fumigant 1,3-dichloropropene (1,3-D) is effective for nematode control and is expected to further replace methyl bromide (MeBr) as MeBr use is phased out. Acute human exposure to soil fumigants is managed in part by using buffer zones between treated fields and occupied structures. The required buffer zone for 1,3-D in California is 91.4 m (300 ft) for all uses. However, a 30.5-m (100-ft) buffer setback is desired for 1,3-D to be an important replacement for MeBr in the orchard and vineyard markets. The Industrial Source Complex Short-Term model, Version 3 (ISCST3) was used to simulate township-wide long-term average and short-term air concentration distributions of 1,3-D. The Gaussian plume model ISCST3 can be used to assess dispersion of air pollutants and pollutant concentrations on receptors from a variety of sources and in diverse airsheds. Long-term and daily-average air concentrations can be compared with the California permitted chronic or acute toxicity endpoints, respectively, to assess the potential risk for individuals living within the township at the proposed buffer setback. Modifications to ISCST3 were made for specific nonpoint-source agricultural constraints and management practices. Chronic and acute air concentration distributions of 1,3-D with a 30.5-m buffer constraint around treated fields are similar to currently permitted air concentration distributions in California. Refinement of exposure as a function of buffer distance, application rate, and field size is possible due to the resolution of the simulation and external post-processing capabilities. Simulated examples of 1,3-D acute and chronic exposure cumulative distributions are presented.

Agriculture↗

A review and numerical assessment of the random walk particle tracking method.

We review the basic mathematical concepts of random walk particle tracking (RWPT) and its advantages and limitations. Three different numerical approaches to overcome the local mass conservation problem of the random walk methodology are examined: (i) the interpolation method, (ii) the reflection principle, and (iii) the generalized stochastic differential equations (GSDE). Analytical solutions of the spatial moments for a two-layer system are compared to model predictions using the different techniques and results demonstrate that the interpolation method reproduces correctly average velocity, but fails to reproduce macrodispersion at higher hydraulic conductivity contrasts between the two layers. On the contrary, the reflection principle and the GSDE approach underestimate average velocity, but reproduce macrodispersion better for high contrasts. The different behavior is based on an artificial shift of mass for increasing heterogeneities for the GSDE approach and the reflection principle, whereas the interpolation method suffers from the smoothing of the dispersion tensor. The behavior of these approaches was furthermore analyzed in two-dimensional heterogeneous hydraulic conductivity fields, which are characterized by different random function models. Solute transport was simulated correctly by all three approaches for the reference fields having Gaussian structures or non-Gaussian structures with an isotropic spatial correlation, even for a variance of the natural log of hydraulic conductivity of sigma(lnK)(2)=4. However, for the non-Gaussian model with a strong anisotropic spatial correlation and a variance of sigma(lnK)(2)=2 and higher, the interpolation method was the only technique modelling solute transport correctly. Furthermore, we discuss the general applicability of random walk particle tracking in comparison to the standard transport models and conclude that in advection-dominated problems using a high spatial discretization or requiring the performance of many model runs, RWPT represents a good alternative for modelling contaminant transport.

Models, Chemical↗

Resolution and noise properties of MAP reconstruction for fully 3-D PET.

We derive approximate analytical expressions for the local impulse response and covariance of images reconstructed from fully three-dimensional (3-D) positron emission tomography (PET) data using maximum a posteriori (MAP) estimation. These expressions explicitly account for the spatially variant detector response and sensitivity of a 3-D tomograph. The resulting spatially variant impulse response and covariance are computed using 3-D Fourier transforms. A truncated Gaussian distribution is used to account for the effect on the variance of the nonnegativity constraint used in MAP reconstruction. Using Monte Carlo simulations and phantom data from the microPET small animal scanner, we show that the approximations provide reasonably accurate estimates of contrast recovery and covariance of MAP reconstruction for priors with quadratic energy functions. We also describe how these analytical results can be used to achieve near-uniform contrast recovery throughout the reconstructed volume.

Algorithms↗

Novel Bayesian multiscale method for speckle removal in medical ultrasound images.

