PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “spatial dependency”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 37 records · Page 2Linked to original sources
PubMed1992

Intensity artifacts in MRI caused by gradient switching in an animal-size NMR magnet.

The switching of magnetic field gradients in MRI gives rise to eddy currents in the structural components of superconducting magnet systems. The associated magnetic fields cause intensity artifacts which are particularly severe in some animal-size systems. We treat theoretically three mechanisms which cause intensity artifacts in one-dimensional projection images obtained by a spin-echo technique. The first is an off-resonance effect, caused by applying the refocusing pulse before the read compensation gradient pulse has decayed sufficiently. The other two mechanisms are caused by a spatial dependence of the phase accumulated by the spins at the time of formation of the echo, as a result of the eddy current fields. First, interference causes a loss of transverse magnetization because of a variation in the phase of spins which lie on the same isochromat during the read gradient pulse. Second, a variation of the phase of the spins in a direction orthogonal to the isochromats causes spins throughout the sample to refocus at different times. These two mechanisms are fundamentally different, since interference can occur even if the main magnetic field is homogeneous, whereas improper refocusing does not. It is shown that there is no loss of intensity by the interference mechanism if phase encoding is used to form two-dimensional images. This may well be a major reason why images obtained by 2DFT have been found to be generally superior to those obtained by projection reconstruction. Experimentally, the distribution of intensity in one-dimensional projection images of a square slice phantom is compared with theoretical intensities, estimated using eddy current field reported in the preceding paper.

Artifacts↗
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↗
PubMed1992

DNA damage caused by ionizing radiation.

A survey is given of continuous-time Markov chain models for ionizing radiation damage to the genome of mammalian cells. In such models, immediate damage induced by the radiation is regarded as a batch-Poisson arrival process of DNA double-strand breaks (DSBs). Enzymatic modification of the immediate damage is modeled as a Markov process similar to those described by the master equation of stochastic chemical kinetics. An illustrative example is the restitution/complete-exchange model. The model postulates that, after being induced by radiation, DSBs subsequently either undergo enzymatically mediated restitution (repair) or participate pairwise in chromosome exchanges. Some of the exchanges 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. Methods for analyzing the Markov chains include using an approximate model for expected values, the discrete-time Markov chain embedded at transitions, partial differential equations for generating functions, normal perturbation theory, singular perturbation theory with scaling, numerical computations, and certain matrix methods that combine Perron-Frobenius theory with variational estimates. Applications to experimental results on expected values, variances, and statistical distributions of DNA lesions are briefly outlined. Continuous-time Markov chains are the most systematic of those radiation damage models that treat DSB-DSB interactions within the cell nucleus as homogeneous (e.g., ignore diffusion limitations). They contain virtually all other relevant homogeneous models and semiempirical summaries as special cases, limiting cases, or approximations. However, the Markov models do not seem to be well suited for studying spatial dependence of DSB interactions, which is known to be important in some situations.

Animals↗
PubMed1991

Polycyclic aromatic hydrocarbon (PAH) concentrations in ambient airborne particles from local traffic and distant sources; variation of the PAH profile.

The temporal and spatial dependence of the PAH profile, i.e. the relative concentrations of polycyclic aromatic hydrocarbons, was investigated for ambient airborne particles during a period with moderate photochemical air pollution. The concentrations of 14 PAH were measured; they differed in volatility, sensitivity to atmospheric chemical conversion and contributing sources. Multivariate analysis (principal-component analysis and factor analysis) revealed that temporal dependence was predominantly determined by five factors clearly linked with volatility, reactivity and sources of the PAH, the first being by far the most important. The results, therefore, indicate that volatilization, conversion and a varying contribution of local sources were the major causes of the variation of the profile with time. The contribution of local sources was investigated by comparison of samples that were taken simultaneously at three different sites, one a background site and two sites downwind of traffic. A marked site dependence was found. The comparison suggested that the differences were not only determined by sources, but also by volatilization and/or conversion during residence of the particles in the air.

Air Pollutants↗
PubMed2026

Lipid metabolism is a key central, systemic and gut microbial feature of the decline in rat hippocampal function during middle age.

