Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “spatial dependency”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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

At least 145 records · Page 8Linked to original sources
PubMed1994

Nonlinear diffusion of a growth inhibitory factor in multicell spheroids.

A mathematical model is presented for the production of a growth inhibitory factor (GIF) within a multicell spheroid. The model is based on the assumption that the GIF diffuses within the spheroid in a nonlinear spatially dependent manner. This is in contrast with previous models, in which the nonlinearity was assumed in the production term. The results of the new model are compared with those of previous models and with experimental data.

Animals↗
PubMed1984

The time-course of rod-cone interaction.

The time-course of rod-cone interaction (change of scotopic sensitivity caused by photopic background stimulation) was measured in the presence of briskly exchanged, scotopically matched, 490- and 630-nm background disks. In all conditions, interaction rose and fell quickly with changes of photopic stimulation. When the background was a small 0.6 degree-diameter disk, photopic stimulation produced relatively constant maintained interaction of about 0.6 log units. When the background was a large 7.8 degree-dia disk, photopic stimulation produced larger initial (0.6-1.0 log unit) than maintained (0.2 log unit) interaction. When a 0.6 degree by 7.8 degree annulus was used instead of a background, photopic stimulation produced substantial interaction only at offset, a transitory interaction. Thus, the spatial dependence of transitory interactions differs from that of maintained interaction: transitory interactions can be large even when maintained interaction is small or absent. The results are discussed in terms of a simple center-surround model of rod-cone interaction that unifies both maintained and transient interaction.

Dark Adaptation↗
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↗
PubMedDate not supplied

Possible applications of digital analysis of ultrasonic images of the placenta.

Analysis of the digitised ultrasonic images of in vivo placentae at 15-18 weeks gestation has revealed various textural differences. These have been correlated with smoking, visual appearance and the subsequent development of hypertension. The total number of patients included in this study was 98, of which 70 had images suitable for analysis. There were no significant textural differences between the images of the placentae of smokers and non-smokers nor did the spatially dependent co-occurrence matrices correlate with visual appearance. Textural differences were however detected when the placentae of the normotensive group were compared to those of patients who subsequently developed hypertension (latent hypertension) in the third trimester of pregnancy (p less than 0.05 Mann Whitney 'U' test).

Female↗
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↗
PubMed1980

Surface-induced lamellar orientation of multilayer membrane arrays. Theoretical analysis and a new method with application to purple membrane fragments.

The orientation of membrane fragments into a lamellar array by a flat surface is analyzed. This analysis includes processes such as centrifugation and drying and physical effects due to membrane fragment steric interactions, finite size, elasticity, and thermal fluctuations. Several model calculations of optimal orientational order in multilayer membrane arrays are presented. The predictions of a smectic A model agree quantitatively with the measured spatial dependence of the fluctuations in layer orientation in a multilamellar arrays. A new technique, based in part on this analysis, for the preparation of well-oriented multilamellar arrays of natural and artificial membranes, isopotential spin-dry centrifugation, is described. The method involves the use of specially designed inserts for the buckets of a standard vacuum ultracentrifuge. The membrane fragments to be oriented are sedimented from solution or suspension onto a substrate of a convenient material which forms a gravitational isopotential surface at high g. Sedimentation is accompanied by removal of the suspending medium at high g to produce oriented films with a selected degree of solvation. In addition, a method is described whereby small solute molecules can be maintained in constant concentration with the membrane fragments during this process. Initial application of the method to the orientation of purple membrane fragments is described. The degree of orientation obtained in this system is evaluated using freeze-fracture and scanning electron microscopy, optical birefringence, linear dichroism, and microscopy.

Bacteriorhodopsins↗
PubMed1989

Current injection into a two-dimensional anisotropic bidomain.

A two-dimensional sheet of anisotropic cardiac tissue is represented with the bidomain model, and the finite element method is used to solve the bidomain equations. When the anisotropy ratios of the intracellular and extracellular spaces are not equal, the injection of current into the tissue induces a transmembrane potential that has a complicated spatial dependence, including adjacent regions of depolarized and hyperpolarized tissue. This behavior may have important implications for the electrical stimulation of cardiac tissue and for defibrillation.

Animals↗
PubMed1997

Stochastic versions of the Hodgkin-Huxley equations.

A Hodgkin-Huxley model algorithm for the numerical simulation of noise in neurons is contracted from a master equation description (cellular automoton) into a Langevin description. This reduction reduces the time required for a simulation by about two orders of magnitude. Earlier work is summarized, condensed, and made explicit to make the algorithm transparent and facilitate applications. Two approximate treatments are reported. An extension of this approach is presented that includes spatial dependence and the propagation of a noisy action potential along an axon.

