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PubMed2004

On diabatization and the topological D-matrix: theory and numerical studies of the H + H2 system and the C2H2 molecule.

This article is divided into two main parts: (1) The theoretical part contains a new derivation of the topological matrix D (M. Baer and A. Alijah, Chem. Phys. Lett., 2000, 319, 489) which is based, solely, on the spatial dependent electronic manifold. This derivation enables more intimate relations between the adiabatic and the diabatic frameworks as is discussed in detail in the manuscript. (2) The numerical part is also divided into two parts: (a) In the first part we extend our previous study on the H + H2 system (G. Halasz, A. Vibok, A. M. Mebel and M. Baer, J. Chem. Phys., 2003, 118, 3052) by calculating the topological matrix for five states (instead of three) and for configuration spaces four times larger than before. These studies are expected to yield detailed information on the possibility of diabatization of this system. (b) We report on preliminary results concerning the C2H2 molecule. So far we established the existence of one (1,2) conical intersection and we have good reasons to believe that this system contains several (2,3) and (3,4) conical intersections as well.

Journal Article↗

PubMed2002

On the role of electron-ion recombination in low vacuum scanning electron microscopy.

Here we demonstrate the effects of electron-ion recombination on imaging signals utilized in low vacuum scanning electron microscopes (SEMs). The presented results show that, under normal operating conditions, recombination of ionized gas molecules with secondary electrons (SEs) suppresses a significant fraction of emitted electrons. If the ion flux (and hence the spatial dependence of the SE-ion recombination rate) is laterally inhomogeneous across the imaged region of a specimen, contrast in SE images can be influenced and in some cases (under conditions of high detector field strength and long ionic mean free path) dominated by variations in the recombination rate. Consequently, SE images of features such as topographic asperities can exhibit edge-darkening, leading to inversion of some topographic contrast. Recognition of the extent and nature of electron-ion recombination is required for a correct understanding of processes occurring in variable pressure SEMs and, subsequently, for models of image formation.

Journal Article↗

PubMed2003

Polarization properties of the in vitro old human crystalline lens.

We have studied the spatially resolved polarization properties of the in vitro intact old human crystalline lens (from 56 to 88 years old) by using Mueller-matrix imaging polarimetry. Analysis was performed within an average of 54 h of death. Results show that the overall retardation is small (7 degrees on average) and decreases from the centre of the lens to the periphery. Lenticular birefringence is linear but has a spatial dependence, reducing outwards along the radius. The distribution of azimuthal angle of the birefringent structure of the crystalline lens changes depending on each individual lens. Diattenuation and polarizance were found to be small, however, depolarization was about 35% for the set of lenses studied here.

Aged↗

PubMed2002

Predicting membrane oxygenator pressure drop using computational fluid dynamics.

Three-dimensional computational fluid dynamic (CFD) simulations of membrane oxygenators should allow prediction of spatially dependent variables and subsequent shape optimization. Fiber bed complexity and current computational limitations require the use of approximate models to predict fiber drag effects in complete device simulations. A membrane oxygenator was modified to allow pressure measurement along the fiber bundle in all cardinal axes. Experimental pressure drop information with water perfusion was used to calculate the permeability of the fiber bundle. A three-dimensional CFD model of a commercial membrane oxygenator was developed to predict pressure drops throughout the device. Darcy's Law was used to account for the viscous drag of the fibers and was incorporated as a momentum loss term in the conservation equations. Close agreement was shown between experimental and simulated pressure drops at lower flow rates, but the simulated pressure drops were lower than experimental results at higher flows. Alternate models of fiber drag effects and flow field visualization are suggested as means to potentially improve the accuracy of the flow simulation. Computational techniques coupled with experimental verification offer insight into model validity and show promise for the development of accurate three-dimensional simulations of membrane oxygenators.

Artificial Organs↗

PubMed1982

[Experimental studies of signal fields of ultrasound broad band transducers].

Quantitative analysis of ultrasonic signals, as increasingly practised, makes it necessary to increase the band width as well as the efficiency of ultrasonic transducers. An broad band ultrasonic transducer is presented which meets the requirements by double lambda/4 layer matching and was specially designed for medical ultrasonic spectroscopy. In an extended measurement programme transmitter characteristic, spatial dependence of the spectral content of the transmitter signals as well as beam geometry and its frequency dependence are investigated and compared with conventional transducers.

