Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “directional diffusion models”

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 397 records · Page 22Linked to original sources

Multi-component apparent diffusion coefficients in human brain.

The signal decay with increasing b-factor at fixed echo time from brain tissue in vivo has been measured using a line scan Stejskal-Tanner spin echo diffusion approach in eight healthy adult volunteers. The use of a 175 ms echo time and maximum gradient strengths of 10 mT/m allowed 64 b-factors to be sampled, ranging from 5 to 6000 s/ mm2, a maximum some three times larger than that typically used for diffusion imaging. The signal decay with b-factor over this extended range showed a decidedly non-exponential behavior well-suited to biexponential modeling. Statistical analyses of the fitted biexponential parameters from over 125 brain voxels (15 x 15 x 1 mm3 volume) per volunteer yielded a mean volume fraction of 0.74 which decayed with a typical apparent diffusion coefficient around 1.4 microm2/ms. The remaining fraction had an apparent diffusion coefficient of approximately 0.25 microm2/ms. Simple models which might explain the non-exponential behavior, such as intra- and extracellular water compartmentation with slow exchange, appear inadequate for a complete description. For typical diffusion imaging with b-factors below 2000 s/mm2, the standard model of monoexponential signal decay with b-factor, apparent diffusion coefficient values around 0.7 microm2/ms, and a sensitivity to diffusion gradient direction may appear appropriate. Over a more extended but readily accessible b-factor range, however, the complexity of brain signal decay with b-factor increases, offering a greater parametrization of the water diffusion process for tissue characterization.

Adult↗

Standardless EDS analysis of bulk and thin specimens.

A direct relationship between the x-ray intensity ratio and the concentration ratio for bulk and thin specimens has been established by use of a revised full-diffusion model of electron scattering. The suitable ionization cross section, the most important parameter influencing the accuracy of the calculated Cliff-Lorimer factors, has been found after comparing the experimental intensity ratio I(L)/I(K) of eight elements (from Ge to Sn) and I(M)/I(L) of six elements (from Sm to Bi) with the calculated values. The quantitative standardless EDS analysis of bulk samples obtained by this direct method is more satisfactory than the commercial indirect method which gives the composition through ZAF correction after calculating the intensity factors of pure elements. The quantitative standardless analysis of thin samples has been improved by the suitable cross section significantly. This method has been applied to the analysis of film on substrate either without any common element or with one common element (P-Si glass film on Si). It has also been used to calculate the intensity factors of pure bulk samples and the backscattering correction factor in Auger electron spectroscopy.

Electron Probe Microanalysis↗

In situ mutagenesis and chemotactic selection of microorganisms in a diffusion gradient chamber.

A new method has been developed to rapidly generate and select microbial strains having increased resistance to an inhibitory compound. The method combines in situ mutagenesis with use of a continuous gradient of the inhibitor to sort cells according to their resistance levels. Microbial chemotaxis is induced to accelerate the selection process. The method was used to develop a strain of E. coli having a feedback-resistant DAHP synthase enzyme. An unsteady-state mathematical model of the process has been developed. The model, that can reproduce key trends observed experimentally, was used to explore the effects of chemotaxis on the efficiency of the selection process.

3-Deoxy-7-Phosphoheptulonate Synthase↗

Evidence against tight channelling of NADH in hepatocytes.

Tritiated substrates at tracer levels were incubated with rat hepatocytes plus 10 mM L-lactate, and the yields of tritium in glucose and water, as well as the tritium distribution on C-6 and C-4 of glucose, determined. Substrates of cytosolic type A NAD-linked dehydrogenases showed some preferential labeling of C-6 of glucose (the pathway involving type A malate dehydrogenase), whereas substrates of cytosolic type B NAD-linked dehydrogenases showed some preferential labeling of C-4 of glucose (the pathway involving type B glyceraldehyde-3P dehydrogenase). The results found are consistent with a classical diffusion model of NADH metabolism, and are at odds with the Srivastava hypothesis (based on isolated enzyme studies) which indicated that direct transfer of NADH can occur between many NAD-linked enzymes but only when they are of opposite (A or B) specificity.

Animals↗

Pancreas oxygenation is limited during preservation with the two-layer method.