Axons↗
PubMed1996

A technique for single-channel MR brain tissue segmentation: application to a pediatric sample.

A segmentation method is presented for gray matter, white matter, and cerebrospinal fluid (CSF) in thin-sliced single-channel brain magnetic resonance (MR) scans. The method is based on probabilistic modeling of intensity distributions and on a region growing technique. Interrater and intrarater reliabilities for the method were high, and comparison with phantom studies and hand-traced results from an experienced rater indicated good validity. The method was designed to account for spatially dependent image intensity inhomogeneities. Segmentation of MR brain scans of 105 (56 male and 49 female) healthy children and adolescents showed that although the total brain volume was stable over age 4-18, white matter increased and gray matter decreased significantly. There were no sex differences in total gray and white matter growth after correction for total brain volume. White matter volume increased the most in superior and posterior regions and laterality effects were seen in hemisphere tissue volumes. These findings are consistent with other reports, and further validate the segmentation technique.

Adolescent↗
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↗
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↗
PubMed1993

CURVATURE: software for the analysis of curved DNA.

Software is presented to plot the sequence-dependent spatial trajectory of the DNA double helix and/or distribution of curvature along the DNA molecule. The nearest-neighbor wedge model is implemented to calculate overall DNA path using local helix parameters: helix twist angle, wedge (deflection) angle and direction (of deflection) angle. The procedures described proved to be very convenient as tools for investigation of a relationship between overall DNA curvature and its gel electrophoretic mobility. All parameters of the model had been estimated from experimental data. Using these wedge parameters the program takes, as input, any DNA sequence and calculates the likely degree of curvature at each point along the molecule. This information is displayed both graphically and in the form of simplified representations of curved double helices. The Software, CURVATURE, can thus be used to investigate possible roles of curvature in modulation of gene expression and for location of curved portions of DNA, which may play an important role in sequence-specific protein--DNA interactions.

Algorithms↗
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↗
PubMed1993

Defense mechanisms in alcoholics attending outpatient treatment. Results from the MCT-test (Meta-Contrast Technique).

Defensive strategies were studied in 72 alcoholics participating in outpatient treatment by using, before the treatment started, the Meta-Contrast Technique, MCT, a percept-genetic method. Alcoholics had less often adaptive strategies than controls. A lack of adaptive defense strategies was related to a more impaired psychic status, more psychological benefits from drinking, and more psychiatric symptoms but not to severity of alcoholism or results of psychometric tests (intellectual level, field-dependence, spatial performance). It does not seem inconceivable that the MCT could be used as a diagnostic tool in treatment planning.

Adaptation, Psychological↗
PubMed1997

Electrophysiology of the right anterior approach to the atrioventricular node: studies in vivo and in the isolated perfused dog heart.

INTRODUCTION: Previous reports have described electrophysiologic properties and rate-dependent responses in the transitional cell zone of the posterior AV nodal input (slow pathway). The purpose of this study was to investigate the electrophysiology of the anterior transitional cell zone (fast pathway) in vivo and in a Langendorff preparation perfused with a nonblood solution containing butanedionemonoxime to inhibit contraction. METHODS AND RESULTS: In five anesthetized dogs, the His-bundle electrogram recorded from the aortic root included atrial activity in close proximity to the anterior limbus of the fossa ovalis. During decremental atrial pacing, the atrial potential exhibited amplitude alternans at a pacing cycle length (CL) of 135 +/- 14 msec. In ten isolated perfused canine hearts, a bipolar electrode catheter was positioned with its tip against the right anterior interatrial septum just superior to the tendon of Todaro. The AV Wenckebach CL (WCL) averaged 262 +/- 21 msec. During further decreases in pacing CL, the bipolar atrial potential developed a 2:1 amplitude alternans (9/10 dogs) at CL = 168 +/- 15 msec and then split into two components with subsequent 2:1 block between these components (10/10 dogs) at CL = 152 +/- 19 msec. Radiofrequency ablation at this site in six dogs prolonged the stimulus to HB interval from 113 +/- 19 to 151 +/- 30 msec (P < 0.01) without changing the WCL, consistent with ablation of the fast AV nodal pathway. In six other isolated perfused canine hearts, an octapolar catheter (2-mm spacing) was positioned along the anterior limbus of the fossa ovalis with the tip electrode located over the anterior portion (apex) of the triangle of Koch. The aforementioned 2:1 amplitude alternans occurred at a longer CL in the distal electrodes located at the tendon of Todaro than in the proximal electrodes at farther distances from the tendon of Todaro (185 +/- 25 vs 171 +/- 20 msec, P < 0.05), as did the 2:1 block between the two components (161 +/- 18 vs 150 +/- 18 msec, P < 0.05). Microelectrode recordings obtained adjacent to the catheter demonstrated 2:1 alternans and block patterns in the action potentials of transitional cells but not in atrial cells, which exhibited 1:1 conduction at all CL. CONCLUSIONS: The transitional cell zone in the anterior interatrial septum exhibits a specific rate-dependent, spatial gradient of conduction block, which can be recorded in bipolar electrograms as well as microelectrode recordings. Electrophysiologic changes induced by radiofrequency ablation of this anterior atrial/transitional cell zone (corroborated by histology) provide strong presumptive evidence that this area constitutes all or a major part of the fast AV nodal pathway.