Fourier Analysis↗

PubMed1994

Chaotic capture of vortices by a moving body. II. Bound pair model.

Previously, we have presented a simple model for the interaction of a fluid vortex structure with a moving bluff body, and demonstrated the existence of a trapping mechanism related to chaotic scattering. This single point vortex model required explicit perturbation to generate chaos and the subsequent complex dynamics. Here, we present a model which attempts to introduce internal degrees-of-freedom in the vortex structure in the simplest manner, by replacing the single vortex with a like-signed pair. We show that this model exhibits chaotic trapping without the need of explicit perturbation, however, the region of parameter space for which trapping occurs is exceedingly small due to the spatially dependent form of the perturbation. We claim that this result explains some the behavior observed in Navier-Stokes simulations of the same vortex-body system, where we find close correspondence between the dynamics of an extended vorticity distribution and the single vortex model. Finally, we generalize the model to unequal strength vortex pairs, and find more complex behavior which includes "partial" capture of the weaker vortex by the body. (c) 1994 American Institute of Physics.

Journal Article↗

PubMed1998

Bogoliubov-Born-Green-Kirkwood-Yvon hierarchy methods for sums of Lyapunov exponents for dilute gases.

We consider a general method for computing the sum of positive Lyapunov exponents for moderately dense gases. This method is based upon hierarchy techniques used previously to derive the generalized Boltzmann equation for the time-dependent spatial and velocity distribution functions for such systems. We extend the variables in the generalized Boltzmann equation to include a new set of quantities that describe the separation of trajectories in phase space needed for a calculation of the Lyapunov exponents. The method described here is especially suitable for calculating the sum of all of the positive Lyapunov exponents for the system, and may be applied to equilibrium as well as nonequilibrium situations. For low densities we obtain an extended Boltzmann equation, from which, under a simplifying approximation, we recover the sum of positive Lyapunov exponents for hard-disk and hard-sphere systems, obtained before by a simpler method. In addition we indicate how to improve these results by avoiding the simplifying approximation. The restriction to hard-sphere systems in d dimensions is made to keep the somewhat complicated formalism as clear as possible, but the method can be easily generalized to apply to gases of particles that interact with strong short-range forces. (c) 1998 American Institute of Physics.

Journal Article↗

PubMed1999

Design criteria of a chemical reactor based on a chaotic flow.

We consider the design criteria of a chemical mixing device based on a chaotic flow, with an emphasis on the steady-state devices. The merit of a reactor, defined as the Q-factor, is related to the physical dimension of the device and the molecular diffusivity of the reactants through the local Lyapunov exponents of the flow. The local Lyapunov exponent can be calculated for any given flow field and it can also be measured in experimental situations. Easy-to-compute formulae are provided to estimate the Q-factor given either the exact spatial dependence of the local Lyapunov exponent or its probability distribution function. The requirements for optimization are made precise in the context of local Lyapunov exponents. (c) 1999 American Institute of Physics.

Journal Article↗

PubMed1999

Dynamics of a nonlinear parametrically excited partial differential equation.

We investigate a parametrically excited nonlinear Mathieu equation with damping and limited spatial dependence, using both perturbation theory and numerical integration. The perturbation results predict that, for parameters which lie near the 2:1 resonance tongue of instability corresponding to a single mode of shape cos nx, the resonant mode achieves a stable periodic motion, while all the other modes are predicted to decay to zero. By numerically integrating the p.d.e. as well as a 3-mode o.d.e. truncation, the predictions of perturbation theory are shown to represent an oversimplified picture of the dynamics. In particular it is shown that steady states exist which involve many modes. The dependence of steady state behavior on parameter values and initial conditions is investigated numerically. (c) 1999 American Institute of Physics.

Journal Article↗

PubMed2006

Ablation of hippocampal neurogenesis impairs contextual fear conditioning and synaptic plasticity in the dentate gyrus.

