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Noise analysis of MAP-EM algorithms for emission tomography.

The ability to theoretically model the propagation of photon noise through PET and SPECT tomographic reconstruction algorithms is crucial in evaluating the reconstructed image quality as a function of parameters of the algorithm. In a previous approach for the important case of the iterative ML-EM (maximum-likelihood-expectation-maximization) algorithm, judicious linearizations were used to model theoretically the propagation of a mean image and a covariance matrix from one iteration to the next. Our analysis extends this approach to the case of MAP (maximum a posteriori)-EM algorithms, where the EM approach incorporates prior terms. We analyse in detail two cases: a MAP-EM algorithm incorporating an independent gamma prior, and a one-step-late (OSL) version of a MAP-EM algorithm incorporating a multivariate Gaussian prior, for which familiar smoothing priors are special cases. To validate our theoretical analyses, we use a Monte Carlo methodology to compare, at each iteration, theoretical estimates of mean and covariance with sample estimates, and show that the theory works well in practical situations where the noise and bias in the reconstructed images do not assume extreme values.

Algorithms↗

Phonetically trained models for speaker recognition.

In this paper, a speaker recognition system that introduces acoustic information into a Gaussian mixture model (GMM)-based recognizer is presented. This is achieved by using a phonetic classifier during the training phase. The experimental results show that, while maintaining the recognition rate, the decrease in the computational load is between 65% and 80% depending on the number of mixtures of the models.

Adult↗

Noise in integrate-and-fire neurons: from stochastic input to escape rates.

We analyze the effect of noise in integrate-and-fire neurons driven by time-dependent input and compare the diffusion approximation for the membrane potential to escape noise. It is shown that for time-dependent subthreshold input, diffusive noise can be replaced by escape noise with a hazard function that has a gaussian dependence on the distance between the (noise-free) membrane voltage and threshold. The approximation is improved if we add to the hazard function a probability current proportional to the derivative of the voltage. Stochastic resonance in response to periodic input occurs in both noise models and exhibits similar characteristics.

Membrane Potentials↗

MEPSIM: a computational package for analysis and comparison of molecular electrostatic potentials.

MEPSIM is a computational system which allows an integrated computation, analysis, and comparison of molecular electrostatic potential (MEP) distributions. It includes several modules. Module MEPPLA supplies MEP values for the points of a grid defined on a plane which is specified by a set of three points. The results of this program can easily be converted into MEP maps using third-parties graphical software. Module MEPMIN allows to find automatically the MEP minima of a molecular system. It supplies the cartesian coordinates of these minima, their values, and all the geometrical relationships between them (distances, angles, and dihedral angles). Module MEPCOMP computes a similarity coefficient between the MEP distributions of two molecules and finds their relative position that maximizes the similarity. Module MEPCONF performs the same process as MEPCOMP, considering not only the relative position of both molecules but also a conformational degree of freedom of one of them. The most recently developed module, MEPPAR, is another modification of MEPCOMP in order to compute the MEP similarity between two molecules, but only taking into account a particular plane. The latter module is particularly useful to compare MEP distributions generated by pi systems of aromatic rings. MEPSIM can use several wavefunction computation approaches to obtain MEP distributions. MEPSIM has a menu type interface to simplify the following tasks: creation of input files from output files of external programs (GAUSSIAN and AMPAC/MOPAC), setting the parameters for the current computation, and submitting jobs to the batch queues of the computer. MEPSIM has been coded in FORTRAN and its current version runs on VMS/VAX computers.

Drug Design↗

Correlation of spatial event plots with simulated population responses of mechanoreceptive fibers.

The experimental setup for generating spatial event plots (SEPs) from single mechanoreceptive fibers of the skin was computationally simulated. The generic fibers used in the simulations were similar to the rapidly adapting fibers (RAs), and had variable refractoriness and receptive-field size. The speed, lateral shift, and the contact width of the drum scanned across the receptive field of the fiber are adjustable parameters. The stimulus patterns used on the drum mimicked stimuli used by several other investigators. These were dot patterns, grating patterns, and the letter "E". First, the effects of simulation parameters on the SEPs were studied. The simulation output confirms the results of physiological experiments that SEPs contain information on the spatiotemporal resolution of the fiber. The next series of simulations involved generating SEPs of fibers obtained from the same or varying spatial distributions of receptive fields. Three hypothetical distributions were used: homogeneous rectangular, uniformly random, and Gaussian. The momentary population response at each case was found using the technique by Johansson and Vallbo (Brain Res 184: 353-366, 1980). The population responses were not isomorphic images of the stimulus patterns due to the variations in field sizes and locations. However, every fiber, no matter which distribution it came from, generated almost identical SEPs given similar response properties. Furthermore, the SEPs looked like the outline of the stimulus. These observations show that SEPs do not contain information about the population response. Therefore, reconstructing the population response using SEPs can result in misleading conclusions on central-nervous-system processing and should be viewed cautiously when formulating psychophysical/physiological linking hypotheses.

