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PubMed1986

In vitro measurement and computer modelling of the diffusion of antibiotic in bone cement.

The diffusion coefficient for a particular antibiotic (benzyl penicillin) in various types of bone cement has been calculated from direct measurement of the passage of radio-labelled penicillin through thin sections of cement at intervals over a period of 90 days, assuming the transport processes to be Fickian. Since the concentration gradient across the test sample is not uniform in the earlier stages of the experiment, a finite-difference approximation to the diffusion equation was used to take account of the transient behaviour in determining the coefficient. This method of analysis may also be used to predict the release, as a function of time, from the surface of antibiotic-loaded bone cement and from implanted pre-loaded PMMA beads used to provide antibiotic cover following bone or joint surgery. Our computer-generated predictions appear to agree very well with previously published figures arising from in vivo and in vitro studies and we conclude therefore, that Fick's Law accurately describes the process, even when the cement mix is inhomogeneous. We have by this means a reliable method by which the diffusion coefficients for various combinations of cement, antibiotic and other additives may be retrospectively determined and compared.

Anti-Bacterial Agents↗
PubMedDate not supplied

Prediction of diffusion coefficients in porous media using tortuosity factors based on interfacial areas.

Determination of aqueous phase diffusion coefficients of solutes through porous media is essential for understanding and modeling contaminant transport. Prediction of diffusion coefficients in both saturated and unsaturated zones requires knowledge of tortuosity and constrictivity factors. No methods are available for the direct measurement of these factors, which are empirical in their definition. In this paper, a new definition for the tortuosity factor is proposed, as the real to ideal interfacial area ratio. We define the tortuosity factor for saturated porous media (tau5) as the ratio S/S(o) (specific surface of real porous medium to that of an idealized capillary bundle). For unsaturated media, tortuosity factor (tau(a)) is defined as a(aw)/a(aw),o (ratio of the specific air-water interfacial area of real and the corresponding idealized porous medium). This tortuosity factor is suitably measured using sorptive tracers (e.g., nitrogen adsorption method) for saturated media and interfacial tracers for unsaturated media. A model based on this new definition of tortuosity factors, termed the interfacial area ratio (IAR) model, is presented for the prediction of diffusion coefficients as a function of the degree of water saturation. Diffusion coefficients and diffusive resistances measured in a number of saturated and unsaturated granular porous media, for solutes in dilute aqueous solutions, agree well with the predictions of the IAR model. A comparison of permeability of saturated sands estimated based on tau(s) and the same based on the Kozeny-Carman equation confirm the usefulness of the tau(s) parameter as a measure of tortuosity.

Diffusion↗
PubMed1994

Modeling and observation of temperature changes in vivo using MRI.

Models have been developed for the signal changes occurring in human peripheral muscle after thermal stress for some methods of measuring temperature in vivo. These include the dependency of T1 on temperature, observed by both direct, and magnetization transfer, experiments, and the temperature sensitivity of the diffusion coefficient and the chemical shift of the water proton line. Results show the relative complexity of the T1-dependent models when there are significant variations in, possibly amongst other things, tissue perfusion, and how the predictions made using them match the behavior of the practical values quite well. Using changes in the diffusion coefficient appears less problematic, although there can still be significant errors in temperature calibrations. The problems with this approach are likely to be due to the consequences of anisotropy in tissue.

Adipose Tissue↗
PubMed1983

Kinetics of the receptor current in bullfrog saccular hair cells.

The receptor current of hair cells from the bullfrog's sacculus was measured by voltage clamp recording across the isolated sensory epithelium. Several hundred hair cells were stimulated en masse by moving the overlying otolithic membrane with a piezoelectrically activated probe. As measured by optical recording of otolithic membrane motion, the step displacement stimuli reached their final amplitudes of up to 1 micrometer within 100 microseconds. The relationship between displacement and steady-state receptor current is an asymmetric, sigmoidal curve about 0.5 micrometer in extent. The time constant of the approach to steady state depends upon the magnitude of the hair bundle displacement and ranges from 100 to 500 microseconds at 4 degrees C; the time course is faster with larger displacements or at higher temperatures. Both the displacement-response curve and the kinetics of the response are changed by alterations in the Ca2+ concentration at the apical surface of the cells. The characteristics of the response are not consistent with simple models for the transduction process that involve enzymatic regulation of channel proteins or diffusible second messengers. Mechanical stimulation is instead posited to act directly by altering the free energy difference between the open and closed forms of the transduction channel, thereby inducing a redistribution between these states. The dependences of the response kinetics on displacement and on temperature suggest that the thermal interconversion between open and closed transduction channels is limited by an enthalpy of activation of about 12 kcal/mol.

