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PubMed2003

Noninvasive imaging of cardiac transmembrane potentials within three-dimensional myocardium by means of a realistic geometry anisotropic heart model.

We have developed a new approach for imaging cardiac transmembrane potentials (TMPs) within the three-dimensional (3-D) myocardium by means of an anisotropic heart model. The cardiac TMP distribution is estimated from body surface electrocardiograms by minimizing objective functions of the "measured" body surface potential maps (BSPMs) and the heart-model-generated BSPMs. Computer simulation studies have been conducted to evaluate the present 3-D TMP imaging approach using pacing protocols. Simulations of single-site pacing at 24 sites throughout the ventricles, as well as dual-site pacing at 12 pairs of sites in the vicinity of atrio-ventricular ring were performed. The present simulation results show that the correlation coefficient (CC) and relative error (RE) between the "true" and inversely estimated TMP distributions were 0.9915 +/- 0.0041 and 0.1266 +/- 0.0326, for single-site pacing, and 0.9889 +/- 0.0034 and 0.1473 +/- 0.0237 for dual-site pacing, respectively, when 10 microV Gaussian white noise (GWN) was added to the BSPMs. The effects of heart and torso geometry uncertainty were also evaluated by shifting the heart position by 10 mm and altering the torso size by 10%. The CC between the "true" and inversely estimated TMP distributions was above 0.97 when these geometry uncertainties were considered. The present simulation results demonstrate the feasibility of noninvasive estimation of TMP distribution throughout the ventricles from body surface electrocardiographic measurements, and suggest that the present method may become a useful alternative in noninvasive imaging of distributed cardiac electrophysiological processes within the 3-D myocardium.

Body Surface Potential Mapping↗

PubMed2006

Constrained Gaussian mixture model framework for automatic segmentation of MR brain images.

An automated algorithm for tissue segmentation of noisy, low-contrast magnetic resonance (MR) images of the brain is presented. A mixture model composed of a large number of Gaussians is used to represent the brain image. Each tissue is represented by a large number of Gaussian components to capture the complex tissue spatial layout. The intensity of a tissue is considered a global feature and is incorporated into the model through tying of all the related Gaussian parameters. The expectation-maximization (EM) algorithm is utilized to learn the parameter-tied, constrained Gaussian mixture model. An elaborate initialization scheme is suggested to link the set of Gaussians per tissue type, such that each Gaussian in the set has similar intensity characteristics with minimal overlapping spatial supports. Segmentation of the brain image is achieved by the affiliation of each voxel to the component of the model that maximized the a posteriori probability. The presented algorithm is used to segment three-dimensional, T1-weighted, simulated and real MR images of the brain into three different tissues, under varying noise conditions. Results are compared with state-of-the-art algorithms in the literature. The algorithm does not use an atlas for initialization or parameter learning. Registration processes are therefore not required and the applicability of the framework can be extended to diseased brains and neonatal brains.

Algorithms↗

PubMed1998

Identification of kinetically hot residues in proteins.

A number of recent studies called attention to the presence of kinetically important residues underlying the formation and stabilization of folding nuclei in proteins, and to the possible existence of a correlation between conserved residues and those participating in the folding nuclei. Here, we use the Gaussian network model (GNM), which recently proved useful in describing the dynamic characteristics of proteins for identifying the kinetically hot residues in folded structures. These are the residues involved in the highest frequency fluctuations near the native state coordinates. Their high frequency is a manifestation of the steepness of the energy landscape near their native state positions. The theory is applied to a series of proteins whose kinetically important residues have been extensively explored: chymotrypsin inhibitor 2, cytochrome c, and related C2 proteins. Most of the residues previously pointed out to underlie the folding process of these proteins, and to be critically important for the stabilization of the tertiary fold, are correctly identified, indicating a correlation between the kinetic hot spots and the early forming structural elements in proteins. Additionally, a strong correlation between kinetically hot residues and loci of conserved residues is observed. Finally, residues that may be important for the stability of the tertiary structure of CheY are proposed.

Amino Acid Sequence↗

PubMed2005

Multidimensional vibrational spectroscopy for tunneling processes in a dissipative environment.

