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 703 records · Page 39Linked to original sources
PubMed1996

Cellular cholesterol efflux mediated by cyclodextrins. Demonstration Of kinetic pools and mechanism of efflux.

The efflux of cholesterol from cells in culture to cyclodextrin acceptors has been reported to be substantially more rapid than efflux induced by other known acceptors of cholesterol (Kilsdonk, E. P. C., Yancey, P., Stoudt, G., Bangerter, F. W., Johnson, W. J., Phillips, M. C., and Rothblat, G. H. (1995) J. Biol. Chem. 270, 17250-17256). In this study, we compared the kinetics of cholesterol efflux from cells with 2-hydroxypropyl-beta-cyclodextrins and with discoidal high density lipoprotein (HDL) particles to probe the mechanisms governing the remarkably rapid rates of cyclodextrin-mediated efflux. The rate of cholesterol efflux was enhanced by shaking cells growing in a monolayer and further enhanced by placing cells in suspension to achieve maximal efflux rates. The extent of efflux was dependent on cyclodextrin concentration, and maximal efflux was observed at concentrations >50 mM. For several cell types, biexponential kinetics of cellular cholesterol efflux were observed, indicating the existence of two kinetic pools of cholesterol: a fast pool (half-time (t1/2) approximately 19-23 s) and a slow pool with t1/2 of 15-30 min. Two distinct kinetic pools of cholesterol were also observed with model membranes (large unilamellar cholesterol-containing vesicles), implying that the cellular pools are in the plasma membrane. Cellular cholesterol content was altered by incubating cells with solutions of cyclodextrins complexed with increasing levels of cholesterol. The number of kinetic pools was unaffected by raising the cellular cholesterol content, but the size of the fast pool increased. After depleting cells of the fast pool of cholesterol, this pool was completely restored after a 40-min recovery period. The temperature dependence of cyclodextrin-mediated cholesterol efflux from cells and model membranes was compared; the activation energies were 7 kcal/mol and 2 kcal/mol, respectively. The equivalent activation energy observed with apo-HDL-phospholipid acceptor particles was 20 kcal/mol. It seems that cyclodextrin molecules are substantially more efficient than phospholipid acceptors, because cholesterol molecules desorbing from a membrane surface can diffuse directly into the hydrophobic core of a cyclodextrin molecule without having to desorb completely into the aqueous phase before being sequestered by the acceptor.

Animals↗
PubMed1992

Formation of a regular dissipative structure: a bifurcation and non-linear analysis.

A non-linear reaction diffusion model of a negative feedback epigenetic control system is presented. The model involves synthesis of the mitotic inducing and inhibiting proteins, simultaneously with intercellular self-diffusion and cross-diffusion of the latter only. The importance of negative cross-diffusion for creating a regular dissipative structure is shown. A bifurcation analysis of the non-linear diffusive system has been performed and it is concluded that bifurcation is supercritical. Lastly, using Liapunov's direct method, it is shown that the pattern evolved by the system is globally asymptotically stable.

Cell Differentiation↗
PubMed1998

The cellular environment in computer simulations of radiation-induced damage to DNA.

Radiation-induced DNA single- and double-strand breaks were modeled for 660 keV photon radiation and scavenger capacity mimicking the cellular environment. Atomistic representation of DNA in B form with a first hydration shell was utilized to model direct and indirect damage. Monte Carlo generated electron tracks were used to model energy deposition in matter and to derive initial spatial distributions of species which appear in the medium following radiolysis. Diffusion of species was followed with time, and their reactions with DNA and each other were modeled in an encounter-controlled manner. Three methods to account for hydroxyl radical diffusion in a cellular environment were tested: assumed exponential survival, time-limited modeling and modeling of reactions between hydroxyl radicals and scavengers in an encounter-controlled manner. Although the method based on modeling scavenging in an encounter-controlled manner is more precise, it requires substantially more computer resources than either the exponential or time-limiting method. Scavenger concentrations of 0.5 and 0.15 M were considered using exponential and encounter-controlled methods with reaction rate set at 3x10(9) dm3 mol(-1) s(-1). Diffusion length and strand break yields, predicted by these two methods for the same scavenger molarity, were different by 20%-30%. The method based on limiting time of chemistry follow-up to 10(-9) s leads to DNA damage and radical diffusion estimates similar to 0.5 M scavenger concentration in the other two methods. The difference observed in predictions made by the methods considered could be tolerated in computer simulations of DNA damage.