Although hippocampal neurogenesis has been described in many adult mammals, the functional impact of this process on physiology and behavior remains unclear. In the present study, we used two independent methods to ablate hippocampal neurogenesis and found that each procedure caused a limited behavioral deficit and a loss of synaptic plasticity within the dentate gyrus. Specifically, focal X irradiation of the hippocampus or genetic ablation of glial fibrillary acidic protein-positive neural progenitor cells impaired contextual fear conditioning but not cued conditioning. Hippocampal-dependent spatial learning tasks such as the Morris water maze and Y maze were unaffected. These findings show that adult-born neurons make a distinct contribution to some but not all hippocampal functions. In a parallel set of experiments, we show that long-term potentiation elicited in the dentate gyrus in the absence of GABA blockers requires the presence of new neurons, as it is eliminated by each of our ablation procedures. These data show that new hippocampal neurons can be preferentially recruited over mature granule cells in vitro and may provide a framework for how this small cell population can influence behavior.

Animals↗

PubMed1998

Subcellular localization of rolipram-sensitive, cAMP-specific phosphodiesterases. Differential targeting and activation of the splicing variants derived from the PDE4D gene.

Biochemical and immunofluorescence analyses revealed that phosphodiesterase variants encoded by the PDE4D gene are targeted to discrete subcellular structures. In quiescent FRTL-5 thyroid cells, the rolipram-sensitive phosphodiesterase (PDE) activity (cAMP-PDE) was recovered both in the soluble and particulate fractions of the homogenate. Although an immunoreactive 93-kDa PDE (PDE4D3) variant was recovered in both compartments, a 105-kDa variant with the properties of PDE4D4 was recovered mostly in the particulate fraction. The PDE4D3 form was readily solubilized with nonionic detergents. Conversely, the PDE4D4 form required buffers containing ionic detergents for extraction, suggesting that different mechanisms target these variants to insoluble structures. A 15-min stimulation with thyroid-stimulating hormone (TSH) led to an activation of the cAMP-PDE in both compartments and was correlated with a shift in electrophoretic mobility of the PDE4D3 polypeptide. Long term incubation with TSH caused an increase of the PDE activity in the soluble fraction and the appearance of a 68-kDa immunoreactive polypeptide with the properties of PDE4D2. Immunofluorescence analysis showed, in addition to diffuse staining, a signal localized on regions adjacent to the plasma membrane on cytoskeletal structures and in a perinuclear region of quiescent cells. Long term incubation with TSH caused an increase in the immunofluorescence signal in the soluble compartment. These data demonstrate that three PDE4D splicing variants are targeted to discrete subcellular compartments and that hormones cause the activation of these isoforms in a temporally and spatially dependent manner.

3',5'-Cyclic-AMP Phosphodiesterases↗

PubMed1995

Phase Transitions and Critical Fluctuations in Rhythmic Coordination of Ipsilateral Hand and Foot.

Four subjects performed rhythmic movements of the ankle and the wrist in time with an auditory metronome, in two modes of coordination, antiphase and in-phase. The forearm was placed in either a prone or a supine position. When movements were prepared in the antiphase mode, spontaneous transitions to the in-phase mode, or to phase wandering were observed as metronome frequency was increased. When prepared in the in-phase mode, transitions between in-phase modes or to phase wandering were occasionally observed. Predicted signature features of nonequilbrium phase transitions were noted, including loss of stability and critical fluctuations. The stability of the movement patterns was determined by spatial (dependent upon the direction of movement) rather than anatomical (dependent on the coupling of specific muscle groups) constraints. The position of the forearm had no consistent bearing upon the variability of the phase relations between the limbs, the frequency of phase transitions, or the time of onset of transitions. These results are discussed with reference to the coordination dynamics (e.g., multistability, loss of stability) of multijoint movements.

Journal Article↗

PubMed2006

Exposure matrix development for the Libby cohort.

