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PubMed2005

Numerical and experimental analysis of an axial flow left ventricular assist device: the influence of the diffuser on overall pump performance.

Thousands of adult cardiac failure patients may benefit from the availability of an effective, long-term ventricular assist device (VAD). We have developed a fully implantable, axial flow VAD (LEV-VAD) with a magnetically levitated impeller as a viable option for these patients. This pump's streamlined and unobstructed blood flow path provides its unique design and facilitates continuous washing of all surfaces contacting blood. One internal fluid contacting region, the diffuser, is extremely important to the pump's ability to produce adequate pressure but is challenging to manufacture, depending on the complex blade geometries. This study examines the influence of the diffuser on the overall LEV-VAD performance. A combination of theoretical analyses, computational fluid (CFD) simulations, and experimental testing was performed for three different diffuser models: six-bladed, three-bladed, and no-blade configuration. The diffuser configurations were computationally and experimentally investigated for flow rates of 2-10 L/min at rotational speeds of 5000-8000 rpm. For these operating conditions, CFD simulations predicted the LEV-VAD to deliver physiologic pressures with hydraulic efficiencies of 15-32%. These numerical performance results generally agreed within 10% of the experimental measurements over the entire range of rotational speeds tested. Maximum scalar stress levels were estimated to be 450 Pa for 6 L/min at 8000 rpm along the blade tip surface of the impeller. Streakline analysis demonstrated maximum fluid residence times of 200 ms with a majority of particles exiting the pump in 80 ms. Axial fluid forces remained well within counter force generation capabilities of the magnetic suspension design. The no-bladed configuration generated an unacceptable hydraulic performance. The six-diffuser-blade model produced a flow rate of 6 L/min against 100 mm Hg for 6000 rpm rotational speed, while the three-diffuser-blade model produced the same flow rate and pressure rise for a rotational speed of 6500 rpm. The three-bladed diffuser configuration was selected over the six-bladed, requiring only an incremental adjustment in revolution per minute to compensate for and ease manufacturing constraints. The acceptable results of the computational simulations and experimental testing encourage final prototype manufacturing for acute and chronic animal studies.

Blood Circulation↗
PubMed2002

Expression of interleukin-6 messenger RNA in a rat model of diffuse axonal injury.

Having demonstrated a transcranial gradient of the cytokine interleukin-6 (IL-6) in patients with either traumatic brain injury or spontaneous subarachnoid haemorrhage we have employed in situ hybridisation for IL-6 messenger RNA (mRNA) to determine the site of this IL-6 production within the central nervous system (CNS). A rodent weight drop model of traumatic brain injury was used. IL-6 mRNA levels in brains were determined 6 h after injury. Sham animals had normal constitutive expression for IL6 mRNA. In traumatised animals an intense area of IL-6 mRNA labelling was found below the hippocampus. Cells strongly expressing IL-6 mRNA were also seen in the dentate gyrus. This inflammatory cytokine is clearly implicated in the response to CNS injury, but whether this response is neuroprotective or pathological is uncertain.

Animals↗
PubMed2005

Adsorption of lignite-derived humic acids on coal-based mesoporous activated carbons.

The adsorption by a coal-based mesoporous activated carbon of humic acids (HAs) isolated from two Polish lignites was studied. For comparison, a commercial Aldrich humic acid was also included into this study. The differences in chemical structure and functional groups of HAs were determined by elemental analysis and infrared spectroscopy DRIFT. Two activated carbons used differed in terms of mesopore volume, mesopore size distribution, and chemical properties of the surface. The kinetics of adsorption of HAs have been discussed using three kinetic models, i.e., the first-order Lagergren model, the pseudo-second-order model, and the intraparticle diffusion model. It was found that the adsorption of HAs from alkaline solution on mesoporous activated carbon proceeds according to the pseudo-second-order model. The correlation coefficients were close to 1. The intraparticle diffusion of HA molecules within the carbon particle was identified to be the rate-limiting step. Comparing the two activated carbons, the carbon with a higher volume of pores with widths of 10-50 nm showed a greater removal efficiency of HA. An increase in the Freundlich adsorption capacity with decreasing carbon content of HA was observed. Among the HAs studied, S-HA shows characteristics indicating the highest contribution of small-size fraction. The S-HA was removed by both activated carbons to the highest extent. The effect of pH solution on the adsorption of HA was examined over the range pH 5.4-12.2. It was found that the extent of adsorption decreased with decreasing pH of the solution.