Acoustic Stimulation↗
PubMed2001

Effect of vasodilator hydralazine on tumor microvascular random flow and blood volume as measured by intravoxel incoherent motion (IVIM) weighted MRI in conjunction with Gd-DTPA-Albumin enhanced MRI.

We studied the effect of hydralazine on tumor blood volume fraction and microvascular random flow velocity magnitude by IVIM weighted MRI in conjunction with dynamic Gd-DTPA-Albumin enhanced MRI. Blood volume fraction maps were obtained from the dynamic Gd-DTPA-Albumin enhanced MRI measurements. The average blood volume fraction of R3230 AC adenocarcinoma decreased from 0.125 +/- 0.022 (s.d.) ml/g to 0.105 +/- 0.018 (s.d.) ml/g (p < 0.001) after the administration of hydralazine at a dose of 5 mg/kg. The microvascular random flow velocity magnitude maps were obtained from the IVIM weighted MRI signals by utilizing the Gd-DTPA-Albumin measured blood volume fractions as an input in the compartmental modeling analysis of the IVIM weighted MRI signal. The random-directional microvascular flow induced MRI signal attenuation was separated from the molecular diffusion induced signal attenuation. Flow induced attenuation was more significant after the administration of hydralazine. The mean microvascular random flow velocity magnitude increased from 0.52 +/- 0.15 (s.d.) mm/sec to 0.73 +/- 0.23 (s.d.) mm/sec (p < 0.05) in the presence of the above blood volume fraction change.

Adenocarcinoma↗
PubMed1993

Influence of diffusion and gravity on the adhesion of a two-component mixture of hard spheres on a flat surface.

The adhesion of hard spheres, modeling particles of biological interest (proteins, bacteria, cells), on flat surfaces is investigated by means of Monte Carlo simulations. These computations include the Brownian diffusion of the particles in the bulk fluid, as well as the systematic displacement due to the gravitational field. The size of the particles influences directly both diffusion coefficient and net weight, with the consequence that the coverage at the jamming limit depends on this parameter. Results obtained in a former paper based on a lattice model are confirmed by the present continuous space model. In order to gain a better understanding of the adsorption competition of two types of particles, the proposed model is applied to the case of binary mixtures of spheres. For polydispersed suspensions, various parameters determine the final coverage, as well as the distribution of the small and large particles on the surface: the radii of the particles and the respective proportions of them in the infinitely large reservoir from which they are randomly selected. In this way, it is shown that the chronology of the adhesion of the small and large particles strongly influences the final number of each type of spheres fixed on the surface. Qualitatively, the present results resemble those obtained with disks placed by means of a classical random sequential adsorption mechanisms. Quantitatively, however, the number densities and coverage values determined in this way are significantly different due to the inclusion of the gravity and of the diffusion in the model.

Adhesiveness↗
PubMed1995

Lateral diffusion of human CD2 wild type and mutants with large deletions in the transmembrane domain.

Integral membrane proteins anchor to the cell surface and span the lipid bilayer by an alpha-helix of 17-30 amino acids, the transmembrane segment. However, little is known about the association of this alpha-helix and the lipid bilayer. In the present study human CD2 molecule was chosen as a model for an integral membrane protein. Truncate forms with transmembrane segments 14 and 12 amino acids long were created by oligonucleotide site-directed mutagenesis. Lateral diffusion revealed that even large deletions in the membrane domain of CD2 do not interfere with its lateral mobility. On the other hand, the fraction of free molecules for diffusion was higher in CD2 protein with transmembrane region 12 amino acids long. These results suggest that deletions in the transmembrane domain can interfere with the stability of the protein within the lipid bilayer.

Amino Acid Sequence↗
PubMed2001

Numerical simulations of angiogenesis in the cornea.