Animals↗

The friction of explanted hip prostheses.

Charnley prostheses, retrieved at revision surgery, were studied to assess the effects of friction on the total hip replacement procedure. Frictional resistance was measured using the Durham hip function simulator under both dry and lubricated conditions. The friction factor values (f) for the explanted prostheses were found to have a non-Gaussian distribution with medians of 0.13 [inter-quartile range (IQR) 0.10-0.16] and 0.06 (IQR 0.005-0.08) for dry and lubricated (n = 0.01 Pa s) regimes, respectively. New Charnley prostheses had values of f equal to 0.11 +/- 0.025 and 0.04 +/- 0.01 under the same conditions, and showed no large deviation from a Gaussian distribution. There was found to be a statistically significant difference in the medians of the friction factors for new and retrieved prostheses in the lubricated regime. Ingression of cement into the worn region of the cup was found to increase the friction factor significantly under dry conditions. There was no evidence of an increase in the friction factor or torque for those joints that had a loose socket with respect to those that were fixed at revision. A decrease in the frictional torque against number of cycles undergone by the joint in vivo may indicate that a fatigue-type process may have a role in the loosening of the socket. However, this relationship was found not to be significant for friction measured under lubricated conditions and it seems unlikely that the frictional torque generated in this type of prosthesis will contribute significantly to the long-term loosening of the socket.

Adult↗

Analysis of bivariate flow karyotypes.

Bivariate flow karyotype analysis is performed using data from chromosomes stained with two fluorescent dyes, typically chromomycin A3 and Hoechst-33258, and measured in a flow cytometer or cell sorter (Carrano et al.: Proceedings of the National Academy of Sciences of the United States of America 76:1382-1384, 1979; Gray et al.: Proceedings of the National Academy of Sciences of the United States of America 72:1231-1234, 1975; Langlois et al.: Proceedings of the National Academy of Sciences of the United States of America 79:7876-7880, 1982). In the resulting bivariate histogram, most chromosome types appear as individual peaks. In sorting of chromosomes to purify a specific chromosomal type, its corresponding peak in the bivariate histogram is delineated by a rectangular region which surrounds it. All events (objects) that fall within this region trigger the sorting process. In most cases, peaks for different chromosomal types overlap to some extent, and in addition there is always an underlying background due to chromosome fragments and clumps. Thus the sorted population will not be pure; it may include more than one chromosome type and will include debris. To determine the purity of a sort, i.e., the percentage of the sorted material that is of the actual chromosomal type desired, two methods of mathematical analysis have been developed. In the more general method, the bivariate data within an analysis region that includes the sort region, are fit with a series of bivariate Gaussian functions, one for each peak. In a simplified method, the data within the analysis region are transformed into a univariate distribution of either chromomycin A3 or Hoechst-33258 fluorescence. The peaks in these univariate distributions are fit with univariate Gaussian functions. In both methods the purity is determined mathematically. The results of both methods agree well with independent methods of analysis.

Animals↗

Parametrical modelling of a premature ventricular contraction ECG beat: comparison with the normal case.

The aim of this paper is to analyse a parametrical Gaussian kernel based model. The proposed model is tested on two types of electrocardiogram (ECG) beats, the normal case beat and the premature ventricular contraction (PVC) one. Basically, the model is constituted of N Gaussians where their corresponding parameters are estimated by optimising a specific criterion. The modelling technique has been validated using MIT/BIH databases. As a result of this study, we show that a normal beat can be modelled using 18 parameters and only 15 parameters are needed to reconstruct the PVC one.

Computer Simulation↗

Absorption microspectroscopy, theory and applications in the case of the photosynthetic compartment.

We performed microspectroscopic evaluation of the pigment composition of the photosynthetic compartments of both algae and higher plants. The feasibility of microspectroscopy for discriminating among species and/or phylogenetic groups was tested on laboratory cultures. Gaussian bands decompositions, and a fitting algorithm, together with fourth-derivative transformation of absorbance spectra, provided a reliable discrimination among chlorophylls, phycobiliproteins and carotenoids. Comparative analysis of absorption spectra highlighted the evolutionary grouping of the algae into three main lineages in accordance with the most recent endosymbiotic theories.