Adsorption↗
PubMed2002

A numerical approach to the study of spatial pattern formation in the ligaments of arcoid bivalves.

In this paper, we employ the novel application of a reaction-diffusion model on a growing domain to examine growth patterns of the ligaments of arcoid bivalves (marine molluscs) using realistic growth functions. Solving the equations via a novel use of the finite element method on a moving mesh, we show how a reaction-diffusion model can mimic a number of different ligament growth patterns with modest changes in the parameters. Our results imply the existence of a common mode of ligament pattern formation throughout the Arcoida. Consequently, arcoids that share a particular pattern cannot be assumed, on this basis alone, to share an immediate common ancestry. Strikingly different patterns within the set can easily be generated by the same developmental program. We further show how the model can be used to make quantitatively testable predictions with biological implications.

Animals↗
PubMed2004

Building an outcome predictor model for diffuse large B-cell lymphoma.

Diffuse large B-cell lymphoma (DLBCL) patients are treated using relatively homogeneous protocols, irrespective of their biological and clinical variability. Here we have developed a protein-expression-based outcome predictor for DLBCL. Using tissue microarrays (TMAs), we have analyzed the expression of 52 selected molecules in a series of 152 DLBCLs. The study yielded relevant information concerning key biological aspects of this tumor, such as cell-cycle control and apoptosis. A biological predictor was built with a training group of 103 patients, and was validated with a blind set of 49 patients. The predictive model with 8 markers can identify the probability of failure for a given patient with 78% accuracy. After stratifying patients according to the predicted response under the logistic model, 92.3% patients below the 25 percentile were accurately predicted by this biological score as "failure-free" while 96.2% of those above the 75 percentile were correctly predicted as belonging to the "fatal or refractory disease" group. Combining this biological score and the International Prognostic Index (IPI) improves the capacity for predicting failure and survival. This predictor was then validated in the independent group. The protein-expression-based score complements the information obtained from the use of the IPI, allowing patients to be assigned to different risk categories.

Adolescent↗
PubMed2004

Period doubling cascade in glow discharges: local versus global differential conductivity.

Short planar glow discharges coupled to a resistive layer exhibit a wealth of spontaneous spatiotemporal patterns. Due to similarities with other pattern forming systems that are described by reaction-diffusion models, several authors have tried to derive such models from discharge physics. We investigate the temporal oscillations of the discharge system and find a cascade of period doubling events. This shows that the inner structure of the discharge is more complex than can be described by a two-component reaction-diffusion-model with negative differential conductivity. We also derive an alternative reduced model.

Journal Article↗
PubMed2003

Experimental evidence against diffusion control of Hg evasion from soils.