Angiogenesis plays important roles in many physiologic and pathologic processes in the body. To understand mechanisms of angiogenesis, we developed a mathematical model for quantitative analysis of various biological events involved in angiogenesis. Our model was focused on two-dimensional angiogenesis in the cornea. The model considered diffusion of angiogenic factors, uptake of these factors by endothelial cells, and randomness in the rate of sprout formation and the direction of sprout growth. Our simulation results indicated that redistribution and uptake of angiogenic factors during angiogenesis had significant effects on the structure of vascular networks. A decrease in the uptake rate resulted in increases in vessel density, self-loop formation, and front migration speed of vascular networks. The randomness in the direction of sprout formation determined the curvature of vessels, whereas the probability of sprout formation from a vessel segment had a significant effect on the total number of vessels in vascular networks. The vascular networks generated in numerical simulations were similar to those observed experimentally. The mathematical model developed in this study can be used to evaluate effects of individual factors on angiogenesis, understand mechanisms of interactions among different factors during angiogenesis, and generate experimentally testable hypotheses.

Animals↗
PubMed2004

Cerebral metabolic reduction in severe malaria: fluorodeoxyglucose-positron emission tomography imaging in a primate model of severe human malaria with cerebral involvement.

Cerebral metabolic changes in Japanese macaques (Macaca fuscata) infected with Plasmodium coatneyi, a primate model of severe human malaria with cerebral involvement, were directly evaluated by fluorodeoxyglucose-positron emission tomography (FDG-PET). We observed diffuse and heterogeneous reduction of metabolism in the cerebral cortex in the acute phase of malaria infection. Neuropathologic examination showed preferential sequestration of parasitized red blood cells in the cerebral microvasculature. However, hemorrhagic change or necrosis was not observed in hematoxylin and eosin-stained and Nissl-stained brain tissues. This suggests that reduction of cerebral metabolism occurs before parenchymal changes appear in the brain. This may be one reason why more than half of the patients with cerebral malaria have no neurologic sequelae after recovery.

Animals↗
PubMed2004

In vivo diffusion tensor imaging of the human prostate.

This study demonstrates the feasibility of in vivo prostate diffusion tensor imaging (DTI) in human subjects. We implemented an EPI-based diffusion-weighted (DW) sequence with seven-direction diffusion gradient sensitization, and acquired DT images from six subjects using cardiac gating with a phased-array prostate surface coil operating in a linear mode. We calculated two indices to quantify diffusion anisotropy. The direction of the eigenvector corresponding to the leading eigenvalue was displayed by means of a color-coding scheme. The average diffusion values of the prostate peripheral zone (PZ) and central gland (CG) were 1.95 +/- 0.08 x 10(-3) mm2 s and 1.53 +/- 0.34 x 10(-3) mm2 s, respectively. The average fractional anisotropy (FA) values for the PZ and CG were 0.46 +/- 0.04 and 0.40 +/- 0.08, respectively. The diffusion ellipsoid in prostate tissue was anisotropic and approximated a prolate model, as shown in the color maps of the anisotropy. Consistent with the tissue architecture, the prostate fiber orientations were predominantly in the superior-inferior (SI) direction for both the PZ and CG. This study shows the feasibility of in vivo DTI and establishes normative DT values for six subjects.

Anisotropy↗
PubMed2004

A model for sedimentation in inhomogeneous media. II. Compressibility of aqueous and organic solvents.

The effects of solvent compressibility on the sedimentation behavior of macromolecules as observed in analytical ultracentrifugation are examined. Expressions for the density and pressure distributions in the solution column are derived and combined with the finite element solution of the Lamm equation in inhomogeneous media to predict the macromolecular concentration distributions under different conditions. Independently, analytical expressions are derived for the sedimentation of non-diffusing particles in the limit of low compressibility. Both models are quantitatively consistent and predict solvent compressibility to result in a reduction of the sedimentation rate along the solution column and a continuous accumulation of solutes in the plateau region. For both organic and aqueous solvents, the calculated deviations from the sedimentation in incompressible media can be very large and substantially above the measurement error. Assuming conventional configurations used for sedimentation velocity experiments in analytical ultracentrifugation, neglect of the compressibility of water leads to systematic errors underestimating sedimentation coefficients by approximately 1% at a rotor speeds of 45000 rpm, but increasing to 2-5% with increasing rotor speeds and decreasing macromolecular size. The proposed finite element solution of the Lamm equation can be used to take solvent compressibility quantitatively into account in direct boundary models for discrete species, sedimentation coefficient distributions or molar mass distributions. Using the analytical expressions for the sedimentation of non-diffusing particles, the ls-g*(s) distribution of apparent sedimentation coefficients is extended to the analysis of sedimentation in compressible solvents. The consideration of solvent compressibility is highly relevant not only when using organic solvents, but also in aqueous solvents when precise sedimentation coefficients are needed, for example, for hydrodynamic modeling.