Middle age is emerging as a turning point in brain ageing, prognostic of future cognitive health and amenable to intervention. Metabolic and proteomic differences during this period are not yet fully understood and may potentially influence functions of the hippocampus, a brain area that regulates memory and anxiety. While the gut microbiota is implicated in brain ageing, the relationship between the gut microbiota, the metabolic state, and hippocampal proteome in middle age has not been investigated. We hypothesise that peripheral metabolic or protein features are associated with hippocampal vulnerability in middle age. Therefore, young adult and middle-aged rats were assessed for behavioural, proteomic, metabolic, and gut microbiota differences. Proteomic profiling of the hippocampus revealed differential expression of proteins indicative of altered synaptic signalling. Concurrently, adult hippocampal neurogenesis was decreased in middle age. Hippocampal microglia exhibited a lipid rich, inflammatory phenotype in middle age which correlated with poorer memory performance. CSF and serum proteomic and metabolomic analyses identified dysregulated lipid-related pathways potentially contributing to hippocampal vulnerability in middle age. Furthermore, 16S rRNA sequencing revealed reduced abundance of bacteria involved in lipid metabolism regulation. However, faecal microbiota transfer from young to middle aged rats was not sufficient to robustly improve hippocampus-dependent spatial memory. Together, these findings highlight dysfunctional lipid metabolism as a key feature of middle age that may contribute to decline in hippocampal function. Given that the scope for intervention is limited during older age, targeting biomarkers involved in metabolic and lipid homeostasis may be pivotal for the development of pharmacological or lifestyle-based interventions during middle age which could ultimately delay future cognitive ageing.

Animals↗
PubMed1978

Quasi-elastic light scattering from migrating chemotactic bands of Escherichia coli.

We report the observation of migrating chemotactic bands of Escherichia coli in a buffer solution. The temporal development of the bacterial density profile is observed by the scattered light intensity as the band migrates through a stationary laser beam. We have made a preliminary analysis of the observed band profile with help of the Keller-Segel theory. The model accounts for only some aspects of the observed time evolution of the density profile. The microscopic motility characteristics of the E. coli in the band are simultaneously studied by photon correlation. The measured correlation functions are analyzed to obtain the spatial dependence of the half-width within the band. A simple analytical model is proposed to account for the contribution of the twiddle motion to the correlation function. By analyzing the correlation function as a superposition of straight-line and twiddle motions, we obtain a satisfactory agreement between the theory and the measured angular dependence of the line shape. As a consequence we are able to extract a parameter beta, which measures the average fraction of twiddling bacteria in the center of the band at a given time.

Cell Movement↗
PubMed2024

SUN2 mediates calcium-triggered nuclear actin polymerization to cluster active RNA polymerase II.

The nucleoskeleton is essential for nuclear architecture as well as genome integrity and gene expression. In addition to lamins, titin or spectrins, dynamic actin filament polymerization has emerged as a potential intranuclear structural element but its functions are less well explored. Here we found that calcium elevations trigger rapid nuclear actin assembly requiring the nuclear membrane protein SUN2 independently of its function as a component of the LINC complex. Instead, SUN2 colocalized and associated with the formin and actin nucleator INF2 in the nuclear envelope in a calcium-regulated manner. Moreover, SUN2 is required for active RNA polymerase II (RNA Pol II) clustering in response to calcium elevations. Thus, our data uncover a SUN2-formin module linking the nuclear envelope to intranuclear actin assembly to promote signal-dependent spatial reorganization of active RNA Pol II.

RNA Polymerase II↗
PubMed2025

Detection of cell-type-specific differentially methylated regions in epigenome-wide association studies.

