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 721 records · Page 40Linked to original sources
PubMed2005

Sedimentation velocity analysis of heterogeneous protein-protein interactions: sedimentation coefficient distributions c(s) and asymptotic boundary profiles from Gilbert-Jenkins theory.

Interacting proteins in rapid association equilibrium exhibit coupled migration under the influence of an external force. In sedimentation, two-component systems can exhibit bimodal boundaries, consisting of the undisturbed sedimentation of a fraction of the population of one component, and the coupled sedimentation of a mixture of both free and complex species in the reaction boundary. For the theoretical limit of diffusion-free sedimentation after infinite time, the shapes of the reaction boundaries and the sedimentation velocity gradients have been predicted by Gilbert and Jenkins. We compare these asymptotic gradients with sedimentation coefficient distributions, c(s), extracted from experimental sedimentation profiles by direct modeling with superpositions of Lamm equation solutions. The overall shapes are qualitatively consistent and the amplitudes and weight-average s-values of the different boundary components are quantitatively in good agreement. We propose that the concentration dependence of the area and weight-average s-value of the c(s) peaks can be modeled by isotherms based on Gilbert-Jenkins theory, providing a robust approach to exploit the bimodal structure of the reaction boundary for the analysis of experimental data. This can significantly improve the estimates for the determination of binding constants and hydrodynamic parameters of the complexes.

Binding Sites↗
PubMed2006

Model-based variational smoothing and segmentation for diffusion tensor imaging in the brain.

This article applies a unified approach to variational smoothing and segmentation to brain diffusion tensor image data along user-selected attributes derived from the tensor, with the aim of extracting detailed brain structure information. The application of this framework simultaneously segments and denoises to produce edges and smoothed regions within the white matter of the brain that are relatively homogeneous with respect to the diffusion tensor attributes of choice. This approach enables the visualization of a smoothed, scale invariant representation of the tensor data field in a variety of diverse forms. In addition to known attributes such as fractional anisotropy, these representations include selected directional tensor components and additionally associated continuous valued edge fields that might be used for further segmentation. A comparison is presented of the results of three different data model selections with respect to their ability to resolve white matter structure. The resulting images are integrated to provide better perspective of the model properties (edges, smoothed image, and so forth) and their relationship to the underlying brain anatomy. The improvement in brain image quality is illustrated both qualitatively and quantitatively, and the robust performance of the algorithm in the presence of added noise is shown. Smoothing occurs without loss of edge features because of the simultaneous segmentation aspect of the variational approach, and the output enables better delineation of tensors representative of local and long-range association, projection, and commissural fiber systems.

Algorithms↗
PubMed1992

Dentin as inhibitor of bacterial toxicity on pulpal cells in vitro.

Many studies have shown that the major cause of pulpal disease is the presence of bacteria or their by-products in the dentinal tubules. The purpose of this investigation was to develop an in vitro model, simulating the pulp chamber, that would permit the study of the transport of bacterial by-products through dentin and their effect on pulpal cells. Human pulpal cells were cultured in a modified Sykes-Moore chamber and exposed through dentin to sonicated extracts of Porphyromonas gingivalis ATCC 33277. The cell response was evaluated with the thymidine incorporation method. The results were compared with the cell response obtained after direct exposure to the same irritant. It was found that dentin significantly restricts the diffusion of bacterial proteins in a 24-h experimental period. The time needed for the first bacterial protein molecule to cross the dentin barrier was 6 h. The "diffusion velocity" of the bacterial proteins was 0.023 microns/s. The proposed model has further applications in biocompatibility and microleakage research.

Bacterial Proteins↗
PubMed2006

Stochastic modeling of CW-ESR spectroscopy of [60]fulleropyrrolidine bisadducts with nitroxide probes.