Centrifugation, Density Gradient↗
PubMed2006

Long-term aging of copper added to soils.

Aging refers to the processes by which the mobility and bioavailability/toxicity of metals added to soil decline with time. Although long-term aging is a key process that needs to be considered in the risk assessment of metals in field soils, the long-term aging of Cu added to soils has not been studied in detail. In this study, the effects of aging on Cu isotopic exchangeability, total Cu in soil pore water, pore water free Cu2+ activity, and "available" Cu measured by the technique of diffusive gradient in thin film (DGT-Cu) were investigated in 19 European soils at two total Cu concentrations shown to inhibit plant (tomato) growth by 10 and 90%. After addition of Cu, the soils were leached, incubated outdoors, and sampled regularly over a 2-year period. The results showed that when water soluble Cu was added to soils, concentrations of Cu determined by each of the techniques tended to decrease rapidly initially, followed by further decreases at slow rates. Soil pH was a vital factor affecting the aging rate of Cu added to soils. The relatively low solubility products and low isotopic exchangeabilities of Cu in calcareous soils immediately after addition of soluble Cu2+ suggested Cu2+ probably precipitated in these soils as Cu2(OH)2CO3 (malachite) and Cu(OH)2. Isotopic dilution was found to be a robust technique for measuring rates of long-term aging reactions. A semi-mechanistic model was developed to describe the rate and extent of Cu aging across soils as affected by soil pH and other physicochemical parameters. Although not measured directly, it is inferred from soil physicochemical controls on Cu aging that processes of precipitation/nucleation of Cu in soils and hydrolysis of Cu2+ followed by a diffusion process controlled the decrease in Cu availability with time. The model was validated by testing it against field soils with different contamination histories and was found to successfully predict the isotopic exchangeability of Cu added to soils based on two parameters: soil pH and time.

Copper↗
PubMed1996

Census and consensus in bacterial ecosystems: the LuxR-LuxI family of quorum-sensing transcriptional regulators.

The importance of accurate demographic information is reflected in the United States Constitution, Article 1, which provides for a decennial census of this country's human population. Bacteria also conduct a census of their population and do so more frequently, more efficiently, and as far we know, with little if any of the political contentiousness caused by human demographers. Many examples have been found of particular bacterial genes, operons, or regulons that are expressed preferentially at high cell densities. Many of these are regulated by proteins related to the LuxR and LuxI proteins of Vibrio fischeri, and by a diffusible pheromone called an autoinducer. LuxR and LuxI and their cognate autoinducer (3-oxohexanoyl homoserine lactone, designated VAI-1) provide an important model to describe the functions of this family of proteins. LuxR is a VAI-1 receptor and a VAI-1-dependent transcriptional activator, and LuxI directs the synthesis of VAI-1. VAI-1 diffuses across the bacterial envelope, and intracellular concentrations of it are therefore strongly increased by nearby VAI-1-producing bacteria. Similar systems regulate pathogenesis factors in Pseudomonas aeruginosa and Erwinia spp., as well as T1 plasmid conjugal transfer in Agrobacterium tumefaciens, and many other genes in numerous genera of gram-negative bacteria. Genetic analyses of these systems have revealed a high degree of functional conservation, while also uncovering features that are unique to each.

4-Butyrolactone↗
PubMed2006

Conditions for propagation and block of excitation in an asymptotic model of atrial tissue.

Detailed ionic models of cardiac cells are difficult for numerical simulations because they consist of a large number of equations and contain small parameters. The presence of small parameters, however, may be used for asymptotic reduction of the models. Earlier results have shown that the asymptotics of cardiac equations are nonstandard. Here we apply such a novel asymptotic method to an ionic model of human atrial tissue to obtain a reduced but accurate model for the description of excitation fronts. Numerical simulations of spiral waves in atrial tissue show that wave fronts of propagating action potentials break up and self-terminate. Our model, in particular, yields a simple analytical criterion of propagation block, which is similar in purpose but completely different in nature to the "Maxwell rule" in the FitzHugh-Nagumo type models. Our new criterion agrees with direct numerical simulations of breakup of reentrant waves.