Simulating tunneling processes as well as their observation are challenging problems for many areas. In this study, we consider a double-well potential system coupled to a heat bath with a linear-linear (LL) and square-linear (SL) system-bath interactions. The LL interaction leads to longitudinal (T1) and transversal (T2) homogeneous relaxations, whereas the SL interaction leads to the inhomogeneous dephasing (T2*) relaxation in the white noise limit with a rotating wave approximation. We discuss the dynamics of the double-well system under infrared (IR) laser excitations from a Gaussian-Markovian quantum Fokker-Planck equation approach, which was developed by generalizing Kubo's stochastic Liouville equation. Analytical expression of the Green function is obtained for a case of two-state-jump modulation by performing the Fourier-Laplace transformation. We then calculate a two-dimensional infrared signal, which is defined by the four-body correlation function of optical dipole, for various noise correlation time, system-bath coupling parameters, and temperatures. It is shown that the bath-induced vibrational excitation and relaxation dynamics between the tunneling splitting levels can be detected as the isolated off-diagonal peaks in the third-order two-dimensional infrared (2D-IR) spectroscopy for a specific phase matching condition. Furthermore, this spectroscopy also allows us to directly evaluate the rate constants for tunneling reactions, which relates to the coherence between the splitting levels; it can be regarded as a novel technique for measuring chemical reaction rates. We depict the change of reaction rates as a function of system-bath coupling strength and a temperature through the 2D-IR signal.

Journal Article↗

PubMed2005

MEDock: a web server for efficient prediction of ligand binding sites based on a novel optimization algorithm.

The prediction of ligand binding sites is an essential part of the drug discovery process. Knowing the location of binding sites greatly facilitates the search for hits, the lead optimization process, the design of site-directed mutagenesis experiments and the hunt for structural features that influence the selectivity of binding in order to minimize the drug's adverse effects. However, docking is still the rate-limiting step for such predictions; consequently, much more efficient algorithms are required. In this article, the design of the MEDock web server is described. The goal of this sever is to provide an efficient utility for predicting ligand binding sites. The MEDock web server incorporates a global search strategy that exploits the maximum entropy property of the Gaussian probability distribution in the context of information theory. As a result of the global search strategy, the optimization algorithm incorporated in MEDock is significantly superior when dealing with very rugged energy landscapes, which usually have insurmountable barriers. This article describes four different benchmark cases that span a diverse set of different types of ligand binding interactions. These benchmarks were compared with the use of the Lamarckian genetic algorithm (LGA), which is the major workhorse of the well-known AutoDock program. These results demonstrate that MEDock consistently converged to the correct binding modes with significantly smaller numbers of energy evaluations than the LGA required. When judged by a threshold of the number of energy evaluations consumed in the docking simulation, MEDock also greatly elevates the rate of accurate predictions for all benchmark cases. MEDock is available at http://medock.csie.ntu.edu.tw/ and http://bioinfo.mc.ntu.edu.tw/medock/.

Algorithms↗

PubMed1996

Spatial phase differences can drive apparent motion.

Can shape differences drive apparent motion? Results from previous research are equivocal. Much of the confusion may be due to the use of relatively complex stimuli: letters or geometric shapes, comprising many spatial frequencies, phases, orientations, and contrasts. We focus on relatively simple stimuli: Gaussian damped f+nf compound sinewave gratings. We examine whether relative phase differences, which are critical for shape perception, can drive apparent motion. We find that some, but not all, phase differences can drive apparent motion. Specifically, stimuli that are easily discriminable and perceptually dissimilar can affect the solution of the correspondence problem. In this case, observers consistently perceive stimuli in one frame moving to the position of perceptually similar stimuli in the next frame. This general result holds over a wide range of spatial frequencies, orientations, and contrasts. Implications for theories of motion processing are discussed.

Attention↗

PubMed1997

Regularized progressive expansion algorithm for recovery of scattering media from time-resolved data.

Reconstructions of the absorption cross sections of dense scattering media from time-resolved data are presented. A progressive expansion (PE) algorithm, similar to a layer-stripping, is developed to circumvent the underdeterminedness of the inverse problem. An overlapping scheme, which used detector readings from several consecutive time intervals, is introduced to reduce the propagation of reconstruction errors that occur at shallower depths. To reduce the sensitivity of the PE algorithm to noise a regularized progressive expansion (RPE) algorithm is proposed, which incorporates regularization techniques into the PE algorithm. The PE and the RPE algorithms are applied to the problem of image reconstruction from time-resolved data. The test media were isotropically scattering slabs containing one or two compact absorbers at different depths below the surface. The data were corrupted by additive white Gaussian noise with various strengths. The reconstruction results show that the PE and the RPE algorithms, when they are combined by proper overlapping, can effectively overcome the underdeterminedness of the inverse problem. The RPE algorithm yields reconstructions that are more accurate and more stable under the same noise level.