MOTIVATION: DNA methylation at cytosine-phosphate-guanine (CpG) sites is one of the most important epigenetic markers. Therefore, epidemiologists are interested in investigating DNA methylation in large cohorts through epigenome-wide association studies (EWAS). However, the observed EWAS data are bulk data with signals aggregated from distinct cell types. Deconvolution of cell-type-specific signals from EWAS data is challenging because phenotypes can affect both cell-type proportions and cell-type-specific methylation levels. Recently, there has been active research on detecting cell-type-specific risk CpG sites for EWAS data. However, existing methods all assume that the methylation levels of different CpG sites are independent and perform association detection for each CpG site separately. Although these methods significantly improve the detection at the aggregated-level-identifying a CpG site as a risk CpG site as long as it is associated with the phenotype in any cell type, they have low power in detecting cell-type-specific associations for EWAS with typical sample sizes. RESULTS: Here, we develop a new method, Fine-scale inference for Differentially Methylated Regions (FineDMR), to borrow strengths of nearby CpG sites to improve the cell-type-specific association detection. Via a Bayesian hierarchical model built upon Gaussian process functional regression, FineDMR takes advantage of the spatial dependencies between CpG sites. FineDMR can provide cell-type-specific association detection as well as output subject-specific and cell-type-specific methylation profiles for each subject. Simulation studies and real data analysis show that FineDMR substantially improves the power in detecting cell-type-specific associations for EWAS data. AVAILABILITY AND IMPLEMENTATION: FineDMR is freely available at https://github.com/JiaRuofan/Detection-of-Cell-type-specific-DMRs-in-EWAS.

DNA Methylation↗
PubMed1991

Non invasive measurement of myocardial motion using magnetic resonance tagging.

Magnetic resonance imaging has become a key modality within the modern radiology department. In addition to the conventional slice images, three dimensional angiographic images, and quantitative flow measurements can be obtained. More recently methods have been developed which enable one to visualize the motion of objects through the application of magnetic resonance markers or tags. Generally the myocardium appears homogeneous with respect to magnetic resonance imaging. Thus at best the displacement of the myocardial surfaces can be observed, but rotational and shear motions are not discernable. With magnetic resonance tagging this all changing. Tagging involves modifying the ability of the tissue to produce a nuclear magnetic resonance signal, in a spatially dependent manner. Typically the pattern is a grid of reduced signal intensity. The tagging grid is applied prior to the heart contraction. Then images are made during systole and diastole. The rotation and shear of the myocardium can be inferred from the distortions of the tagging grid. Here our work in this field is reviewed.

Heart Diseases↗
PubMed1991

The ability of cationic amphiphilic compounds to depress the transition temperature of dipalmitoylphosphatidic acid liposomes depends on the spatial arrangement of the lipophilic moiety.

The hypothesis was tested with the help of model compounds that the ability of cationic amphiphilic drugs to depress the phase-transition temperature Tt of dipalmitoylphosphatidic acid (DPPA) liposomes depends on the spatial arrangement of the lipophilic moiety. The main structure of the compounds with identical cationic side chain was 1-dimethylamino-3-phenylpropane (compound I). A further phenyl ring was introduced either at C3 of the propane chain (compound II) to broaden the lipophilic moiety, or in para-position of the phenyl ring (compound III) to elongate it. As shown by differential scanning calorimetry, the reduction of Tt (control 64 degrees) amounted for compound I to 29 degrees, for compound II to 28 degrees and for compound III to 53 degrees. In order to assess the binding affinity of the compounds to DPPA, their inhibitory effect on 45Ca(2+)-binding to DPPA films was measured. The IC50 values were 2100 microM for compound I, 40 microM for compound II, and 9 microM for compound III. Thus, binding affinity corresponded with the hydrophobicity of the compounds. In contrast, the depressing effect on the transition temperature was only augmented by the additional phenyl ring when substituted in the elongating position.

Calcium↗
PubMedDate not supplied

The spatial and energy dependence of bremsstrahlung production about beta point sources in H2O.

A Monte Carlo simulation was performed to characterize the spatial and energy distribution of bremsstrahlung radiation from beta point sources important to radioimmunotherapy (RIT). Using the EGS4 Monte Carlo code, the isotropic emission and transport of monoenergetic 0.1-, 0.5-, 1.0-, 2.0-, and 3.0-MeV electrons and 32P and 90Y beta particles was simulated in an infinite, homogeneous H2O phantom. The probability of bremsstrahlung production for each Monte Carlo-simulated electron step was accumulated in energy intervals not exceeding 5 keV and stored as a function of radial position. To validate this scheme, the EGS4 code was tested in the continuous slowing down approximation (csda) mode, with resulting radiation yields seen to agree with values in ICRU Report No. 37 (ICRU, Bethesda, MD, 1984) to better than 1.6%. The radiation yield calculated with the simulation of secondary particles is seen to be 3%-5% greater than the csda yield. The photon energy distributions are characterized by a typically broad bremsstrahlung spectrum with the probability of photon generation decreasing with radial distance. In the energy range 0.05-0.511 MeV, the probability for bremsstrahlung production from 90Y (2.76 x 10(-2) decay-1) is twice that from 32P (1.35 x 10(-2) decay-1). When passed through 10 cm of H2O and put upon a standard NaI scintillation camera, count rates of 2.3 x 10(-6) and 1.2 x 10(-6) counts s-1 Bq-1 are estimated from point sources of 90Y and 32P. These results predict the inherent spatial resolution limitation and provide the initial data required for modeling and analyzing the scatter, attenuation, and image formation processes in quantitative imaging of bremsstrahlung for RIT dosimetry.