Biological Evolution↗

The spatial tuning of color and luminance peripheral vision measured with notch filtered noise masking.

We have measured the spatial bandwidths of the bandpass red-green chromatic and luminance mechanisms at four locations in the nasal visual field (0, 10, 20 and 30 degrees) using a method of notch filtered noise masking which effectively removes the artifact of off-frequency looking for our stimuli. Detection thresholds were measured for luminance or isoluminant red-green Gaussian enveloped test gratings of 0.5 cpd embedded in 1/f noise. Firstly, thresholds were obtained as a function of increasing noise spectral density and were fitted using a standard noise masking model. These results support the existence across the visual field of independent, red-green chromatic and luminance mechanisms with similar sampling efficiencies. Secondly, we measured thresholds in notch filtered noise as a function of notch width and derived the spatial bandwidth of the detection mechanism. We find both color and luminance mechanisms have similar bandwidths which remain virtually constant across eccentricity. These results indicate strong overall similarities between the early processing of color and luminance vision, and lend support to the role of color as an 'intrinsic image' in spatial vision. The results are discussed in the light of the anchored channel and shifting channel models of peripheral contrast sensitivity and pattern detection.

Color Perception↗

EPR study of non-covalent spin labeled serum albumin and hemoglobin.

Electron Paramagnetic Resonance (EPR) was used to investigate the Tempyo spin label (3-carbamoyl-2,2,5,5-tetramethyl-3-pyrrolin-1-yloxy) as a report group for the interactions and the conformational changes of lyophilized bovine serum albumin (BSA) and bovine hemoglobin (BH), as function of pH values in the range 2.5-11. The EPR spectra are similar with those of other non-covalently spin label porphyrins in frozen solution at very low temperatures. This behavior indicated a possible spin-spin interaction between the hemic iron and the nitroxide group. The changes in the EPR spectra as function of the pH are discussed in terms of conformational changes of the proteins. Spectral simulations and magnetic EPR parameters reveal the following: (i) one single paramagnetic species, with Gaussian line shape, was used for the best fits of experimental spectra in the case of serum albumin samples; and (ii) a weighted sum of Lorentzian and Gaussian line shape in the case of hemoglobin samples. The representation of correlation time vs. pH, reveals a dependence of degree of immobilization of spin label on the conformational changes of proteins in acidic and basic environment.

Animals↗

Estimation of initial conditions and parameters of a chaotic evolution process from a short time series.

Tracing back to the initial state of a time-evolutionary process using a segment of historical time series may lead to many meaningful applications. In this paper, we present an estimation method that can detect the initial conditions, unobserved time-varying states and parameters of a dynamical (chaotic) system using a short scalar time series that may be contaminated by noise. The technique based on the Newton-Raphson method and the least-squares algorithm is tolerant to large mismatch between the initial guess and actual values. The feasibility and robustness of this method are illustrated via the numerical examples based on the Lorenz system and Rossler system corrupted with Gaussian noise.

Journal Article↗

Iterative reconstruction for helical CT: a simulation study.

Iterative reconstruction algorithms for helical CT are presented. The algorithms are derived from two-dimensional reconstruction algorithms, by adapting the projector/backprojector to the helical orbit of the source, and by constraining the axial frequencies with a Gaussian sieve. Simulations have been carried out and the performance of the iterative algorithms is compared to that of filtered backprojection of synthetic (interpolated) two-dimensional sinograms. The iterative algorithms produce superior bias-noise curves. Axial resolution is superior, but disturbing edge-artefacts are introduced.

Algorithms↗

A docking analysis of the statistical physics of protein-protein recognition.

We describe protein-protein recognition within the frame of the random energy model of statistical physics. We simulate, by docking the component proteins, the process of association of two proteins that form a complex. We obtain the energy spectrum of a set of protein-protein complexes of known three-dimensional structure by performing docking in random orientations and scoring the models thus generated. We use a coarse protein representation where each amino acid residue is replaced by its Voronoï cell, and derive a scoring function by applying the evolutionary learning program ROGER to a set of parameters measured on that representation. Taking the scores of the docking models to be interaction energies, we obtain energy spectra for the complexes and fit them to a Gaussian distribution, from which we derive physical parameters such as a glass transition temperature and a specificity transition temperature.

Biophysics↗

Application of fractal and morphological methods in radioecology.