Cells↗
PubMed1991

Several new approaches to improvement of alpha interferon therapy in chronic myelogenous leukaemia.

Several basic experimental and clinical studies were carried out in an attempt to improve the efficacy of alpha interferon therapy for chronic myelogenous leukaemia (CML). First, the combined use of hydroxyurea (HU) and interferon (500-1000 mg daily) in interferon-resistant cases facilitated maintenance of reduced leucocyte production, or a reduction in the dose of interferon, although suppression of Philadelphia chromosome (Ph1)-positive clones was not observed in most cases. In order to try and decrease the rate of lymphoblastic crisis during the course of interferon therapy, we recently added methotrexate (MTX) (10-15 mg, weekly) to the treatment protocol. Since then, no lymphoblastic crisis has been observed. Second, the in vitro expression of alpha interferon-stimulated gene (ISG) mRNA was shown to be markedly decreased in granulocytes of one representative interferon-resistant case, compared to that in granulocytes of the three interferon-sensitive cases. Interestingly, it was found that the transcriptional activity in this case became almost normal when the blood granulocytes were controlled by the addition of HU. These findings suggest that the in vitro transcriptional assay of ISG mRNA may be clinically useful for predicting alpha interferon efficacy. Third, when genetically manipulated, alpha interferon-producing NIH/3T3 cells were co-transplanted using diffusion chambers into nude mice bearing a CML cell line, KU812, the CML tumour growth was shown to be markedly suppressed. This experimental model for alpha interferon replacement gene therapy suggests some directions for future studies on interferon therapy.

Animals↗
PubMed2004

Comparative permeability of various chemical markers through human vaginal and buccal mucosa as well as porcine buccal and mouth floor mucosa.

A number of drugs undergo extensive first-pass metabolism after oral administration, necessitating large doses for effective therapeutic responses in the body. Buccal administration of drugs is becoming more popular because the drugs diffuse into the systemic circulation directly, circumventing the first-pass metabolism. Lower concentrations thus need to be administered and side effects may be minimized. In this study, one of the classic models for human buccal permeability, i.e. the porcine buccal mucosal model, is compared with the more recent human vaginal model and both these are in turn further compared to porcine mouth floor mucosa. To determine the permeability of the different markers (arecoline, 17beta-estradiol, water and vasopressin), a continuous flow-through perfusion system was used (20 degrees C, 24h). Mean steady state flux values were compared statistically using a t-test at a significance level of 5%. Porcine buccal mucosa showed a consistently lower permeability towards all the markers than the other mucosae tested. Porcine mouth floor mucosa was found to be more permeable than porcine buccal mucosa. From these studies we concluded that human vaginal and porcine mouth floor mucosae were superior models for human buccal mucosa than porcine buccal mucosa, using in vitro permeability studies with various chemical markers.

Administration, Buccal↗
PubMed2002

The effect of associative strength on priming in the cerebral hemispheres.

Recent studies have suggested that semantic memory is more diffusely organized in the right hemisphere of the brain and that words directed to this hemisphere are more likely to activate meanings distantly related to the input. It is argued that this model of language processes predicts that variations in the associative strength of word pairs should give rise to different patterns of priming in each hemisphere. Specifically, the right hemisphere should exhibit relatively more facilitation than the left in response to weaker associative relationships, whereas the left hemisphere should exhibit relatively more facilitation than the right in the context of stronger relationships. This study varied the strength of the semantic association between prime and target in a divided visual field priming procedure. The results were unequivocal in demonstrating similar associative strength functions in each hemisphere, under conditions that encouraged either automatic or controlled processing. Visual field differences in absolute RTs to words and in magnitude of facilitation effects support the claim that the data collected in this study are veridical with respect to priming processes in the hemispheres. It is suggested that current models of hemispheric language processes require further refinement.