Elemental Hg (Hg(0)) evolution from soils can be an important process and needs to be measured in more ecosystems. The diffusion model for soil gaseous efflux has been applied to modeling the fluxes of several gases in soils and deserves testing with regard to Hg(0). As an initial test of this model, we examined soil gaseous Hg(0) and CO(2) concentrations at two depths (20 and 40 cm) over the course of a controlled environment study conducted in the EcoCELLs at the Desert Research Institute in Reno, Nevada. We also compared small, spatially distributed gas wells against the more commonly used large gas wells. In this study, two EcoCELLs were first watered (June 2000) and then planted (July 2000) with trembling aspen (Populus tremuloides). Following that, trees were harvested (October 2000) and one EcoCELL (EcoCELL 2) was replanted with aspen (25 April 2001). During most of the experiment, there was a strong vertical gradient of CO(2) (increasing with depth, as is typical of a diffusion-driven process), but no vertical gradient of soil gaseous Hg(0). Strong diel variations in soil gas Hg(0) concentration were noted, whereas diel variations in CO(2) were small and not statistically significant. Initial watering and planting caused increases in both soil gas CO(2) and Hg(0). Replanting in EcoCELL 2 caused a statistically significant increase in soil gas CO(2) but not Hg(0). Calculated Hg(0) effluxes using the diffusion model produced values two orders of magnitude lower than those measured using field chambers placed directly on the soil or whole-cell fluxes. Neither soil gas Hg(0) concentrations nor calculated fluxes were correlated with measured Hg(0) efflux from soil or from whole EcoCELLs. We conclude that (1) soil gas Hg(0) flux is not diffusion-driven and thus soil gas Hg(0) concentrations cannot be used to calculated soil Hg(0) efflux; (2) soil gas Hg(0) concentrations are increased by watering dry soil, probably because of displacement/desorption processes; (3) soil gas Hg(0) concentrations were unaffected by plants, suggesting that roots and rhizosphere processes are unimportant in controlling Hg(0) evasion from the soil surface. We recommend the use of the small wells in all future studies because they are much easier to install and provide more resolution of spatial and temporal patterns in soil gaseous Hg(0).

Carbon Dioxide↗
PubMed2004

Increase of dermal blood volume fraction reduces the threshold for laser-induced purpura: implications for port wine stain laser treatment.

BACKGROUND AND OBJECTIVES: The average success rate in achieving total blanching of port wine stain (PWS) lesions treated with laser-induced selective photothermolysis is below 25%, even after multiple treatments. This is because smaller diameter (5-20 microm) PWS blood vessels are difficult to destroy with selective photothermolysis since the volumetric heat generated by absorption of laser light is insufficient to adequately heat the entire vessel wall. The aim of this study was to investigate a potential technique for more efficient photocoagulation of small diameter PWS blood vessels in PWS that respond poorly to selective photothermolysis. STUDY DESIGN/MATERIALS AND METHODS: The blood volume fraction (BVF) in the upper dermis of the forearm of human volunteers was increased by placing an inflated blood pressure cuff on the upper arm. Applied pressures were in the range of 80-100 mm Hg for up to 5 minutes. The increased BVF was determined by matching reflectance spectra measured with that computed using a diffusion model. The impact of increased BVF on purpura formation induced by a 0.45 milliseconds pulsed dye laser (PDL) at 585 nm wavelength was investigated in normal and in PWS skin. RESULTS: In the presence of a 100 mm Hg pressure cuff, the BVF, as determined from the diffusion model, increased by a factor of 3 in the forearm and by 6 in the hand. Increasing BVF by a factor of 3 corresponds to an increase in blood vessel diameters by a factor of radical 3 approximately 1.7. BVF increased at 1-3 minutes after application of the pressure cuff, remained constant at 3-5 minutes, and returned to baseline values at 3 minutes after removal of the pressure cuff. Approximately 40% less radiant exposure was needed to induce the same amount of purpura after PDL irradiation when the blood pressure cuff was used. Applying an 80 mm Hg pressure cuff reduced the required radiant exposure for purpura formation by 30%. Heating of blood vessels was calculated as a function of vessel diameter and of radiant exposure (at 585 nm and at 0.5 and 1.5 milliseconds pulse duration). CONCLUSIONS: Enlarging the vessel lumen, for example, by obstructing venous return, can significantly reduce the "small-vessel-limitation" in PDL treatment of PWS. Dilation of PWS blood vessels enables a more efficient destruction of smaller vessels without increasing the probability of epidermal damage.

Adult↗
PubMed2006

Stochastic models of decisions about motion direction: behavior and physiology.