A novel speckle suppression method for medical ultrasound images is presented. First, the logarithmic transform of the original image is analyzed into the multiscale wavelet domain. We show that the subband decompositions of ultrasound images have significantly non-Gaussian statistics that are best described by families of heavy-tailed distributions such as the alpha-stable. Then, we design a Bayesian estimator that exploits these statistics. We use the alpha-stable model to develop a blind noise-removal processor that performs a nonlinear operation on the data. Finally, we compare our technique with current state-of-the-art soft and hard thresholding methods applied on actual ultrasound medical images and we quantify the achieved performance improvement.

Bayes Theorem↗

An image analysis on MR imaging of the brain for hepatic encephalopathy.

Through the Magnetic Resonance Imaging (MRI) sequences with T1 weighting (TR 600 msec/TE 20 msec) of the brain, the high intensity lesions due to hepatic encephalopathy have been demonstrated markedly. The data have been collected were based upon eleven patients with clinically proven hepatic encephalopathy. Three sets of normal brain MRI which were identified with no evidence of brain or liver diseases were also included in this study. After the brain MRI slices have been identified, it showed that the affected regions of interest (ROI) were around the largest third ventricle. The histogram which was generated out of that particular slice is composed of two distinguished peaks lumped together. After the decomposition and curve fitting procedures, the Gaussian distributions were identified with the mean value and the standard deviation. One was assumed to be gray index region for gray and white matter, the other with higher gray index value was the contribution of hepatic encephalopathy. Once the range of the distribution has been determined, the affected portion can be marked and highlighted. This mechanism of histogram decomposition and curve fitting techniques shows the valuable correlation with the clinical status of MR findings.

Brain↗

Kinetic differences at low temperatures between R and T state carbon monoxide-carp hemoglobin.

We use the low-temperature recombination kinetics of carbon monoxide with carp hemoglobin to determine that the R and T states of hemoglobin exhibit different low-temperature geminate recombination kinetics. The peak of the fitted Gaussian activation energy spectrum is at 1.5 kcal/mol for R state and 1.8 kcal/mol for T state. The distribution in activation energies is fit well by the Agmon-Hopfield linear strain model. The T state is fit with a stronger elastic constant than R, and has a larger displacement of the protein conformation coordinate than does the R state, indicating that the T state does have a significantly greater rigidity and also stores more strain energy in its conformational states than does R hemoglobin. The pre-exponential in the activation energy spectrum is only a factor of two greater in the R than the T state and the low-temperature activation energy spectrum does not correctly predict the difference in the on rates for R and T states at 300 degrees K, indicating that processes removed from the binding site are important in cooperativity.

Animals↗

Automatic determination of the number of targets present when using the time reversal operator.

Acoustical time reversal mirrors have been shown to provide a highly accurate means of studying and focusing on acoustical sources. The DORT method is a derivation of the time reversal process, which allows for focusing on multiple targets. An important step in this process is the determination of the number of targets or sources present. This is achieved by examining the eigenvalues of the time reversal operator (TRO). The number of significant eigenvalues is then chosen as the number of sources present. However, as mentioned in [N. Mordant, C. Prada, and M. Fink, J. Acoust. Soc. Am. 105, 2634-2642 (1999) and C. Prada, M. Tanter, and M. Fink, in Proceedings of the IEEE Symposium, 1997, pp. 679-683], factors such as low signal to noise ratio (SNR), small data sample, array configuration and the target location may result in the eigenvalues corresponding to the targets no longer being distinguishable from the background noise eigenvalues. This paper proposes a robust method of automatically determining the number of targets even in the presence of a small number of snapshots. For white Gaussian noise, the profile of the ordered eigenvalues is seen to fit an exponential law. The observed eigenvalues are then compared to this model and a mismatch is detected between the observed profile and the noise-only model. The index of the mismatch gives the number of scatterers present.

Journal Article↗

Prediction of seizure onset in an in-vitro hippocampal slice model of epilepsy using Gaussian-based and wavelet-based artificial neural networks.