Adult↗
PubMed2004

Peroxynitrite-mediated protein nitration and lipid peroxidation in a mouse model of traumatic brain injury.

The role of reactive oxygen-induced oxidative damage to lipids (i.e., lipid peroxidation, LP) and proteins has been strongly supported in previous work. Most notably, a number of free radical scavengers and lipid antioxidants have been demonstrated to be neuroprotective in traumatic brain injury (TBI) models. However, the specific sources of reactive oxygen species (ROS), the time course of oxidative damage and its relationship to post-traumatic neurodegeneration in the injured brain have been incompletely defined. The present study was directed at an investigation of the role of the ROS, peroxynitrite (PON), in the acute pathophysiology of TBI and its temporal relationship to neurodegeneration in the context of the mouse model of diffuse head injury model. Male CF-1 mice were subjected to a moderately severe head injury and assessed at 1-, 3-, 6-, 12-, 24-, 48-, 72, 96- and 120-h post-injury for neurodegeneration using quantitative image analysis of silver staining and semi-quantitative analysis of PON-mediated oxidative damage to proteins (3-nitrotyrosine, 3-NT) and lipids (4-hydroxynonenal, 4-HNE). Significant evidence of silver staining was not apparent until 24-h post-injury, with peak staining seen between 72- and 120-h. This time-course of neurodegeneration was preceded by intense immunostaining for 3-NT and 4-HNE, which occurred within the first hour post-injury. The time course and staining pattern for 3-NT and 4-HNE were similar, with the highest staining intensity noted within the first 48-h in areas surrounding trauma-induced contusions. In the case of 3-NT, neuronal perikarya and processes and microvessels displayed staining. The temporal and spatial coincidence of protein nitration and LP damage suggests that PON is involved in both. However, lipid-peroxidative (4-HNE) immunoreactivity was broader and more diffuse than 3-NT, suggesting that other reactive oxygen mechanisms, such as iron-dependent LP, may also contribute to the more widespread 4-HNE immunoreactivity. This indicates that optimal pharmacological inhibition of post-traumatic oxidative damage in TBI may need to combine two functionalities: one to scavenge PON or PON-derived radicals, and the second to inhibit LP caused by multiple ROS species.

Aldehydes↗
PubMed2001

Segregation of granular media by diffusion and convection.

A diffusion-convection equation is used to model granular segregation within a mixture of particles of different size, shape, or surface structure in a vertical vessel. Convection describes competition between species in vertical direction whereas random noise (shaking) allows particles to exchange positions. For two species it is shown that the moving grains converge to a unique distribution along the vertical scale. For more than two species it is shown that at least one equilibrium distribution exists (there are examples with multiple equilibria). For a class of models with simple competition laws, uniqueness of the equilibrium in all dimensions is shown.

Journal Article↗
PubMed2005

A 3-d surface reconstruction approach based on postnonlinear ICA model.

