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Results for “spatial dependency”

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At least 451 records · Page 25Linked to original sources

PubMed1998

Quantitative spectroscopic imaging of the human brain.

A method to provide B1 correction and cerebrospinal fluid (CSF) referencing is developed and applied to spectroscopic imaging of the human brain at 4.1 T using a volume head coil. The B1 image allows rapid determination of the spatially dependent B1 that is then used to compensate for the B1 sensitivity of the spectroscopic sequence. The reference signal is acquired from CSF located in a lateral ventricular position using a point-resolved echo spectroscopy (PRESS) acquisition. The CSF spectrum is also corrected for B1 dependence. Together with T2 and T1 corrections, this method is used to provide quantitative values of N-acetylaspartate (NAA), creatine (Cr), and choline (Ch). The metabolite concentrations obtained from a spectroscopic imaging slice through the ventricles in seven normal controls are in good agreement with previously published literature values. This method is applied in a patient with secondary progressive multiple sclerosis, showing separate areas of abnormalities in both NAA and Cr.

Aspartic Acid↗

PubMed2004

Correction for gradient nonlinearity in continuously moving table MR imaging.

Recently, a number of methods have been demonstrated for large field of view MR imaging using continuous table motion. As with conventional, fixed-table MRI, the spatial encoding is performed using magnetic field gradients. However, it is demonstrated in this work that as a consequence of every measurement being made at a slightly different displacement between the object and the gradient field, gradient nonlinearities are manifest as blurring in addition to spatial distortion. Moreover, the blurring is spatially dependent. It is also shown that correcting all phase-encoding steps individually or in groups can reduce these effects. Phantom and in vivo results are shown which demonstrate the effectiveness of the correction.

Humans↗

PubMed2005

Analysis and correction of gradient nonlinearity and B0 inhomogeneity related scaling errors in two-dimensional phase contrast flow measurements.

Phase contrast flow measurements will be increasingly biased at eccentric positions, where nonlinearity of gradients and inhomogeneity of the main field become important. In theory, they scale the result of phase contrast flow values in two ways: incorrect velocity encoding of moving spins and geometric distortion of the vessel cross-sectional area. A flow phantom, consisting of a 3D grid of interconnected tubes, was used to determine the spatial dependence of the associated scaling factors, which demonstrate that scaling errors in flow can be as large as 20% within the examined volume of 336 x 336 x 336 mm(3). The same phantom was also used to determine and minimize concomitant gradient effects. Correction of the off-center flow values with the local scaling factors and the concomitant gradient phase improves the measurement accuracy substantially, both in the flow phantom and in a volunteer study.

Adult↗

PubMed2006

Fast 3D radiofrequency field mapping using echo-planar imaging.

An inhomogeneous radiofrequency (RF) magnetic field is an essential source of error for the quantification of MRI and MRS parameters. To correct for effects of RF inhomogeneities in 3D data sets, it is necessary to have knowledge of the 3D RF distribution in the sample. In this paper a method for fast 3D RF mapping is presented. The method is based on the simultaneous acquisition of a spin echo (SE) and a stimulated echo (STE) using echo-planar imaging (EPI). The acquisition of the 3D RF map using 64 partitions and TR = 500 ms requires 1.5 min. The use of the sequence in vivo is demonstrated by the calculation of the RF maps in the human brain at 3T. The comparison of calculated flip angles with the flip angles obtained by fitting signal behavior in the 3D stimulated-echo acquisition mode (STEAM)-EPI sequence and the analysis of errors due to spatially dependent T(1) values in the brain show that the accuracy of the calculated flip angles in the human brain is about 2 degrees.

Algorithms↗

PubMed2006

Disease cluster detection: a critique and a Bayesian proposal.