In this work, we address the interpretation of continuous wave electron spin resonance (CW-ESR) spectra of fulleropyrrolidine bisadducts with nitroxide addends. Our approach is based on a definition of the spin Hamiltonian which includes exchange and dipolar interactions and on a complete numerical solution of the resulting stochastic Liouville equation, with inclusion of diffusive rotational dynamics. CW-ESR spectra are simulated for a series of C60 bisadducts made up of four trans isomers and the equatorial isomer. A nonlinear least-squares fitting procedure allows extraction directly from the available experimental spectra of a wide range of parameters, namely interprobe relative distances, diffusion tensors, and values of the exchange parameter J. Results are in good agreement with previous, more phenomenological estimates, proving that the combination of sensitive ESR spectroscopy based on multiple spin labeling with nitroxide radicals and sophisticated modeling can be highly helpful in providing structural and dynamic information on molecular systems.

Journal Article↗
PubMed1993

Cellular automaton simulation of pulsed field gel electrophoresis.

We describe simulation techniques well suited to detailed investigation of the microscopic behavior of DNA during electrophoretic separation in the diffusive regime. Long polymers moving diffusively in a medium are simulated using microscopic Monte-Carlo steps. Simulations rely upon a recently introduced two-space abstract polymer that enables fine-grained massively parallel simulation. Tests of the two-space polymer dynamics are reviewed. The scaling with polymer length of the size and relaxation time of isolated polymers are shown to agree with universal scaling relations. The relaxation time is found to be significantly faster than the alternative bond-fluctuation method. Simplicity of implementation enables simulation on cellular automaton machines (CAM) including CAM-6, and a prototype of the new CAM-8, as well as other massively parallel architectures. Preliminary simulations of polymers migrating under an external field through a random medium of obstacles in two dimensions are described. Two sequences of simulations are performed, with different obstacle densities corresponding to pore sizes larger and smaller than the polymer radius of gyration. In the dilute medium polymers are characteristically draped on single obstacles. In the denser medium draping across multiple obstacles results in reduced orientation in the field direction. A demonstration of rapid 90 degrees field direction switching results in polymer motion toward the expected intermediate direction.

Algorithms↗
PubMed2002

Identification of a C-terminal region that is required for the nuclear translocation of ERK2 by passive diffusion.

Extracellular signal-regulated kinase 2 (ERK2) is located in the cytoplasm of resting cells and translocates into the nucleus upon extracellular stimuli by active transport of a dimer. Passive transport of an ERK2 monomer through the nuclear pore is also reported to coexist. We attempted to characterize the cytoplasmic retention and nuclear translocation of fusion proteins between deletion and site-directed mutants of ERK2 and green fluorescent protein (GFP). The overexpressed ERK2-GFP fusion protein is usually localized to both the cytoplasm and the nucleus unless a cytoplasmic anchoring protein is coexpressed. Deletion of 45 residues, but not 43 residues, from the C terminus of ERK2 prevented the nuclear distribution of the ERK2-GFP fusion protein. Substitution of a part of residues 299-313 to alanine residues also prevented the nuclear distribution of the ERK2-GFP fusion protein without abrogation of its nuclear active transport. These observations may indicate that the passive diffusion of ERK2 into the nucleus is not simple diffusion but includes a specific interaction process between residues 299-313 and the nuclear pore complex and that this interaction is not required for the active transport. We also showed that substitution of Tyr(314) to alanine residue abrogated the cytoplasmic retention of the ERK2-GFP fusion protein by PTP-SL but not by MEK1.

Active Transport, Cell Nucleus↗
PubMed1981

Surface charge asymmetry and a specific calcium ion effect in chloroplast photosystem II.