BACKGROUND: The two-layer method (TLM) for pancreas preservation reportedly improves islet yield and transplantation outcome relative to previous methods. Increased ATP concentrations support the hypothesis that these improvements are related to better oxygenation from the perfluorocarbon solution. However, there are limited direct measurements of oxygen partial pressure, (pO(2)) in pancreata preserved with the TLM. Theory predicts that only a small fraction of a human pancreas can be oxygenated externally. In this report we examine pancreas oxygenation with the TLM using theory and direct pO(2) measurements. METHODS: pO(2) profiles in cylindrical pancreata were calculated at various temperatures with a diffusion-reaction model. The pO(2) was measured using fiber optic sensors in the core of porcine pancreatic tissue preserved with the TLM in media saturated with 100% oxygen. RESULTS: The model predicts that at 8 degrees C, even in the absence of an external pO(2) gradient, oxygen penetration depth is about 1 mm and insensitive to pancreas diameter, while the oxygenated volume fraction is about 15% for a 2.5-cm-diameter pancreas. Experimental measurements verified that pO(2) is virtually zero in the core of a 1-cm-thick pancreatic piece preserved with the TLM. Penetration of solution around the sensor may be responsible for the observed lag and for the previously reported nonzero pO(2) measurements. Reoxygenation of heat-treated tissue took several hours. CONCLUSIONS: The TLM can oxygenate only a small volume fraction of a human pancreas. Pancreas oxygenation through the native vasculature should be explored to further improve yield of viable islets.

Humans↗

Determination of cell membrane permeability in concentrated cell ensembles.

The method of volume averaging is used to analyze the process of diffusion in concentrated cell ensembles in which significant resistance to mass transfer is caused by the cellular membrane. A general closure scheme is given that allows for direct theoretical prediction of effective diffusivities for any cellular geometry. Numerical results are presented for the classical parallelepiped arrangement used to model cellular systems, and these results are used in conjunction with experimental studies of concentrated cell ensembles to determine membrane permeabilities for solute diffusion in several cellular systems. Membrane permeabilities are compared with predictions from other models of diffusion in cellular systems.

Animals↗

Diffusion dynamics of the li atom on amorphous carbon: A direct molecular orbital-molecular dynamics study.

Direct molecular orbital-molecular dynamics (MO-MD) calculation was applied to diffusion processes of the Li atom on a model surface of amorphous carbon and compared with the diffusion mechanism of Li+ ion. A carbon sheet composed of C96H24 was used as the model surface. The total energy and energy gradient on the full dimensional potential energy surface of the LiC96H24 system were calculated at each time step in the trajectory calculation. The optimized structure, where the Li atom is located at the center of mass of the model surface, was used as the initial structure at time zero. Simulation temperatures were chosen in the range of 200-1250 K. The dynamics calculations showed that the Li atom vibrates around the initial position below 250 K, and it moves above 300 K. At middle temperature, the Li atom translates freely on the surface. At higher temperature (1000 K), the Li atom moves from the center to edge region of the model surface and is trapped in the edge. The activation energy calculated for the Li atom is larger than that for the Li+ ion. This difference is due to the fact that the Li atom diffuses together with an unpaired electron on the carbon surface. The diffusion mechanism of the Li atom was discussed on the basis of the theoretical results.

Journal Article↗

Metal-induced assembly of a semiconductor island lattice: Ge truncated pyramids on Au-patterned Si.

We report the two-dimensional alignment of semiconductor islands using rudimentary metal patterning to control nucleation and growth. In the Ge on Si system, a square array of submicron Au dots on the Si (001) surface induces the assembly of deposited Ge adatoms into an extensive island lattice. Remarkably, these highly ordered Ge islands form between the patterned Au dots and are characterized by a unique truncated pyramidal shape. A model based on patterned diffusion barriers explains the observed ordering and establishes general criteria for the broader applicability of such a directed assembly process to quantum dot ordering.

Journal Article↗

Propagation failures, breathing pulses, and backfiring in an excitable reaction-diffusion system.

We report results from experiments with a pseudo-one-dimensional Belousov-Zhabotinsky reaction that employs 1,4-cyclohexanedione as its organic substrate. This excitable system shows traveling oxidation pulses and pulse trains that can undergo complex sequences of propagation failures. Moreover, we present examples for (i) breathing pulses that undergo periodic changes in speed and size and (ii) backfiring pulses that near their back repeatedly generate new pulses propagating in opposite direction.

Animals↗

Incorporation of a disaccharide nucleoside into the backbone of double-stranded DNA: crystallization and preliminary X-ray diffraction.

Incorporation of a disaccharide nucleoside into double-stranded DNA can be considered as a chemical (non-enzymatic) alternative for site-specific cleavage of DNA. Crystals of the sequence d(CGCGAATT*CGCG), where * is an incorporated ribose, were obtained by hanging-drop vapour diffusion and diffracted to 2.6 A. The crystals belong to the orthorhombic space group P222(1), with unit-cell parameters a = 41.52, b = 57.63, c = 81.39 A, indicating a new crystal packing motif for an oligonucleotide dodecamer sequence.