Algorithms↗

PubMed2006

Single particle tracking across sequences of microscopical images: application to platelet adhesion under flow.

A versatile and automated image processing technique and data extraction procedure from videomicroscopic data is presented. The motivation is a detailed quantification of blood platelet adhesion from laminar flow onto a surface. The characteristics of the system under observation (type of cells, their speed of movement, and the quality of the optical image to analyze) provided the criteria for developing a new procedure enabling tracking for long image sequences. Specific features of the novel method include: automatic segmentation methodology which removes operator bias; platelet recognition across the series of images based on a probability density function (two-dimensional, Gaussian-like) tailored to the physics of platelet motion on the surface; options to automatically tune the procedure parameters to explore different applications; integrated analysis of the results (platelet trajectories) to obtain relevant information, such as deposition and removal rates, displacement distributions, pause times and rolling velocities. Synthetic images, providing known reference conditions, are used to test the method. The algorithm operation is illustrated by application to images obtained by fluorescence microscopy of the interaction between platelets and von Willebrand factor-coated surfaces in parallel-plate flow chambers. Potentials and limits are discussed, together with evaluation of errors resulting from an inaccurate tracking.

Algorithms↗

PubMed1981

A computer implementation of a theory of human stereo vision.

Recently, Marr & Poggio (1979) presented a theory of human stereo vision. An implementation of that theory is presented, and consists of five steps. (i) The left and right images are each filtered with masks of four sizes that increase with eccentricity; the shape of these masks is given by delta 2G, the Laplacian of a Gaussian function. (ii) Zero crossings in the filtered images are found along horizontal scan lines. (iii) For each mask size, matching takes place between zero crossings of the same sign and roughly the same orientation in the two images, for a range of disparities up to about the width of the mask's central region. Within this disparity range, it can be shown that false targets pose only a simple problem. (iv) The output of the wide masks can control vergence movements, thus causing small masks to come into correspondence. In this way, the matching process gradually moves from dealing with large disparities at a low resolution to dealing with small disparities at a high resolution. (v) When a correspondence is achieved, it is stored in a dynamic buffer, called the 2 1/2-dimensional sketch. To support the adequacy of the Marr-Poggio model of human stereo vision, the implementation was tested on a wide range of stereograms from the human stereopsis literature. The performance of the implementation is illustrated and compared with human perception. Also statistical assumptions made by Marr & Poggio are supported by comparison with statistics found in practice. Finally, the process of implementing the theory has led to the clarification and refinement of a number of details within the theory; these are discussed in detail.

Computers↗

PubMed1977

Quantitative evaluation of the loss of human platelet dense bodies following stimulation by thrombin or A23187.

1. Distributions of dense bodies per platelet were evaluated in unstimulated human platelets and in platelets stimulated to secrete by the addition of varying amounts of thrombin or the ionophore A23187. Since distributions were not Gaussian, they were compared by non-parametric methods. 2. Most distribution obtained following varying levels of dense-body release differed significantly from the control (unstimulated) distribution. In general, distribution from points widely separated in terms of per cent release of total dense-body content also differed significantly. Distributions obtained at points where the total number of dense bodies lost was approximately the same did not differ significantly, regardless of the drug and incubation conditions used to produce the dense-body loss. 3. Dense bodies were lose from platelets during the secretory process (measured as the release of either calcium or ATP), and the number of dense bodies lost correlated at a significant level with the amounts of both substances secreted. 4. Following maximal secretion produced by either thrombin or A23187, a population of dense bodies (refractory dense bodies) remained in platelets. The refractory dense bodies could not have been distributed uniformly among the control populations of either platelets or dense bodies. The distribution of refractory dense bodies could, however, be described by a model in which platelets containing large numbers of dense bodies had a greater proportion of their dense-body complement refractory than did platelets containing fewer dense bodies.