We have used the decay kinetics of Signal IIf in Tris-washed chloroplasts as a direct probe to reactions on the oxidizing side of Photosystem II. A study of the salt concentration dependence of the rate of reduction of Z . + by the ascorbate monoanion has been interpreted by using the Gouy-Chapman diffuse double layer model and allows the calculation of an inner membrane surface charge density of -3.4 +/- 0.3 microC . cm-2 at pH = 8.0 in the vicinity of Photosystem II. We have also measured the outer membrane surface charge density at this pH in Tris- and sucrose-washed chloroplasts by monitoring the rate of potassium ferricyanide oxidation of Q-, and arrive at values of -2.2 +/- 0.3 microC . cm-2 and -2.1 microC . cm-2, respectively. From these experiments we conclude that in dark-adapted chloroplasts at pH 8.0 there exists a transmembrane electric field in the vicinity of Photosystem II which arises from this surface charge asymmetry. In the presence of 10 mM monovalent salts, the transmembrane potential difference is of the order of 20 mV, corresponding to a field of 4 . 10(4) V . cm-1 (negative inside) for a 50A membrane. It is both smaller in magnitude and in the opposite direction compared to the photoinduced transmembrane field which gives rise to the 515 nm absorption change. We have also found non-double layer Ca2+ effects on the decay kinetics of Signal IIf with both charged (ascorbate monoanion) and neutral (diphenylcarbazide) donors. These results suggest a change in the environment of Z from lipophilic to hydrophilic upon specific binding of Ca2+.

Calcium↗
PubMed1992

Mutation of serine residue 318 in the class C beta-lactamase of Enterobacter cloacae 908R.

The involvement of the serine residue 318 in the specificity of a class C beta-lactamase was investigated. Multiple site-directed mutants at this position were generated using a polymerase chain reaction technique. These mutants were then probed for their activity towards various beta-lactam compounds. One mutant, S318G was further purified and its physico-chemical and catalytic properties determined. It was shown that the observed minimal inhibitory concentration values of this mutant could be correlated to its kinetic properties using a 'diffusion-hydrolysis' model. However, the data showed that residue 318 has little influence on the specificity of class C beta-lactamases.

Base Sequence↗
PubMed2003

Binding of NAP-22, a calmodulin-binding neuronal protein, to raft-like domains in model membranes.

The cholesterol-binding protein NAP-22 is a major component of the detergent-insoluble low-density fraction of rat brain. In this study, we found, using fluorescence microscopy, that native NAP-22, but not a demyristoylated form, binds to cholesterol-rich raft-like domains in planar-supported monolayers and remains bound after nonionic detergent extraction. NAP-22 also protects the cholesterol-rich domains during extraction by methyl-beta-cyclodextrin. The lateral mobility of this protein is much lower than that of other raft components in model membranes, suggesting that both cholesterol binding and inter-NAP-22 interactions markedly reduce its lateral diffusion. This study suggests that NAP-22 binding may be employed to image cholesterol-rich regions, such as caveolae/rafts, on the plasma membrane of cells, and preliminary efforts in that direction are presented.

3T3 Cells↗
PubMed2006

Diffusion tensor feature in vasogenic brain edema in cats.

We investigated the correlation between the changes in diffusion tensor magnetic resonance imaging, regional water content, and tissue ultrastructure after vasogenic brain edema induced by cortical cold lesioning. In this cat model, E3 in the white matter was dominantly increased while fractional anisotropy (FA) was significantly decreased 8 hours after cortical cold lesioning. This finding indicates that water diffusion in the cortical white matter mainly increased perpendicularly rather than parallel to the direction of the nerve fibers. Additionally, in the area where edema is mild or moderate (tissues with water content of 65% to 75%), FA in the chronic phase was significantly lower than that in the acute phase. Histological examination demonstrated disordered arrangement of nerve fibers, highly dissociated neuronal fibers due to extracellular accumulation of protein rich-fluid, and enlarged interfiber spaces in the acute phase.

Animals↗
PubMed2002

Modelling of DNA damage induced by energetic electrons (100 eV to 100 keV).

Modelling and calculations are presented for the spectrum of initial DNA damage produced by 100 eV to 100 keV energetic electrons. Analysis of the initial spectrum of damage, based upon the source (direct energy deposition and reactions with diffusing OH radicals) and complexity of damage, indicates that the majority of the interactions cause no damage to DNA and any damage that does occur is most likely to be a simple single strand break (SSB). The fraction of complex damage for energetic electrons is lower than that induced by low energy electrons and ultrasoft X rays but still represents an appreciable fraction (20-30%) of the total double strand breaks (DSBs). Relative yields of strand breaks are investigated for dependence on the assumed energy deposition threshold and on the probability of the hydroxyl radicals to produce a single strand break. The ratio of direct to indirect damage does not change significantly across the electron energy range investigated and the values lie well within the experimental data. The direct energy deposition in DNA represents a larger proportion of the damage although the contribution from the hydroxyl radicals is also substantial, both in terms of the absolute yield of the breaks and the complexity of the damage.