Crystallization↗

A technology transfer model for effective HIV/AIDS interventions: science and practice.

The widespread use of effective, science-based interventions to motivate and sustain behavior change provides an important approach to reducing the spread of HIV. The process of disseminating information about effective interventions and building capacity for implementing them in field settings must be improved, however. Starting with a review of diffusion of innovations and technology transfer literature, we offer a technology transfer model for HIV interventions. We identify participants and activities directed toward the use of effective interventions by prevention services providers (e.g., health departments and community-based organizations) in each phase of technology transfer: preimplementation, implementation, and maintenance and evolution. Preimplementation activities focus on selecting an intervention and preparing for implementation. Implementation activities include initial implementation and process evaluation. Maintenance and evolution are ongoing with continued support for and evaluation of the intervention. This article takes the perspective of providers. Other perspectives are presented elsewhere in this issue.

HIV Infections↗

Ag-PIE: a GIS-based screening model for assessing agricultural pressures and impacts on water quality on a European scale.

Diffuse pollution of water resources from agricultural sources is a major environmental issue in the European Union, and has been dealt with by specific legislation: the Nitrate Directive of 1991 and the Water Framework Directive of 2000. These attempts to provide a coordinated approach to solving environmental problems require methods and tools for spatial analysis and modelling on a continental scale, with river basins being used as spatial units. This paper presents a screening model (Ag-PIE), developed in a GIS environment, for the assessment of pressures from agricultural land use and the consequent impacts on surface and groundwater. Ag-PIE has been applied at the European scale (EU15), with focus on nitrogen pollution from chemical fertilisers and manure. The model adopts a multi-criteria evaluation procedure applied to spatial data layers which represent the variety of factors affecting the pollution process. The DPSIR (Driving forces, Pressures, State, Impact, Responses) approach is applied to provide the modelling approach with a conceptual framework and to further analyse and communicate results. Ag-PIE is ultimately aimed at providing a tool making use of state-of-the-art geographical databases to support policy-makers at the European level. The scale of reference adopted is the river basin, in particular those that extend across national boundaries. The quality of the results obtained has been assessed against existing related studies and monitoring reports and by means of sensitivity analysis. Conclusions are driven by considering the potential of Ag-PIE in devising policy support and its strengths and weaknesses in view of identifying future research needs.

Agriculture↗

Quantifying the Gurken morphogen gradient in Drosophila oogenesis.

Quantitative information about the distribution of morphogens is crucial for understanding their effects on cell-fate determination, yet it is difficult to obtain through direct measurements. We have developed a parameter estimation approach for quantifying the spatial distribution of Gurken, a TGFalpha-like EGFR ligand that acts as a morphogen in Drosophila oogenesis. Modeling of Gurken/EGFR system shows that the shape of the Gurken gradient is controlled by a single dimensionless parameter, the Thiele modulus, which reflects the relative importance of ligand diffusion and degradation. By combining the model with genetic alterations of EGFR levels, we have estimated the value of the Thiele modulus in the wild-type egg chamber. This provides a direct characterization of the shape of the Gurken gradient and demonstrates how parameter estimation techniques can be used to quantify morphogen gradients in development.

Animals↗

On the time-dependent diffusion of macromolecules through transient open junctions and their subendothelial spread. I. Short-time model for cleft exit region.

In this two-part study we shall quantitatively study, using time-dependent models, the hypothesis that transient open junctions associated with widely scattered endothelial cells undergoing mitosis are the structural equivalent for the large pore pathway via which macromolecules the size of albumin or larger cross the vascular endothelium. In an earlier steady-state model [Am. J. Physiol. 248, H945-960 (1985)], the authors demonstrated that such an open-junction pathway could quantitatively account for the regional differences in macromolecular permeability observed in various mammalian arteries in regions of enhanced cell turnover as indicated by 3H-thymidine although these cells were less than 1% of the population and the open junctions occupied less than 10(-5) of the endothelial surface. The time-dependent models described herein have been used to identify a time window and size of probe molecule wherein this hypothesis could be tested experimentally in the larger blood vessels. The first stages of these experiments have now been completed and provide convincing evidence that the junctions of virtually all endothelial cells in the M phase of the cell cycle are leaky to macromolecules (Lin et al., 1988). The statistical frequency of such leakage sites has also been determined. The time-dependent models developed herein contain two important refinements that were not contained in the earlier steady state model. First the finite resistance of the open cleft as a function of molecular size is accounted for by introducing a diffusion coefficient ratio Dj/Dz describing the relative resistance of the open cleft compared to the subendothelial tissue in the direction normal to the endothelial surface. Second the non-isotropy of the vessel wall due to the elastic lamina is considered by introducing a second diffusion coefficient ratio Dx/Dz describing the relative resistance in the lateral as compared to the normal direction. This second ratio can be as large as 100 for the arterial intima, but is of order unity for capillaries. In Part I a short time model is presented to describe the initial labeling of the open cleft and the subendothelial space in the vicinity of the cleft exit following the introduction of a tracer macromolecule. This model is valid for both larger vessels and capillaries since wall thickness and curvature and the interaction between leakage sites does not enter into the model description. In Part II (Wen et al., 1988) a long-time model is developed for larger vessels only which is valid for greater times including steady-state labeling.