This paper reviews issues in the analysis of non-focussed clustering, and proposes a novel approach to cluster modelling that can be used in a surveillance context. The novel approach involves the use of local likelihood models for the analysis of clustering in small area health data. Local likelihood is used when interdependence between data events at locations is modelled directly, as opposed to the modelling of a hidden process of cluster centres. This approach allows the use of conventional posterior sampling. It also allows a less parameterized approach to the form of clusters detected. The idea of a spatially dependent lasso which provides the local maxima for the aggregation of locations is considered as an approximation. The methods are applied to a well known data set and compared with Satscan, and a conditional logistic Bayesian model.

Air Pollutants↗

PubMed1993

Disease mapping using empirical Bayes and Bayes methods on mortality statistics in The Netherlands.

Data from the 64 public health service districts in the Netherlands, describing the health status of the Dutch population, were used to construct maps for several causes of deaths. The choice and estimation of the relative risk measure is described. The prior expected number of deaths was modelled using a Poisson regression approach based on a model with main effects of district and age. Desirable properties of risk parameters for disease mapping are that they both reflect the level of risk and cope with the instability in the observed measure caused by the numbers at risk in each district. Different techniques for estimation of parameters were applied: empirical Bayes estimation (EB) using a nonparametric prior and a gamma prior, and a Bayesian approach (B) with a uniform prior. For the parametric EB also a constrained estimator was used. The EB techniques studied in this paper shift or smooth the values of the risk parameter towards a global mean. In the Bayesian method applied here, spatial dependence among districts can be modelled, that is the estimates are smoothed towards a local mean. The three EB estimates gave by and large similar results, although the constrained EB estimate smoothed less, as was expected. The Bayesian estimates smoothed the estimates more or less similarly to the constrained EB.

Bayes Theorem↗

PubMed1998

Estrogen-mediated structural and functional synaptic plasticity in the female rat hippocampus.

Light and electron microscopic studies have shown that ovarian steroids regulate the density and number of excitatory synaptic inputs to hippocampal pyramidal cells in the adult female rat; elevated levels of estradiol are associated with a higher density of dendritic spine synapses on CA1 pyramidal cells. Electrophysiological analyses indicate that these hormone-induced synapses increase hippocampal excitability as well as the potential for synaptic plasticity. Importantly, correlation of dendritic spine density and sensitivity to synaptic input of individual CA1 pyramidal cells from estradiol-treated and control animals suggests that synapses induced by estradiol may be a specialized subpopulation that contains primarily the NMDA subtype of glutamate receptor. The apparent NMDA receptor specificity of these synapses may be key to understanding their functional significance. Currently, the behavioral consequences of additional spine synapses are unknown. Numerous studies have aimed at correlating hormone-induced changes in hippocampal connectivity with differences in hippocampus-dependent spatial learning ability in mazes, but the results of these efforts have been equivocal. Anatomical, electrophysiological, and behavioral studies of estradiol-mediated hippocampal plasticity are reviewed. In conclusion, it is suggested that standard behavioral tests of hippocampal function are not sufficient to reveal the behavioral consequences of hormone-induced hippocampal plasticity. Rather, understanding the behavioral consequences of estradiol and progesterone effects on hippocampal connectivity may require analysis of the hippocampus' cognitive and spatial information processing functions in relation to alternative biologically relevant behaviors. A (nonexclusive) proposal that hormone-induced hippocampal plasticity may facilitate appropriate prepartum/maternal behavior is discussed.

Animals↗

PubMed1999

Pulsed field gradients in simulations of one- and two-dimensional NMR spectra.

A method for the inclusion of the effects of z-axis pulsed field gradients in computer simulations of an arbitrary pulsed NMR experiment with spin (1/2) nuclei is described. Recognizing that the phase acquired by a coherence following the application of a z-axis pulsed field gradient bears a fixed relation to its order and the spatial position of the spins in the sample tube, the sample is regarded as a collection of volume elements, each phase-encoded by a characteristic, spatially dependent precession frequency. The evolution of the sample's density matrix is thus obtained by computing the evolution of the density matrix for each volume element. Following the last gradient pulse, these density matrices are combined to form a composite density matrix which evolves through the rest of the experiment to yield the observable signal. This approach is implemented in a program which includes capabilities for rigorous inclusion of spin relaxation by dipole-dipole, chemical shift anisotropy, and random field mechanisms, plus the effects of arbitrary RF fields. Mathematical procedures for accelerating these calculations are described. The approach is illustrated by simulations of representative one- and two-dimensional NMR experiments.