Photometric stereo technique deals with the reconstruction of three-dimensional (3-D) shape of an object by using several images of the same surface taken from the same viewpoint but under illuminations from different directions. In this paper, we propose a new photometric stereo scheme based on a new reflectance model and the postnonlinear (PNL) independent components analysis (ICA) method. The proposed nonlinear reflectance model consists of diffuse components and specular components for modeling the surface reflectance of a stereo object in an image. Unlike the previous approaches, these two components are not separated and processed individually in the proposed model. An unsupervised learning adaptation algorithm is developed to estimate the reflectance model based on image intensities. In this algorithm, the PNL ICA method is used to obtain the surface normal on each point of an image. Then, the 3-D surface model is reconstructed based on the estimated surface normal on each point of image by using the enforcing integrability method. Two experiments are performed to assess the performance of the proposed approach. We test our algorithm on synthetically generated images for the reconstruction of surface of objects and on a number of real images captured from the Yale Face Database B. These testing images contain variability due to illumination and varying albedo in each point of surface of human faces. All the experimental results are compared to those of the existing photometric stereo approaches tested on the same images. The results clearly indicate the superiority of the proposed nonlinear reflectance model over the conventional Lambertian model and the other linear hybrid reflectance model.

Algorithms↗
PubMed1991

A new method for crystalloid cardioplegic oxygenation.

A new model of in vitro cardioplegic oxygenation was evaluated by placing Ringer's infusion bags in a pressure resistant barrel filled with pure oxygen maintaining 380mmHg. In this hyperbaric environment, oxygen gradually diffused directly through the wall of the infusion bag reaching a concentration exceeding four volumes percent after 96 hours. Decay in oxygen content was less than 1.5% after one week refrigerated at 4 degrees C. In conclusion, the method described above offers an alternative approach to cardioplegic oxygenation, with the advantage of being safe, simple and without any extra expenditure.

Cardioplegic Solutions↗
PubMed1997

Gamma-delta T cells in BAL fluid of chronic lower respiratory tract infection.

Gamma-delta (gamma/delta) T cells are thought to represent the first line of defense against various pathogenic microorganisms. The aim of the present study was to investigate whether gamma/delta T cells were increased in BAL fluid (BALF) of patients with diffuse panbronchiolitis (DPB), a model of chronic lower respiratory tract infection. The study population consisted of four groups, including patients with DPB, sarcoidosis, idiopathic pulmonary fibrosis, and normal subjects. Two-color direct immunofluorescence and flow cytometry were used for analysis of peripheral blood or BALF from these patients. The percentage of peripheral blood or BALF gamma/delta T cells relative to the total number of lymphocytes was similar in the four groups. Although the absolute number of gamma/delta T cells in BALF was significantly higher in DPB patients compared with the other three groups, the total lymphocyte number in BALF in DPB patients was increased and the number of BALF gamma/delta T cells correlated with the total lymphocyte number in BALF. Furthermore, the percentage and number of BALF gamma/delta T cells were not related to a certain group of pathogenic organisms or the number of colony-forming units. Our results suggest that gamma/delta T cells are unlikely to play a part in chronic lower respiratory tract infection.

Adult↗
PubMedDate not supplied

Dynamic swelling behaviour of gelatin/poly(acrylic acid) bioadhesive microspheres loaded with oxprenolol.

The dynamic swelling of gelatin/poly(acrylic acid) microspheres loaded with oxprenolol has been evaluated. The movement of two distinct and characteristic swelling boundaries was measured directly using an optical microscope. Swelling rate constants associated with the inner moving front and the outer swelling boundary were determined. A polynomial equation incorporating both Fickian diffusion and case II relaxational models was used to fit the kinetics of liquid uptake. The influence of the concentration of the cross-linking agent, the poly(acrylic acid) load, the pH of the swelling medium and the particle size of the microspheres, on the swelling kinetics, was evaluated and discussed.

Acrylic Resins↗
PubMed2000

Photon migration through fetal head in utero using continuous wave, near-infrared spectroscopy: development and evaluation of experimental and numerical models.