Computer Simulation↗
PubMed1989

Regulation of mast cell differentiation.

Mast cells are a unique class of blood cell. Unlike most blood cells, undifferentiated precursors of mast cells migrate in the bloodstream, invade tissues, proliferate there and then differentiate. Even after differentiation, some mast cells may proliferate extensively. Differentiation of mast cells is regulated by both diffusible growth factors and direct contact with fibroblasts.

Animals↗
PubMed1997

NMR structural studies of human cystatin C dimers and monomers.

Human cystatin C undergoes dimerization before unfolding. Dimerization leads to a complete loss of its activity as a cysteine proteinase inhibitor. A similar process of dimerization has been observed in cells, and may be related to the amyloid formation seen for the L68Q variant of the protein. Dimerization is barrier controlled, and no dimer/monomer interconversion can be observed at physiological conditions. As a consequence, very stable, "trapped" dimers can be easily separated from monomers. A study of the structural aspects of cystatin C dimer formation was undertaken using NMR spectroscopy. The monomer/dimer model was verified by (pulse field gradient NMR) self-diffusion molecular mass measurements. Complete backbone resonance assignments and secondary structure determination were obtained for the monomer using data from triple resonance experiments performed on 13C/15N doubly labeled protein. A marked similarity of the cystatin C secondary structure to that of chicken cystatin was observed. Using uniformly and amino-acid-specific 15N-enriched protein, backbone NH signals were assigned for cystatin C in its dimeric state. Comparison of 1H -15N correlation NMR spectra of the monomer and dimer shows that the three-dimensional structure remains unchanged in the dimer and that only local perturbations occur. These are localized to the amino acid residues comprising the cysteine proteinase binding site. Such a mode of dimerization readily explains the complete loss of the inhibitory activity in the dimer. The NMR results also demonstrate that the dimer is symmetric.

Amino Acid Sequence↗
PubMed2006

Local field effects on electron transport in nanostructured TiO2 revealed by terahertz spectroscopy.

We study electron mobilities in nanoporous and single-crystal titanium dioxide with terahertz time domain spectroscopy. This ultrafast technique allows the determination of the electron mobility after carrier thermalization with the lattice but before equilibration with defect trapping states. The mobilities reported here for single-crystal rutile (1 cm2/(V s)) and porous TiO2 (10(-2) cm2/(V s)) therefore represent upper limits for electron transport at room temperature for defect-free materials. The large difference in mobility between bulk and porous samples is explained using Maxwell-Garnett effective medium theory. These results demonstrate that electron mobility is strongly dependent on the material morphology in nanostructured polar materials due to local field effects and cannot be used as a direct measure of the diffusion coefficient.

Computer Simulation↗
PubMed1983

Bithorax phenocopy and pattern formation. II. A model of prepattern formation.

Phenocopy maps are constructed from the spatial pattern of the phenocopy spots using a distance function defined on the frequencies with which two compartments transform separately and jointly. The temporal changes in distances between different compartments in turn enable us to make inferences concerning the diffusion-like processes involved in prepattern formation of the metathorax. A model is presented which accounts for the data in terms of the propagation of two wavefronts in sequence and in approximately orthogonal directions. Sensitivity to transformation by ether is limited in time to the interval between the passing of the two wavefronts. Changes caused by 13 successive generations of ether treatment can be interpreted in terms of alterations in the timing and rates of wave propagation. A comparison of phenocopy and fate maps suggests that the prepatterning processes affect primarily the blastoderm cytoplasm or surface membrane.