Anisotropy↗

PubMed2001

Computer simulation of the spin-echo spatial distribution in the case of restricted self-diffusion.

This article concerns the question of a proper stochastic treatment of the spin-echo self-diffusion attenuation of confined particles that arises when short gradient pulse approximation fails. Diffusion is numerically simulated as a succession of random steps when motion is restricted between two perfectly reflecting parallel planes. With the magnetic field gradient perpendicular to the plane boundaries, the spatial distribution of the spin-echo signal is calculated from the simulated trajectories. The diffusion propagator approach (Callaghan, "Principles of Nuclear Magnetic Resonance Microscopy," Oxford Univ. Press, Oxford, 1991), which is just the same as the evaluation of the spin-echo attenuation by the method of cumulant expansion in the Gaussian approximation, with Einstein's approximation of the velocity correlation function (VCF) (delta function), agrees with the results of simulation only for the particle displacements that are much smaller than the size of the confinement. A strong deviation from the results of the simulation appears when the bouncing rate from the boundaries increases at intermediate and long gradient sequences. A better fit, at least for intermediate particle displacements, was obtained by replacing the VCF with the Oppenheim--Mazur solution of the Langevin equation (Oppenheim and Mazur, Physica 30, 1833--1845, 1964), which is modified in a way to allow for spatial dependence of particle displacements. Clearly, interplay of the correlation dynamics and the boundary conditions is taking place for large diffusion displacements. However, the deviation at long times demonstrates a deficiency of the Gaussian approximation for the spin echo of diffusion inside entirely closed pores. Here, the cumulants higher than the second one might not be negligible. The results are compared with the experiments on the edge enhancement by magnetic resonance imaging of a pore.

Journal Article↗

PubMed1994

A new model for bacterial growth in heterogeneous systems.

A general theory of spatially dependent bacterial growth in heterogeneous systems is developed by combining a structured-cell kinetic model of bacterial metabolism with reaction-diffusion equations describing the transport of nutrients in the growth medium. Rate constants in the theory are determined for Listeria monocytogenes by fitting the viable count batch growth data acquired in homogeneous, shake-flask cultures. The rate constants are then used to calculate the form of bacterial growth when it occurs as localized microcolonies in structured systems. The same theory is used to analyse the effects of transient variations in environmental variables.

Bacteriological Techniques↗

PubMed1999

A Model for the Propagation of Action Potentials in Non-Uniformly Excitable Media.

Electrophysiological properties of cardiac tissue change as a function of position. We define the "excitability" as the propagation velocity of an excitation pulse through the tissue, and study a simple FitzHugh-Nagumo (FHN) model of heart tissue whose excitability changes with position. The propagation velocity is shown to be a good continuous measure of the excitability for both limit cycle and excitable tissue. The influence of the spatial dependence of the excitability is examined for several normal and pathological situations. A novel transient effect is observed for a train of pulses propagating across an excitability step. Copyright 1999 Academic Press.

Journal Article↗

PubMed2003

A unified statistical and information theoretic framework for multi-modal image registration.

We formulate and interpret several registration methods in the context of a unified statistical and information theoretic framework. A unified interpretation clarifies the implicit assumptions of each method yielding a better understanding of their relative strengths and weaknesses. Additionally, we discuss a generative statistical model from which we derive a novel analysis tool, the auto-information function, as a means of assessing and exploiting the common spatial dependencies inherent in multi-modal imagery. We analytically derive useful properties of the auto-information as well as verify them empirically on multi-modal imagery. Among the useful aspects of the auto-information function is that it can be computed from imaging modalities independently and it allows one to decompose the search space of registration problems.