Humans↗
PubMed1978

Mapping the ATP-binding site in the catalytic subunit of adenosine-3':5'-monophosphate-dependent protein kinase. Spatial relationship with the ATP site of the undissociated enzyme.

A set of 24 ATP analogs modified at various positions of the ATP molecule was used for mapping the ATP-binding site in the free catalytic subunit (C) of cAMP-dependent protein kinase (type I). Ki values for these analogs (of which 23 were shown to be competitive with ATP) were measured and compared with Ki values previously obtained for the same set of analogs upon binding to the undissociated form of the enzyme (R2C2). It was found that modifications at the adenine part of ATP bring about a considerable reduction in affinity between C and the resulting analog. The other parts of the ATP molecule play a less important, though definite, role in the binding of this nucleotide to C. By measuring the effect of each given modification in ATP on its binding to C, and comparing the effect of this modification on the binding of the same analog to R2C2, it was possible to obtain 'specificity profiles' for both forms of the kinase. Using such profiles it is shown that the adenine-binding subsite in C may well coincide with the adenine-binding subsite in R2C2. Two plausible models describing the spatial relationship between the ATP sites in C and R2C2 are proposed.

Adenosine Triphosphate↗
PubMedDate not supplied

[The dependence of spatial-motor asymmetry on the nature of the reinforcement].

Spatial-motor asymmetry (SMA) of rats goal-directed running was studied in condition of numerous alternative choices in complex T-maze. In condition of free choices SMA in trained rats depended on reinforcement biological significance, volume and disposition scheme. In condition of non-free choices a change was possible of asymmetry of sequence of goal-directed motor acts adequate to situation, i.e. SMA regulation. Examples of the presence of properties of ego- and allocentric systems in SMA are given. The results of experiments testify to SMA dependence on the motivation of running, to rightfulness of SMA interpretation as behavioural tactics and to non-coming of SMA of goal-directed running to a simple rotation of animals.

Animals↗
PubMed1992

Visual hemispheric asymmetries depend on which spatial frequencies are task relevant.

Observers classified sine-wave and square-wave gratings on the basis of fundamental frequency (Are the bars wide or narrow?) or on the basis of higher harmonic frequencies (Are the bars sharp or fuzzy?). Stimuli were presented in either the left (LVF) or right (RVF) visual field. When the classification was made on the basis of the fundamental frequencies (1 or 3 c/deg), there was a LVF/right hemisphere advantage. However, when the classification was on the basis of a sharp/fuzzy distinction which involved searching for the higher harmonic frequencies, then a RVF/left hemisphere advantage was found.

Adult↗
PubMed1992

Responses of cat horizontal cells to sinusoidal gratings.

The spatiotemporal properties of cat horizontal (H-) cells were studied by recording the intracellular responses in the optically intact, in vivo, eye to sinusoidal gratings at a photopic mean illumination level. In order to investigate the linearity of spatial summation a "null test" was performed in which the responses to contrast reversal gratings were measured at different positions of the grating relative to the receptive field. Spatial and temporal transfer functions were measured using drifting sinusoidal gratings of variable spatial and temporal frequencies. The amplitudes of cat H-cell responses to contrast reversal gratings modulated with a square wave time-course showed a sinusoidal dependence on spatial phase. When zero crossings of the grating were lined up with the receptive field center, as defined by the maximum of the measured line weighting function, contrast reversal produced no response modulation. This result did not depend on the spatial frequency of the grating or the temporal frequency of contrast modulation over substantial ranges. The response waveform was found not to depend on the spatial phase of the grating. The spatial transfer function of cat H-cells has low-pass characteristics with a cut-off frequency in the range of about 0.4-1.5 c/deg. The shape of the spatial transfer function was roughly the same for temporal frequencies ranging from 3 to 10 Hz. The temporal transfer function exhibited band-pass characteristics with a maximum response amplitude at 3-6 Hz. The amplitude fall-off for low and high temporal frequencies was independent of the spatial frequency of the grating. The results obtained with sine gratings were found not to agree with the receptive field profiles measured with narrow slits flashed at different positions in the receptive field.