In this work experimental tissue phantoms and numerical models were developed to estimate photon migration through the fetal head in utero. The tissue phantoms incorporate a fetal head within an amniotic fluid sac surrounded by a maternal tissue layer. A continuous wave, dual-wavelength (lambda = 760 and 850 nm) spectrometer was employed to make near-infrared measurements on the tissue phantoms for various source-detector separations, fetal-head positions, and fetal-head optical properties. In addition, numerical simulations of photon propagation were performed with finite-difference algorithms that provide solutions to the equation of radiative transfer as well as the diffusion equation. The simulations were compared with measurements on tissue phantoms to determine the best numerical model to describe photon migration through the fetal head in utero. Evaluation of the results indicates that tissue phantoms in which the contact between fetal head and uterine wall is uniform best simulates the fetal head in utero for near-term pregnancies. Furthermore, we found that maximum sensitivity to the head can be achieved if the source of the probe is positioned directly above the fetal head. By optimizing the source-detector separation, the signal originating from photons that have traveled through the fetal head can drastically be increased.

Cerebrovascular Circulation↗
PubMed2007

Analysis of oxygen transport in a diffusion-limited model of engineered heart tissue.

Cardiac tissue engineering has made notable progress in recent years with the advent of an experimental model based on neonatal cardiomyocytes entrapped in collage gels and purified basement membrane extract, known as "engineered heart tissues" (EHTs). EHTs are a formidable display of tissue-level contractile function and cellular-level differentiation, although they suffer greatly from mass transport limitations due to the high density of metabolically active cells and the diffusion-limited nature of the hydrogel. In this report, a mathematical model was developed to predict oxygen levels inside a one-dimensional, diffusion-limited model of EHT. These predictions were then compared to values measured in corresponding experiments with a hypoxia-sensitive stain (pimonidazole). EHTs were cast between two plastic discs, which allowed for mass transfer with the culture medium to occur in only the radial direction. EHTs were cultured for up to 36 h in the presence of pimonidazole, after which time they were snap-frozen, histologically sectioned, and stained for bound pimonidazole. Quantitative image analysis was performed to measure the distance from the culture medium at which hypoxia first occurs under various conditions. As tested by variation of simple design parameters, the trends in oxygen profiles predicted by the model are in reasonable agreement with those obtained experimentally, although a number of ambiguities related to the specific model parameters led to a general overprediction of oxygen concentrations. Based on the sensitivity analysis in the present study, it is concluded that diffusion-reaction models may offer relatively precise predictions of oxygen concentrations in diffusion-limited tissue constructs.

Biological Transport↗
PubMed2005

Visualisation of the extent of damage in a rat spinal cord injury model using MR microsopy of the water diffusion tensor.

Magnetic Resonance Diffusion Tensor Imaging (DTI) of the control and traumatic injured spinal cord of a rat in vitro is reported. Experiments were performed on excised spinal cords from 10 Wistar rats, using a home-built 6.4 T MR microscope. MRI and histopathological results were compared. Presented results show that DTI of the spinal cord, perfused with formalin 10 minutes after the injury, can detect changes in water diffusion in white matter (WM) and in gray matter (GM), in areas extending well beyond the region of direct impact. Histology of neurons of the GM shows changes that can be attributed to ischemia. This is in agreement with the observed decrease of diffusion in the injured regions, which may be attributed to the cytotoxic edema due to ischemia. However, the diffusion changes in highly anisotropic WM seem to be caused by a direct action of mechanical force of impact, which significantly distorts the nerve fibers.

Animals↗
PubMed2004

A new mathematical model for chemotactic bacterial colony growth.

A new continuum model for the growth of a single species biofilm is proposed. The geometry of the biofilm is described by the interface between the biomass and the surrounding liquid. Nutrient transport is given by the solution of a semi-linear Poisson equation. In this model we study the morphology of a chemotactic bacterial colony, which grows in the direction of increasing nutrient concentration. Numerical simulations using the level set method and finite difference schemes are presented. The results show rich heterogeneous morphology.

Bacteria↗
PubMed1981

Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor--operator interaction: kinetic measurements and conclusions.