Algorithms↗

PubMed1993

DNA damage in non-proliferating cells subjected to ionizing irradiation at high or low dose rates.

Ionizing radiation damage to the genome of a non-cycling mammalian cell is analyzed using continuous time Markov chains. Immediate damage induced by the radiation is modeled as a batch Poisson arrival process of DNA double strand breaks (DSBs). Different kinds of radiation, for example gamma rays or alpha particles, have different batch probabilities. Enzymatic modulation of the immediate damage is modeled as a Markov process similar to the processes described by the master equation of stochastic chemical kinetics. An illustrative example is the restitution/complete exchange model, which postulates that radiation induced DSBs can subsequently either undergo enzymatically mediated repair (restitution) or can participate pairwise in chromosome exchanges, some of which make irremediable lesions such as dicentric chromosome aberrations. One may have rapid irradiation followed by enzymatic DSB processing or have prolonged irradiation with both DSB arrival and enzymatic DSB processing continuing throughout the irradiation period. A complete solution of the Markov chain is known for the case that the exchange rate constant is negligible so that no irremediable chromosome lesions are produced and DSBs are the only damage to the genome. Using PDEs for generating functions, a perturbation calculation is made assuming the exchange rate constant is small compared to the repair rate constant. Some non-perturbative results applicable to very prolonged irradiation are also obtained using matrix methods: Perron-Frobenius theory, variational methods and numerical approximations of eigenvalues. Applications to experimental results on expected values, variances and statistical distributions of DNA lesions are briefly outlined. Continuous time Markov chain models are the most systematic of those current radiation damage models which treat DSB-DSB interactions within the cell nucleus as homogeneous (e.g. ignore diffusion limitations). They contain most other homogeneous models as special cases, limiting cases or approximations. However, applying the continuous time Markov chain models to studying spatial dependence of DSB interactions, which is generally believed to be very important in some situations, presents difficulties.

Animals↗

PubMedDate not supplied

Characteristics of fatty acid-binding proteins and their relation to mammary-derived growth inhibitor.

Based on sequence relationships the cytoplasmic fatty acid-binding proteins (FABPs) of mammalian origin are divided into at least three distinct types, namely the hepatic-, intestinal- and cardiac-type. Highly conserved sequences of FABPs within the same type correlate with immunological crossreactivities. Isoforms of hepatic-type FABP are found in several mammalian species and for bovine liver FABP specific shifts in isoelectric points upon lipidation with fatty acids are observed. Isoforms of intestinal-type FABP are not known and the occurrence of cardiac-type isoforms so far is confined to bovine heart tissue. A bovine mammary-derived growth inhibitor (MDGI) is 95% homologous to the cardiac-type FABP from bovine heart. Dissociation constants of FABP/fatty acid complexes are in the range of 1 microM and 1:1 stoichiometries are usually found, but the neutral isoform of hepatic FABP from bovine liver binds 2 fatty acids. On subcellular levels hepatic- and cardiac-type FABPs are differently distributed. Though mainly cytosolic in either case, immunoelectron microscopy as well as a gelchromatographic immunofluorescence assay demonstrate the association of hepatic FABP in liver cells with microsomal and outer mitochondrial membranes and with nuclei, whereas in heart cells cardiac FABP is confined to mitochondrial matrix and nuclei. In mammary epithelial cells MDGI is associated with neither mitochondria nor endoplasmic reticulum, and is expressed in a strictly developmental-dependent spatial and temporal pattern. The specific role proposed for MDGI is to arrest growth of mammary epithelial cells when they become committed to differentiation in the mammary gland.

Amino Acid Sequence↗

PubMed1992

Sarcolemmal calcium binding sites in heart: II. Mathematical model for diffusion of calcium released from the sarcoplasmic reticulum into the diadic region.