We propose that artificial neural networks (ANNs) can be used to predict seizure onsets in an in-vitro hippocampal slice model capable of generating spontaneous seizure-like events (SLEs) in their extracellular field recordings. This paper assesses the effectiveness of two ANN prediction schemes: Gaussian-based artificial neural network (GANN) and wavelet-based artificial neural network (WANN). The GANN prediction system consists of a recurrent network having Gaussian radial basis function (RBF) nonlinearities capable of extracting the estimated manifold of the system. It is able to classify the underlying dynamics of spontaneous in-vitro activities into interictal, preictal and ictal modes. It is also able to successfully predict the onsets of SLEs as early as 60 s before. Improvements can be made to the overall seizure predictor design by incorporating time-varying frequency information. Consequently, the idea of WANN is considered. The WANN design entails the assumption that frequency variations in the extracellular field recordings can be used to compute the times at which onsets of SLEs are most likely to occur in the future. Progressions of different frequency components can be captured by the ANN using appropriate frequency band adjustments via pruning, after the initial wavelet transforms. In the off-line processing comprised of 102 spontaneous SLEs generated from 14 in-vitro rat hippocampal slices, with half of them used for training and the other half for testing, the WANN is able to predict the forecoming ictal onsets as early as 2 min prior to SLEs with over 75% accuracy within a 30 s precision window.

Animals↗

Stochastic pulse stimulation in chemoreceptors and its properties.

Orientation towards food and mate, especially in insects, is an olfactory-controlled behavior which relies on the detection of small amounts of odorant molecules delivered in turbulent atmospheric conditions, so that randomness in magnitude and time is a major feature of the natural stimulus. The effect of random delivery on the initial step of olfactory transduction, the formation of the receptor-ligand complex, is analyzed in the case of the moth pheromonal system. Two types of randomness are compared, Gaussian (regular) and exponential (irregular). The influence of noise is quantified either with the maxima of the receptor-ligand complex, or with the times at which the concentration of complex crosses a given threshold level. It is shown that the stochastic features of the stimulus helps its detection and that the exponential distribution appears not only as a better description of the natural stimulus, but also as the most efficient from a biological point of view.

Animals↗

Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition.

We present an approach to integrate physical properties of DNA, such as DNA bendability or GC content, into our probabilistic promoter recognition system McPROMOTER. In the new model, a promoter is represented as a sequence of consecutive segments represented by joint likelihoods for DNA sequence and profiles of physical properties. Sequence likelihoods are modeled with interpolated Markov chains, physical properties with Gaussian distributions. The background uses two joint sequence/profile models for coding and non-coding sequences, each consisting of a mixture of a sense and an anti-sense submodel. On a large Drosophila test set, we achieved a reduction of about 30% of false positives when compared with a model solely based on sequence likelihoods.

Animals↗

Color and luminance spatial tuning estimated by noise masking in the absence of off-frequency looking.

We assessed the contribution of off-frequency looking for pattern detection and obtained bandwidths for chromatic and luminance mechanisms in conditions free from this effect. We used a simultaneous spatial masking technique with Gaussian enveloped sinusoidal test stimuli (0.5 cycle/deg) and filtered one-dimensional static-noise masks whose spectral power was uniformly distributed per octave. Stimuli were modulated in the chromatic (isoluminant red-green) or the luminance (yellow-black) domain. Color and luminance detection thresholds were compared for low-pass, high-pass, and notch- (band-stopped) filtered noise. We obtained the following results: (1) at high-noise spectral densities, masking by notched noise is greater than the summed masking of the high- and low-pass noise, indicating the presence of off-frequency looking for both color and luminance detection. There is no evidence for off-frequency looking at lower power densities. (2) Using notch-filtered noise, which avoids the problem of off-frequency looking, we found that color processing is subserved by bandpass channels with bandwidths similar to those revealed for luminance processing. (3) Both color and luminance mechanisms appear to have bandwidths proportional to their center frequency (constant in octaves). (4) The lower and upper sides of the color and luminance tuning functions were estimated individually by use of high-pass and low-pass noise of a low power density and are revealed to be asymmetric, with the lower side declining more steeply than the upper side.

Color Perception↗