Animals↗
PubMedDate not supplied

Antibiotic-impregnated bone cement: an in vitro comparative analysis.

This manuscript examines the in vitro antibacterial activity of eight different antibiotics when mixed with polymethyl methacrylate. Two different parameters are presented as being important considerations in the choice of antibiotic. One parameter is the bacterial inhibition created by the direct contact of the antibiotic-impregnated bone cement. The second parameter is the bacterial inhibition produced by diffusion of antibiotic from the bone cement into the surrounding liquid medium. These two experimental models were created to establish the contiguous and remote antimicrobial effects of antibiotic-impregnated bone cement.

Anti-Bacterial Agents↗
PubMed1993

Development and assessment of two fixed-array microphones for use with hearing aids.

Hearing-impaired listeners often have great difficulty understanding speech in situations with background noise (e.g., meetings, parties). Conventional hearing aids offer insufficient directivity to significantly reduce background noise relative to the desired speech signal. Based on array techniques, microphone prototypes have been developed with strongly directional characteristics to be incorporated into the frame and the "temples" of a pair of eyeglasses. Particular emphasis was on optimization and electronic stability. Computer simulations show that a directivity index of more than 10 dB can be obtained at the higher frequencies. Simulations were verified with free-field measurements. To investigate the influence of the human head on directivity, two portable models were also tested with a KEMAR manikin. The measurements show that the two models give an improvement of the signal-to-noise ratio of approximately 7 dB in a diffuse background noise field compared with an omnidirectional microphone. For the clinical assessment of these microphone arrays in the diffuse noise field (simulating a cocktail party situation), the speech-reception threshold in noise for simple Dutch sentences was determined with a normal single omnidirectional microphone and with one of the microphone arrays. The results of monaural listening tests of 30 subjects with normal hearing and 45 subjects with hearing impairment show that the microphone arrays give a mean improvement of the speech reception threshold in noise of about 7 dB compared with an omnidirectional microphone.

Adult↗
PubMed2006

Polyoxyethylene fatty acid esters as potential promotors of transdermal absorption for morphine hydrochloride and sulphate.

The presence of opioid receptors mu in pathologically changed skin and mucosa justifies application of preparations with morphine salts to obtain topical analgesic activity. Numerous factors associated with the vehicle and therapeutic agent physiochemical properties affect the capability and rate of penetration of a therapeutic substance in the form of a drug into dermis. Promotors of transcutaneous absorption, which weaken the integrity of epidermal corneal layer and thus, increase therapeutic substance penetration play more and more important role. In this study non-ionic macromolecular surface active compounds from Rokacets group were suggested as potential promotors of transdermal absorption for morphine sulphate and hydrochloride. The aim of the study was to work out prescription composition of ointment with morphine salts of optimal rheological and morphological parameters and high pharmaceutical availability of the therapeutic agent (morphine sulphate, hydrochloride). Three model emulsive ointment vehicles were prepared and selected promoters of transdermal absorption were introduced into them. On the basis of the formed vehicles ointments were made with morphine sulphate and hydrochloride. The obtained vehicles and ointment preparations were subjected to rheological tests. Spreadness was determined by extensometric method and viscosity with digital cone-plate rheometer. Morphological parameters of the vehicles and ointments, such as: pH and pharmacopeal density were estimated. Carrying out direct diffusion from the surface of the preparation to acceptor fluid (to water), the amount of the released therapeutic substance in time function was determined by spectrophotometric method. The performed tests demonstrated that the investigated vehicles and ointments are non-Newtonian systems, viscoelastic and highly thixotropic. The kind of morphine salt affects the spreadness and viscosity of model ointments. Preparations with morphine hydrochloride have higher spreadness than viscosity and more alkaline pH. From among the investigated non-ionic surface active compounds Rokacet R-40 appeared to be the most beneficial promotor of transdermal absorption for both pharmacopeal morphine salts. Pharmaceutical availability of morphine sulphate and hydrochloride is the highest from ointments with its content in the vehicle prescription.

Administration, Cutaneous↗