We present a model for predicting the temporal and spatial dependence of [Ca] in the cardiac subsarcolemmal diadic region (cleft), following Ca release from the "feet" of the sarcoplasmic reticulum. This region is modeled as a disc 10 nm thick, 430 nm in radius, with or without Ca binding sites and open at its periphery to the cytosol. [Ca] is computed for three diffusion coefficients (100, 20 and 4% of aqueous diffusion), following release of a 20-msec square pulse sufficient to produce 50% maximal contractile force, or repetitive release (400/min) of such pulses. Numerical solutions are obtained for the general diffusion/binding problem and analytic solutions for the case of no binding sites. For the middle value of diffusion coefficient, and in the absence of binding sites, [Ca] rises to approximately 1.5 mM in 20-msec and then falls to approximately 0.1 microM in less than 3 msec. Adding binding sites reduces peak [Ca] to approximately 0.6 mM but prolongs its decline, requiring approximately 200 msec to reach 20 microM. For repetitive release [Ca] is greater than 100 microM for roughly half of each cycle. Two major implications of the predicted [Ca] are: (i) The effect of Ca binding sites on [Ca] will cause Ca efflux from the cleft via the Na-Ca exchanger (Km(Ca) approximately 20 microM) to continue at a significant level for greater than 200 msec. (ii) The time constant for inactivation of release from the "feet" must be much greater than for activation if Ca-induced Ca release is to continue for greater than 1-2 msec.

Animals↗

PubMed1989

The asymptotic transectional/circumferential homogeneity of the solutions of reaction-diffusion systems in/on cylinder-like domains.

It is often reported that an animal with spotty coat markings on its body has a tail with stripe-shaped pattern. In other various biological and chemical phenomena in/on cylinder-like domains, longitudinally periodic band patterns are observed much more often than the other non-uniform patterns. This paper mathematically explains these observations by proving that, in/on a long and narrow cylinder-like domain, any solution of reaction-diffusion system asymptotically loses its spatial dependence in the transectional/circumferential direction.

Animals↗

PubMed1985

Mechanics of the transduction of sound in the tympanal organ of adults and larvae of locusts.

The mechanical transmission of sound in the tympanal organ of adults and 5th instar larvae of Locusta migratoria and Schistocerca gregaria has been investigated by means of stroboscopic measurements within a frequency range from 1-20 kHz. Frequency dependent spatial distributions of amplitudes and phases of oscillation on the tympanal membrane and the Müller's organ could be demonstrated. Cuticular structures on the membrane may act as a lever arm (e.g. elevated process) and cause a transformation of the (unidimensional) membrane motion into components of displacements in the Müller's organ perpendicular, as well as even parallel, to the membrane. Sites of maximum relative displacements at distinct frequencies are found to be correlated to the course of the dendrites of the acoustic receptor cells. Differences in morphology of the tympanal organ between the two species as well as between adults and larvae always correspond to differences in the mechanical properties (resonances etc.). Consequently, differences or changes in the neurophysiological response characteristics of the different receptor cells have been found. Based upon these findings a correlation between the anatomical and physiological classification of the receptor cell groups is presented.

Animals↗

PubMed1999

Two-dimensional deghosting for EPI.

A residual ghost artefact in echo-planar imaging (EPI) remains after the standard correction procedure based on a 1-dimensional phase-modulation of the spectra of even or odd echoes. A better reduction of this artefact is demonstrated using a 2-dimensional phase correction. The phase correction map is measured inside the ghost-free region of the image, preferably in a reference scan with an increased field of view, as the phase difference between complex images reconstructed separately from even and odd echoes. An extrapolated map consisting of spatial components up to the second order (constant, x, y, xy and x2-y2) is then found by a fit to the measured values. This map is used to correct the phase of even- and odd-reconstructed images before adding them. This procedure may cause some spatially dependent loss of signal, but if the level of the residual artefact is less than 20% of the image intensity, such losses are negligible.

Artifacts↗