Animals↗
PubMed1982

A study of the motion of organelles which undergo retrograde and anterograde rapid axonal transport in Xenopus.

1. Axonally transported organelles were detected optically in myelinated axons from Xenopus laevis at room temperature (21-23 degrees C). Details of the motion of organelles which were transported in the retrograde and anterograde directions were studied using filmed records.2. A group of 133 organelles with a mean retrograde velocity of 0.91 mum/sec was compared with a group of thirty-nine organelles with a mean anterograde velocity of 0.93 mum/sec.3. Averaged power spectra of the positional deviations about the mean positional change through time were constructed for organelles which travelled in the retrograde and anterograde directions. Most of the power in the two spectra was at frequencies below 0.2 Hz and each contained a single peak at 0.02-0.04 Hz. The power spectrum for retrograde organelle motion had a magnitude about twice that for anterograde organelle motion.4. Estimates of the instantaneous velocity of organelles which travelled in either direction varied smoothly with time. Instantaneous velocity was not a smooth function of organelle position, (i.e. was ;saltatory').5. Histograms of the estimates for the groups of organelles whose major motion was retrograde or anterograde were broad, covering a range of about 3 mum/sec, were unimodal, and passed through zero to include a small group of values which indicated motion in the opposite (minor) direction.6. Organelles spent, on average, more time moving in the minor direction the lower their mean velocity.7. The variation in instantaneous velocity was greater for organelles which travelled in the retrograde direction than for those which travelled in the anterograde direction. No correlation was found between the variation of instantaneous velocity and the mean velocity of the organelles.8. Images of organelles occasionally appeared to rotate while the organelle continued to move in the major direction of travel.9. Evidence is presented that spatially related properties of the axon influence organelle velocity and that this influence is common to organelles which travel in the two major directions.10. A hypothesis is presented to account for the findings. This supposes that each organelle travels through a stationary axoplasm and is propelled by the resultant of two opposing driving forces whose relative magnitude fluctuates with time. Spatially dependent properties of the axoplasm modify the postulated time-related cycle of motion.

Animals↗
PubMed1993

Active motion of polymorphonuclear leukocytes in response to chemoattractant in a micropipette.

A novel experimental method of producing and observing the active motion of polymorphonuclear leukocytes (PMNs) using a micropipette technique has been recently developed (Usami et al., 1992). The present paper develops a quantitative theory for the chemoattractant gradients and cell locomotion observed in these experiments. In previous experimental methods (e.g., the Boyden chamber, the Zygmond chamber and the Dunn chamber) for study chemotaxis of leukocytes, fibroblasts, and PMNs, the exact nature of the concentration gradient of the chemoattractant is unknown. The cells may themselves modify the local gradient of the chemoattractant. In experiments using the micropipette, an internal source of chemoattractant provides well-defined boundary and initial conditions which allow the computation of the chemoattractant concentration gradient during the active locomotion of the PMNs. Since the cell completely fills the pipette lumen, convection is limited to the motion of the cells themselves. In coordinates moving with cell, it is assumed that diffusion is the only mechanism of mass transport of the chemoattractant (fMLP). Computations of the fMLP concentration during locomotion of the cell were carried out for a range of rates of fMLP binding by the receptors expressed on the front face of the cell membrane. The results show that the front face of the cell is subjected to increasing fMLP concentration during the cell motion. The sequence of events involve receptor binding of fMLP, signal transduction, polymerization of the cell cytoskeleton at the membrane of the front face, spatially dependent adhesion to the pipette wall, and localized contraction of the cytoskeleton. This sequence of events leads to the steady locomotion of the leukocytes in the micropipette. The computation of the distribution of the fMLP concentration during cell locomotion with constant velocity in micropipette experiments shows that the cell is exposed to increasing concentration of fMLP. This suggests that chemotaxis maybe induced by temporal gradient of an attractant.

Cell Movement↗