Adenosine Triphosphate↗

PubMed2000

LQG controller design using GUI: application to antennas and radio-telescopes

The Linear Quadratic Gaussian (LQG) algorithm has been used to control the JPL's beam wave-guide, and 70-m antennas. This algorithm significantly improves tracking precision in a wind disturbed environment. Based on this algorithm and the implementation experience a Matlab based Graphical User Interface (GUI) was developed to design the LQG controllers applicable to antennas and radiotelescopes. The GUI is described in this paper. It consists of two parts the basic LQG design and the fine-tuning of the basic design using a constrained optimization algorithm. The presented GUI was developed to simplify the design process, to make the design process user-friendly, and to enable design of an LQG controller for one with a limited control engineering background. The user is asked to manipulate the GUI sliders and radio buttons to watch the antenna performance. Simple rules are given at the GUI display.

Journal Article↗

PubMedDate not supplied

Magnetic resonance visualisation of single- and two-phase flow in porous media.

Three-dimensional MRI and flow visualisation data are presented for single and two-phase flow occurring within packed beds of glass spheres. The initial motivation for this work has been to understand the operation of fixed-bed reactors used in many chemical processing operations; these systems also serve as model porous media in which to investigate the effect of the structure of a pore space on the flow phenomena occurring within it. For the case of single-phase flow, maps of the liquid shear rate components are calculated from which forces on individual spheres within the bed are obtained. The velocity histogram for flow transverse to the direction of superficial flow is exponential in both negative and positive directions. This form of the velocity histogram implies an exponential form for the displacement propagator, in contrast to the Gaussian distribution obtained by pulsed gradient spin echo measurements. This difference arises because the spatially resolved velocity imaging sequence measures only the average velocity within each voxel and is insensitive to the effects of incoherent (diffusive) motion. Visualisations of air-water flow through a sphere pack are also reported and the capability of MRI to yield information on rivulet formation and surface wetting characteristics is illustrated.

Glass↗

PubMed2003

Distance distributions and electron-density characteristics of protein models.

The analytical expression for the distribution of an interatomic distance resulting from a known error-free distance and a Gaussian perturbation of the atomic coordinates is presented. This is used to estimate the coordinate error on the basis of known geometric features of protein models via the nearest-neighbour or the radial distance distribution. A simple relation is presented that describes the dependence of the map correlation on the positional error of the protein model, the resolution of the X-ray data and the overall atomic displacement parameter. The distribution of geometrical features and the relation between the map correlation and the positional error can be used in assisting the decision-making process during automated model-building procedures.

Crystallography, X-Ray↗

PubMed1990

Aperture optimization for emission imaging: effect of a spatially varying background.

A method for optimizing the aperture size in emission imaging is presented that takes into account limitations due to the Poisson nature of the detected radiation stream as well as the conspicuity limitation imposed by a spatially varying background. System assessment is based on the calculated performance of two model observers: the best linear observer, also called the Hotelling observer, and the nonprewhitening matched-filter observer. The tasks are the detection of a Gaussian signal and the discrimination of a single from a double Gaussian signal. When the background is specified, detection is optimized by enlarging the aperture; an inhomogeneous background results in an optimum aperture size matched naturally to the signal. The discrimination task has a finite optimum aperture for a flat background; a nonuniform background drives the optimum toward still-finer resolution.

Image Processing, Computer-Assisted↗

PubMed2000

Robust parametric and semi-parametric spot fitting for spot array images.

In this paper we address the problem of reliably fitting parametric and semi-parametric models to spots in high density spot array images obtained in gene expression experiments. The goal is to measure the amount of label bound to an array element. A lot of spots can be modelled accurately by a Gaussian shape. In order to deal with highly overlapping spots we use robust M-estimators. When the parametric method fails (which can be detected automatically) we use a novel, robust semi-parametric method which can handle spots of different shapes accurately. The introduced techniques are evaluated experimentally.

Animals↗

PubMed1991

Bi-spectral analysis of bioelectric phenomena: a survey.

This article presents five examples of bi-spectral analysis of bioelectric phenomena which show non-Gaussian statistics. Examples include: analysis of the electroencephalogram (EEG), electrical response of retinal horizontal cells to light stimuli, the evoked potential (EVP), the electromyogram (EMG) and spontaneous synaptic potentials (SSP). Readers may find the higher-order spectral analysis useful in extracting information underlying various kinds of bioelectric phenomena.