Action Potentials↗
PubMed2006

Distance traveled by random walkers before absorption in a random medium.

We consider the penetration length l of random walkers diffusing in a medium of perfect or imperfect absorbers of number density rho. We solve this problem on a lattice and in the continuum in all dimensions D, by means of a mean-field renormalization group. For a homogeneous system in D > 2, we find that l is similar to max(xi,rho(-1/2)), where is the absorber density correlation length. The cases of D = 1 and D = 2 are also treated. In the presence of long-range correlations, we estimate the temporal decay of the density of random walkers not yet absorbed. These results are illustrated by exactly solvable toy models, and extensive numerical simulations on directed percolation, where the absorbers are the active sites. Finally, we discuss the implications of our results for diffusion limited aggregation (DLA), and we propose a more effective method to measure l in DLA clusters.

Journal Article↗
PubMed1992

A proposed tolerance criterion for diffuse axonal injury in man.

The head injury criterion (HIC) is currently the government-accepted head injury indicator. The HIC is not injury-specific, does not relate to injury severity, nor does it take into account variations in the brain mass or load direction. This report focuses on one type of inertial brain injury, diffuse axonal injury (DAI), and utilizes animal studies, physical model experiments, and analytical model simulations to determine the kinematics of DAI in the subhuman primate and to scale these results to man. A human injury tolerance for moderate to severe DAI, which includes the influences of rotational loads and brain mass, is proposed.

Acceleration↗
PubMed2003

Polarised transport of monocarboxylic acid type drugs across rat jejunum in vitro: the effect of mucolysis and ATP-depletion.

The transport characteristics of monocarboxylic acid type drugs (ketoprofen, ibuprofen and gemfibrozil) across the excised jejunal segments and artificial (octanol impregnated) membrane in side-by-side diffusion cells were studied. All three model drugs permeated faster across the intestinal tissue in the mucosal-to-serosal direction than in the opposite direction. No polarised transport of tested drugs was observed when the mucosal side of the intestine was treated with mucus disrupting agent, L-cysteine 1% (w/v), which significantly increased the microclimate pH at the mucosal surface of the intestine. Similar effects on the transport characteristics of model drugs and microclimate pH were observed when metabolic inhibitor, sodium azide (10mM), was present in the incubation medium. Furthermore, the direction of proton gradient across the artificial membrane was shown to significantly influence the transport of model drugs across this membrane. The results of this study indicate that the inwardly directed proton gradient maintained by the acidic microclimate pH at the intestinal surface could be considered as a driving force for the transport of monocarboxylic acid type drugs across the intestinal epithelia and could explain rapid absorption of these drugs after oral application.

Adenosine Triphosphate↗
PubMed1986

The DNA scanning mechanism of T4 endonuclease V. Effect of NaCl concentration on processive nicking activity.

T4 endonuclease V is a pyrimidine dimer-specific endonuclease which generates incisions in DNA at the sites of pyrimidine dimers by a processive reaction mechanism. A model is presented in which the degree of processivity is directly related to the efficacy of the one-dimensional diffusion of endonuclease V on DNA by which the enzyme locates pyrimidine dimers. The modulation of the processive nicking activity of T4 endonuclease V on superhelical covalently closed circular DNA (form I) which contains pyrimidine dimers has been investigated as a function of the ionic strength of the reaction. Agarose gel electrophoresis was used to separate the three topological forms of the DNA which were generated in time course reactions of endonuclease V with dimer-containing form I DNA in the absence of NaCl, and in 25, 50, and 100 mM NaCl. The degree of processivity was evaluated in terms of the mass fraction of form III (linear) DNA which was produced as a function of the fraction of form I DNA remaining. Processivity is maximal in the absence of NaCl and decreases as the NaCl concentration is increased. At 100 mM NaCl, processivity is abolished and endonuclease V generates incisions in DNA at the site of dimers by a distributive reaction mechanism. The change from the distributive to a processive reaction mechanism occurs at NaCl concentrations slightly below 50 mM. The high degree of processivity which is observed in the absence of NaCl is reversible to the distributive mechanism, as demonstrated by experiments in which the NaCl concentration was increased during the time course reaction. In addition, unirradiated DNA inhibited the incision of irradiated DNA only at NaCl concentrations at which processivity was observed.

DNA↗