The association and dissociation kinetics of the Escherichia coli lac repressor--operator (RO) complex have been examined as a function of monovalent ion concentration and operator-containing DNA fragment length in order to investigate the mechanisms used by repressor in locating (and dissociating from) the operator site. Association rate constants (ka) measured with an 80- or a 203-base-pair lac operator containing DNA fragment are 3--5-fold smaller than those determined with a 6700-base-pair operator fragment or with intact lambda plac5 DNA (50000 base pairs) at all salt concentrations tested. At salt concentrations less than approximately 0.1 M KCl, association rate constants to all operator-containing DNA fragments (except lambda plac5 DNA) are insensitive to variations in salt concentration, but the limiting low salt value of ka appears to depend upon operator-containing DNA length. The value of ka for lambda plac5 DNA decreases significantly from the approximately 0.1 M KCl maximum at low salt. Above approximately 0.1 M KCl, repressor--operator association rate constants for all operator-containing DNA substrates tested show a similar decrease with increasing salt concentration, which does not appear to depend upon the length of the DNA molecule (except for the very small DNA fragments). In contrast to the association reaction, kd, the dissociation rate constant, decreases linearly (on a log kd vs. log [KCl] plot) with decreasing salt concentration over virtually the entire salt concentration range studied (0.05--0.2 M KCl). These results are consistent with the explanation of the unusually fast association kinetics for this system in terms of a two-step model in which repressor initially diffuses to a nonoperator DNA binding site (forming an RD complex) and then rapidly "scans" (in a locally correlated fashion) adjacent sites until the operator is located or the repressor dissociates from the chain. Dissociation of the RO complex follows the same two-step process in reverse. Quantitative comparisons are made between these results and the theoretical predictions of the two facilitating translocation mechanisms (one-dimensional "sliding" along the DNA double helix and direct transfer between DNA segments) developed in the first paper of this series [Berg, O. G., Winter, R. B., & von Hippel, P. H. (1981) Biochemistry (first paper of three in this issue)]. We conclude that the experimental data for the "faster-than-diffusion-controlled" interaction of repressor and operator can be quantitatively modeled by a two-step process in which sliding is the dominant transfer mechanism. Molecular models of the initial nonspecific binding event (including "hopping") as well as sliding and interchain transfer are discussed, and the possible roles of facilitated translocation mechanisms of the diffusion-driven type in this and other in vitro and in vivo protein--nucleic acid interaction processes are considered.

DNA, Bacterial↗
PubMed1990

Permanent dipole moment of tRNA's and variation of their structure in solution.

The structure of six different tRNA molecules has been analyzed in solution by electrooptical measurements and by bead model simulations. The electric dichroism measured as a function of the field strength shows that tRNA's are associated with substantial permanent dipole moments, which are in the range of 1 x 10(-27) cm(identical to 300 D; before correction for the internal directing field). Rotational diffusion time constants of tRNA molecules in their native state at 2 degrees C show a considerable variation. A particularly large value found for tRNA(Tyr) (50 ns) can be explained by its nine additional nucleotide residues. However, remarkable variations remain for tRNA molecules with the standard number of 76 nucleotide residues (tRNA(Phe) [yeast] 41.6 ns, tRNA(Val) [Escherichia coli] 44.9 ns, tRNA(Glu) [E. coli] 46.8 ns; tRNA(Phe) [E. coli] 48.3 ns). These variations indicate modulations of the tertiary structure, which may be due to a change of the L-hinge angle. Bead models are used to simulate both electric and hydrodynamic parameters of tRNA molecules according to the crystal structure of tRNA(Phe) (yeast). The asymmetric distribution of phosphate charges with respect to the center of diffusion leads, under the assumption of a constant charge reduction to 15% by ion condensation, to a theoretical dipole moment of 7.2 x 10(-28) cm, which is in reasonable agreement with the measurements. The dichroism decay curve calculated for tRNA(Phe) (yeast) is also consistent with the measurements and thus the structure in solution and in the crystal must be very similar in this case. However, our measurements also indicate that the structure of some other tRNA's in solution is different, even in cases with the same number of nucleotide residues.

Magnesium↗