Animals↗

PubMed2000

Effects of acid pH and urea on the spectral properties of the LHII antenna complex from the photosynthetic bacterium Ectothiorhodospira sp.

The aim of this study was to investigate the spectral modifications of the LHII antenna complex from the purple bacterium Ectothiorhodospira sp. upon acid pH titration both in the presence and absence of urea. A blue shift specifically and reversibly affected the B850 band around pH 5.5-6.0 suggesting that a histidine residue most probably participated in the in vivo absorption red shifting mechanism. This transition was observed in the presence and absence of urea. Under strong chaotropic conditions, a second transition occurred around pH 2.0, affecting the B800 band irreversibly and the B850 reversibly. Under these conditions a blue shift from 856 to 842 nm occurred and a new and strong circular dichroism signal from the new 842 nm band was observed. Reverting to the original experimental conditions induced a red shift of the B850 band up to 856 nm but the circular dichroism signal remained mostly unaffected. Under the same experimental conditions, i.e. pH 2.1 in the presence of urea, part of the B800 band was irreversibly destroyed with concomitant appearance of a band around 770 nm due to monomeric bacteriochlorophyll from the disrupted B800. Furthermore, Gaussian deconvolution and second derivative of the reverted spectra at pH 8.0 after strong-acid treatment indicated that the new B850 band was actually composed of two bands centered at 843 and 858 nm. We ascribed the 858 nm band to bacteriochlorophylls that underwent reversible spectral shift and the 843 nm band to oligomeric bacteriopheophytin formed from a part of the B850 bacteriochlorophyll. This new oligomer would be responsible for the observed strong and mostly conservative circular dichroism signal. The presence of bacteriopheophytin in the reverted samples was definitively demonstrated by HPLC pigment analysis. The pheophytinization process progressed as the pH decreased below 2.1, and at a certain point (i.e. pH 1.5) all bacteriochlorophylls, including those from the B800 band, became converted to oligomeric bacteriopheophytin, as shown by the presence of a single absorption band around 843 nm and by the appearance of a single main elution peak in the HPLC chromatogram which corresponded to bacteriopheophytin.

Bacterial Proteins↗

PubMed2004

Ab initio studies of alkyl radical reactions: Combination and disproportionation reactions of CH3 with C2H5, and the decomposition of chemically activated C3H8.

This paper reports the first quantitative ab initio prediction of the disproportionation/combination ratio of alkyl+alkyl reactions using CH3+C2H5 as an example. The reaction has been investigated by the modified Gaussian-2 method with variational transition state or Rice-Ramsperger-Kassel-Marcus calculations for several channels producing (1) CH4+CH2CH2, (2) C3H8, (3) CH4CH3CH, (4) H2+CH3CHCH2, (5) H2+CH3CCH3, and (6) C2H6+CH2 by H-abstraction and association/decomposition mechanisms through singlet and triplet potential energy paths. Significantly, the disproportionation reaction (1) producing CH4+C2H4 was found to occur primarily by the lowest energy path via a loose hydrogen-bonding singlet molecular complex, H3CHC2H4, with a 3.5 kcal/mol binding energy and a small decomposition barrier (1.9 kcal/mol), instead of a direct H-abstraction process. Bimolecular reaction rate constants for the formation of the above products have been calculated in the temperature range 300-3000 K. At 1 atm, formation of C3H8 is dominant below 1200 K. Over 1200 K, the disproportionation reaction becomes competitive. The sum of products (3)-(6) accounts for less than 0.3% below 1500 K and it reaches around 1%-4% above 2000 K. The predicted rate constant for the disproportionation reaction with multiple reflections above the complex well, k1=5.04 x T(0.41) exp(429/T) at 200-600 K and k1=1.96 x 10(-20) T(2.45) exp(1470/T) cm3 molecule(-1) s(-1) at 600-3000 K, agrees closely with experimental values. Similarly, the predicted high-pressure rate constants for the combination reaction forming C3H8 and its reverse dissociation reaction in the temperature range 300-3000 K, k2(infinity)=2.41 x 10(-10) T(-0.34) exp(259/T) cm3 molecule(-1) s(-1) and k(-2)(infinity)=8.89 x 10(22) T(-1.67)exp(-46 037/T) s(-1), respectively, are also in good agreement with available experimental data.

Journal Article↗