The Libby, MT, cohort includes current and former residents with potential historical exposure to asbestos-contaminated vermiculite. This cohort includes individuals with a broad range of exposure experiences and work histories. While both occupational and nonoccupational exposure pathways were found to be relevant in recent investigations of health effects among this cohort, there has not been a comprehensive approach to characterizing these varied exposure pathways. Any approach toward assessing historical exposures among this population must account for three general categories: (1) occupational exposures, (2) residential exposures, and (3) exposures related to a variety of nonoccupational activities thought to be associated with vermiculite/asbestos exposure in this community. First, a job exposure matrix is commonly used in occupational epidemiology to assess historical worker exposures, allowing for the incorporation of numerous occupational categories and weighting factors applied to specific jobs for different time periods. Second, residential exposures can best be quantified by integrating individuals' residential histories with data on environmental asbestos contamination in the community. Previous soil or sediment sampling as well as air modeling could inform estimates of time- and spatial-dependent exposure concentrations for a residential exposure matrix. Finally, exposure opportunities due to nonoccupational activities could be weighted by factors such as time, geography, environmental sampling, and an assessment of the relative importance for each pathway. These three matrices for occupational, residential, and activity exposure pathways could be combined or used separately to provide a more comprehensive and quantitative, or semiquantitative, assessment of individual exposure in future epidemiological studies of this cohort.

Aluminum Silicates↗

PubMed2003

Support vector machines based analysis of brain SPECT images for determining cerebral abnormalities in asymptomatic diabetic patients.

PURPOSE: An image processing method was developed to investigate whether brain SPECT images of patients with diabetes mellitus type II (DMII) and no brain damage differ from those of normal subjects. MATERIALS AND METHODS: Twenty-five DMII patients and eight healthy volunteers underwent brain 99mTc-Bicisate SPECT examination. A semi-automatic method, allowing for physician's interaction, was developed to delineate specific brain regions (ROIs) on the SPECT images. Twenty-eight features from the grey-level histogram and the spatial-dependence matrix were computed from numerous small image-samples collected from each specific ROI. Classification into 'diabetics' and 'non-diabetics' was performed for each ROI separately. The classical least squares-minimum distance (LSMD) classifier and the recently developed support vector machines (SVM) classifier were used. System performance was evaluated by means of the leave-one-out method; one sample was left out, the classifier was trained by the rest of the samples, and the left-out sample was classified. By repeating for all samples, the classifier's performance could be tested on data not incorporated in its design. RESULTS: Highest classification accuracies (LSMD: 97.8%, SVM: 99.1%) were achieved at the right occipital lobule employing two features, the standard deviation and entropy. For the rest of the ROIs classification accuracies ranged between 84.5 and 98.6%. CONCLUSION: Our findings indicate cerebral blood flow disruption in patients with DMII. The proposed system may assist physicians in evaluating cerebral blood flow in patients with DMII undergoing brain SPECT.

Adult↗

PubMed1981

Intercellular communication in normal and regenerating rat liver: a quantitative analysis.

We have compared intercellular communication in the regenerating and normal livers of weanling rats. The electrophysiological studies were conducted at the edge of the liver, and we have found that here as elsewhere in the liver there is a dramatic decrease in the number and size of gap junctions during regeneration. The area of hepatocyte membrane occupied by gap junctions is reduced 100-fold 29-35 h after hepatectomy. By combining observations made with the scanning electron microscope with our freeze fracture data we have estimated the number of "communicating interfaces" (areas of contact between hepatocytes that include at least one gap junction) formed by hepatocytes in normal and regenerating liver. In normal liver a hepatocyte forms gap junctions with every hepatocyte it contacts (approximately 6). In regenerating liver a hepatocyte forms detectable gap junctions with, on average, only one other hepatocyte. Intercellular spread of fluorescent dye and electric current is reduced in regenerating as compared with normal liver. The incidence of electric coupling is reduced from 100% of hepatocyte pairs tested in control liver to 92% in regenerating liver. Analysis of the spatial dependence of electronic potentials indicates a substantial increase in intercellular resistance in regenerating liver. A quantitative comparison of our morphological and physiological data is complicated by tortuous pattern of current flow and by inhomogeneities in the liver during regeneration. Nevertheless we believe that our results are consistent with the hypothesis that gap junctions are aggregates of channels between cell interiors.

Animals↗

PubMed2006

Bayesian graphical models for genomewide association studies.