Albumins↗

Diffusion with evolving sources and competing sinks: development of angiogenesis.

Tumors ensure their long-time growth by emitting molecular messengers that induce cellular modifications in neighboring capillaries. These modifications are conducive to the enlargement of the vascular system feeding the tumor. This phenomenon, termed angiogenesis, is controlled by the diffusion and competitive trapping of nutrients and molecular messengers by several cell species. The number, location, and properties of these traps change continuously. The angiogenic process also implies that nutrient sources are time dependent. Starting from assumptions at the cellular level, we formulate a mathematical model that predicts the evolution of angiogenesis and the increase in the blood flow to the tumor. The model also predicts the emergence of directed growth and the possibility of therapeutical synergy. Simulations permit a careful analysis of the influence of the main parameters.

Absorption↗

Divisability of diltiazem matrix sustained-release tablets.

The objective of this work was to study the possibility of a solid sustained-release dosage form, like a tablet, be divided without changing its release characteristics. Diltiazem hydrochloride Sustained-Release (SR) tablets with a standard groove on one face, were tested and the following dissolution parameters were evaluated: t10%, t25%, and t50% dissolution time, and dissolution efficiency at t120, and at t360. To analyze the release mechanism, several release models were tested such as Higuchi, zero order, first order, Baker-Lonsdale, Hixson-Crowell, Weibull, and Korsmeyer-Peppas. The similarities between two in vitro dissolution profiles were assessed by the difference factor (f1), the similarity factor (f2) and the Rescigno index (xi(i)). The in vitro release kinetics of diltiazem hydrochloride tablets were evaluated using USP apparatus 4. Using a one-way ANOVA (a = 0.05), statistically significant differences were found for t10%, t25%, and t50% dissolution times with a constant and with a variable pH dissolution fluid. The variation coefficient for the divisibility assay (Portuguese Pharmacopoeia VI) was lower than the limit value of 10%. The diltiazem release rate from this pharmaceutical system was not constant, and diminished with the square root of time (Higuchi model) showing that the phenomenon controlling drug release was the diffusion occurring inside the swelled polymeric matrix. Diltiazem release rate was a function of the area in direct contact with the dissolution fluid and not of the pharmaceutical matrix volume. The results obtained permit us to conclude that the division, in this case, affects the drug release characteristics.

Analysis of Variance↗

The random collision model and a critical assessment of diffusion and collision in mitochondrial electron transport.

This review focuses on our studies over the past ten years which reveal that the mitochondrial inner membrane is a fluid-state rather than a solid-state membrane and that all membrane proteins and redox components which catalyze electron transport and ATP synthesis are in constant and independent diffusional motion. The studies reviewed represent the experimental basis for the random collision model of electron transport. We present five fundamental postulates upon which the random collision model of mitochondrial electron transport is founded: All redox components are independent lateral diffusants; Cytochrome c diffuses primarily in three dimensions; Electron transport is a diffusion-coupled kinetic process; Electron transport is a multicollisional, obstructed, long-range diffusional process; The rates of diffusion of the redox components have a direct influence on the overall kinetic process of electron transport and can be rate limiting, as in diffusion control. The experimental rationales and the results obtained in testing each of the five postulates of the random collision model are presented. In addition, we offer the basic concepts, criteria and experimental strategies that we believe are essential in considering the significance of the relationship between diffusion and electron transport. Finally, we critically explore and assess other contemporary studies on the diffusion of inner membrane components related to electron transport including studies on: rotational diffusion, immobile fractions, complex formation, dynamic aggregates, and rates of diffusion. Review of all available data confirms the random collision model and no data appear to exist that contravene it. It is concluded that mitochondrial electron transport is a diffusion-based random collision process and that diffusion has an integral and controlling affect on electron transport.

Adenosine Triphosphate↗