Animals↗
PubMed1979

Receptive field mechanisms of cat X and Y retinal ganglion cells.

We investigated receptive field properties of cat retinal ganglion cells with visual stimuli which were sinusoidal spatial gratings amplitude modulated in time by a sum of sinusoids. Neural responses were analyzed into the Fourier components at the input frequencies and the components at sum and difference frequencies. The first-order frequency response of X cells had a marked spatial phase and spatial frequency dependence which could be explained in terms of linear interactions between center and surround mechanisms in the receptive field. The second-order frequency response of X cells was much smaller than the first-order frequency response at all spatial frequencies. The spatial phase and spatial frequency dependence of the first-order frequency response in Y cells in some ways resembled that of X cells. However, the Y first-order response declined to zero at a much lower spatial frequency than in X cells. Furthermore, the second-order frequency response was larger in Y cells; the second-order frequency components became the dominant part of the response for patterns of high spatial frequency. This implies that the receptive field center and surround mechanisms are physiologically quite different in Y cells from those in X cells, and that the Y cells also receive excitatory drive from an additional nonlinear receptive field mechanism.

Action Potentials↗
PubMed1992

Phosphorylation-dependent changes in the spatial relationship between Ca-ATPase polypeptide chains in sarcoplasmic reticulum membranes.

In order to investigate possible structural changes associated with the coupling mechanisms of the Ca-ATPase in sarcoplasmic reticulum membranes, we have utilized fluorescence resonance energy transfer between spectroscopic probes covalently bound to different domains of the ATPase. Using time-correlated single photon counting, we have directly measured the energy transfer efficiency between 5-[2-[(iodoacetyl)amino]ethyl]aminonaphthalene-1-sulfonic acid (IAEDANS), that is specifically bound to the B trypic fragment at cysteines 670 and 674 and acceptors covalently bound either near the nucleotide binding site, i.e. fluorescein 5-isothiocyanate at lysine 515, also on the B fragment, or maleimide-directed probes specifically located on the A1, tryptic fragment, i.e. 4-dimethylaminoazobenzene-4'-maleimide (DABmal) or fluorescein-5-maleimide (Fmal), probably at cysteines 344 and 364. All of these donor-acceptor pairs exhibit energy transfer both within and between Ca-ATPase molecules allowing us to investigate spatial relationships between the A1 and B domains and between different ATPase polypeptide chains. Differentiation between the intra- and intermolecular components of energy transfer was accomplished in two ways: 1) by comparing the transfer efficiencies in native membranes before and after detergent solubilization and 2) by reconstituting ATPase chains that have already been labeled with either the donor or acceptor chromophores. Using this approach, we find no significant change in the intramolecular transfer efficiency between any of these donor-acceptor pairs either upon binding of calcium to the high affinity sites or upon stabilization of the phosphoenzyme intermediate, indicating that there are no large structural changes within the B tryptic fragment or, alternatively, between the A1 and B fragments. With respect to intermolecular energy transfer, we observe no effect of calcium binding on the unliganded enzyme with either donor-acceptor pair. However, formation of the phosphoenzyme intermediate results in a measurable increase in the transfer efficiency between IAEDANS and DABmal (or Fmal); this increase is reversible upon phosphoenzyme destabilization by subsequent addition of calcium. There is no corresponding change in the intermolecular component of fluorescence resonance energy transfer between IAEDANS and fluorescein 5-isothiocyanate, indicating that the change in fluorescence resonance energy transfer probably occurs as a result of reorientation of associated ATPase polypeptide chains with respect to one another.

Animals↗