As the extent of human genetic variation becomes more fully characterized, the research community is faced with the challenging task of using this information to dissect the heritable components of complex traits. Genomewide association studies offer great promise in this respect, but their analysis poses formidable difficulties. In this article, we describe a computationally efficient approach to mining genotype-phenotype associations that scales to the size of the data sets currently being collected in such studies. We use discrete graphical models as a data-mining tool, searching for single- or multilocus patterns of association around a causative site. The approach is fully Bayesian, allowing us to incorporate prior knowledge on the spatial dependencies around each marker due to linkage disequilibrium, which reduces considerably the number of possible graphical structures. A Markov chain-Monte Carlo scheme is developed that yields samples from the posterior distribution of graphs conditional on the data from which probabilistic statements about the strength of any genotype-phenotype association can be made. Using data simulated under scenarios that vary in marker density, genotype relative risk of a causative allele, and mode of inheritance, we show that the proposed approach has better localization properties and leads to lower false-positive rates than do single-locus analyses. Finally, we present an application of our method to a quasi-synthetic data set in which data from the CYP2D6 region are embedded within simulated data on 100K single-nucleotide polymorphisms. Analysis is quick (<5 min), and we are able to localize the causative site to a very short interval.

Bayes Theorem↗

PubMed1999

Non-invasive optical monitoring of the newborn piglet brain using continuous-wave and frequency-domain spectroscopy.

We have used continuous-wave (CW) and frequency-domain spectroscopy to investigate the optical properties of the newborn piglet brain in vivo and non-invasively. Three anaesthetized, intubated, ventilated and instrumented newborn piglets were placed into a stereotaxic instrument for optimal experimental stability, reproducible probe-to-scalp optical contact and 3D adjustment of the optical probe. By measuring the absolute values of the brain absorption and reduced scattering coefficients at two wavelengths (758 and 830 nm), frequency-domain spectroscopy provided absolute readings (in contrast to the relative readings of CW spectroscopy) of cerebral haemoglobin concentration and saturation during experimentally induced perturbations in cerebral haemodynamics and oxygenation. Such perturbations included a modulation of the inspired oxygen concentration, transient brain asphyxia, carotid artery occlusion and terminal brain asphyxia. The baseline cerebral haemoglobin saturation and concentration, measured with frequency-domain spectroscopy, were about 60% and 42 microM respectively. The cerebral saturation values ranged from a minimum of 17% (during transient brain asphyxia) to a maximum of 80% (during recovery from transient brain asphyxia). To analyse the CW optical data, we have (a) derived a mathematical relationship between the cerebral optical properties and the differential pathlength factor and (b) introduced a method based on the spatial dependence of the detected intensity (dc slope method). The analysis of the cerebral optical signals associated with the arterial pulse and with respiration demonstrates that motion artefacts can significantly affect the intensity recorded from a single optode pair. Motion artefacts can be strongly reduced by combining data from multiple optodes to provide relative readings in the dc slope method. We also report significant biphasic changes (initial decrease and successive increase) in the reduced scattering coefficient measured in the brain after the piglet had been sacrificed.

Animals↗

PubMed2000

Non-iterative methods incorporating a priori source distribution and data information for suppression of image noise and artefacts in 3D SPECT.

Non-iterative methods have been developed for image reconstruction in 3D SPECT with uniform attenuation and distance-dependent spatial resolution. It was observed that these methods can, in general, be susceptible to data noise and other errors, yielding conspicuous image artefacts. In this work, we developed and evaluated a regularized inverse-filtering approach for effective suppression of noise and artefacts in 3D SPECT images without significantly compromising image resolution. The proposed approach allows the incorporation of a priori random image field and data information and can thus robustly control the degree of suppression of noise and artefacts in 3D SPECT images. Using computer simulations, we evaluated and compared quantitatively images reconstructed from data sets of various noise levels by the use of the proposed methods and the existing non-iterative methods. These numerical results clearly demonstrated that the proposed regularized inverse-filtering approach can effectively suppress image noise and artefacts that plague the existing non-iterative methods, thus yielding quantitatively more accurate 3D SPECT images. The proposed regularized inverse-filtering approach can also be generalized to other imaging modalities.

Algorithms↗