Effective management of radioactive contamination requires comprehensive knowledge of pollutants' characteristics. The complicated character of the problem is due to a number of issues, such as the very wide range of contamination, the presence of a mixture of radioactive isotopes, the highly variable diffusion of radionuclides in soil, water, and air, and the effect of climatic conditions. The resultant field has an irregular mosaic structure, which restricts the choice of measurement methods and data processing. In view of this, application of classical statistics techniques is often inappropriate in modeling such an environment. Application of the tools of fractal and stochastic geometry provides a good insight and helps to distinguish between distribution characteristics of natural and man-made isotopes. Several techniques are implemented to determine scaling aspects of contaminated fields. The discovery of multifractal scaling leads to the hierarchical structure of contamination spots on different scales and intensity and places restrictions on the measurement net for detecting anomalies. The method of stochastic geometry further demonstrates that topological characteristics of contamination fields differ from those of the Gaussian fields and the topology of man-made isotopes differs from natural ones.

Air Pollutants, Radioactive↗

Nonlinear nonstationary Wiener model of infant EEG seizures.

This paper presents the estimation of a nonstationary nonlinear model of seizures in infants based on parallel Wiener structures. The model comprises two parts and is partly derived from the Roessgen et al. seizure model. The first part consists of a nonlinear Wiener model of the pure background activity, and the second part in a nonlinear Wiener model of the pure seizure activity with a time-varying deterministic input signal. The two parts are then combined in a parallel structure. The Wiener model consists of an autoregressive moving average filter followed by a nonlinear shaping function to take into account the non-Gaussian statistical behavior of the data. Model estimation was performed on 64 infants of whom four showed signs of clinical and electrical seizures. Model validation is performed using time-frequency-based entropy distance and shows an averaged improvement of 50% in modeling performance compared with the Roessgen model.

Electroencephalography↗

Fractal analysis of cytoskeleton rearrangement in cardiac muscle during head-down tilt.

Head-down tilt by tail suspension of the rat produces a volume, but not pressure, load on the heart. One response of the heart is cytoskeleton rearrangement, a phenomenon commonly referred to as disruption. In these experiments, we used fractal analysis as a means to measure complexity of the microtubule structures at 8 and 18 h after imposition of head-down tilt. Microtubules in whole tissue cardiac myocytes were stained with fluorescein colchicine and were visualized by confocal microscopy. The fractal dimensions (D) of the structures were calculated by the dilation method, which involves successively dilating the outline perimeter of the microtubule structures and measuring the area enclosed. The head-down tilt resulted in a progressive decrease in D (decreased complexity) when measured at small dilations of the perimeter, but the maximum D (maximum complexity) of the microtubule structures did not change with treatment. Analysis of the fold change in complexity as a function of the dilation indicates an almost twofold decrease in microtubule complexity at small kernel dilations. This decrease in complexity is associated with a more Gaussian distribution of microtubule diameters, indicating a less structured microtubule cytoskeleton. We interpret these data as a microtubule rearrangement, rather than erosion, because total tubulin flourescence was not different between groups. This conclusion is supported by F-actin fluorescence data indicating a dispersed structure without loss of actin.

Actins↗

A feasibility study of multispectral image analysis of skin tumors.

To develop a noninvasive, early-detection method for skin cancers, a feasibility study of multispectral image analysis was investigated. The three most frequently occurring skin cancer types, ten basal-cell carcinomas (BCCs), ten squamous-cell carcinomas (SCCs) and five malignant melanomas (MMs) were studied, along with ten normal moles. Images were acquired by a charge-coupled device camera using eight narrow-band filters ranging from 450 nm to 800 nm, at 50-nm intervals. To extract main features of these tumors, principal components analysis (PCA) was performed, because it projects the multidimensional (here, eight-dimensional) data in the direction of maximum data variance. Then, the primary PCA components for red, green, and blue subset images were analyzed in terms of hue-saturation-intensity (HSI). By hue distributions, the BCCs and SCCs were differentiated from the MMs and normal moles. Texture information was used to further classify tumor types after the HSI analysis. The texture analysis, performed using a spatial gray-level co-occurrence matrix (SGCM), could separate MMs from normal moles. The BCCs and SCCs were further studied by Fisher's linear discriminant analysis. Distribution was described as a Gaussian mixture model. By this classification procedure, seven BCCs, eight SCCs, five MMs, and ten NMs were correctly classified. Three BCCs and two SCCs were unseparable. Thus, multispectral skin cancer image analysis has potential to diagnose skin cancers.

Algorithms↗