Roitman and Shadlen [Roitman J. D., & Shadlen M. N. (2002). Response of neurons in the lateral intraparietal area during a combined visual discrimination reaction time task. Journal of Neuroscience, 22, 9475-9489] have published a non-human primate study on visual decision making. They collected both behavioral and neurophysiological data and provided evidence that the data are qualitatively consistent with a mechanism based on accumulating sensory evidence up to a decision threshold. I have previously demonstrated that a time-variant diffusion model can account quite well quantitatively for both the behavioral and the neural data. In this manuscript I discuss how well the data constrains different components and parameters of the computational process. I also discuss the biological plausibility of the model parameters. I will demonstrate that a relatively large class of models, both with and without temporal integration and both stationary and time-variant could account for the behavioral data. Both the single cell recordings from the parietal cortex and previously published data from the extrastriate visual cortex provide additional constraints. Overall, the data favor a diffusion model with time-variant gain and leaky integrators. The integration time constant, however, turns out not to be well-constrained by the data.

Action Potentials↗
PubMed2006

Evaluating a three dimensional model of diffuse photosynthetically active radiation in maize canopies.

Diffuse photosynthetically active radiation (DPAR) is important during overcast days and for plant parts shaded from the direct beam radiation. Simulation of DPAR interception by individual plant parts of a canopy, separately from direct beam photosynthetically active radiation (PAR), may give important insights into plant ecology. This paper presents a model to simulate the interception of DPAR in plant canopies. A sub-model of a virtual maize canopy was reconstructed. Plant surfaces were represented as small triangular facets positioned according to three-dimensionally (3D) digitized data collected in the field. Then a second sub-model to simulate the 3D DPAR distribution in the canopy was developed by dividing the sky hemisphere into a grid of fine cells that allowed for the anisotropic distribution of DPAR over the sky hemisphere. This model, DSHP (Dividing Sky Hemisphere with Projecting), simulates which DSH (Divided Sky Hemisphere) cells are directly visible from a facet in the virtual canopy, i.e. not obscured by other facets. The DPAR reaching the center of a facet was calculated by summing the amounts of DPAR present in every DSH cell. The distribution of DPAR in a canopy was obtained from the calculated DPARs intercepted by all facets in the canopy. This DSHP model was validated against DPAR measurements made in an actual maize (Zea mays L.) canopy over selected days during the early filling stage. The simulated and measured DPAR at different canopy depths showed a good agreement with a R (2) equaling 0.78 (n=120).

Light↗
PubMed1999

Theory of spiral wave dynamics in weakly excitable media: asymptotic reduction to a kinematic model and applications.

In a weakly excitable medium, characterized by a large threshold stimulus, the free end of an isolated broken plane wave (wave tip) can either rotate (steadily or unsteadily) around a large excitable core, thereby producing a spiral pattern, or retract, causing the wave to vanish at boundaries. An asymptotic analysis of spiral motion and retraction is carried out in this weakly excitable large core regime starting from the free-boundary limit of the reaction-diffusion models, valid when the excited region is delimited by a thin interface. The wave description is shown to naturally split between the tip region and a far region that are smoothly matched on an intermediate scale. This separation allows us to rigorously derive an equation of motion for the wave tip, with the large scale motion of the spiral wave front slaved to the tip. This kinematic description provides both a physical picture and exact predictions for a wide range of wave behavior, including (i) steady rotation (frequency and core radius), (ii) exact treatment of the meandering instability in the free-boundary limit with the prediction that the frequency of unstable motion is half the primary steady frequency, (iii) drift under external actions (external field with application to axisymmetric scroll ring motion in three dimensions, and spatial- or/and time-dependent variation of excitability), and (iv) the dynamics of multiarmed spiral waves with the prediction that steadily rotating waves with two or more arms are linearly unstable. Numerical simulations of FitzHugh-Nagumo kinetics are used to test several aspects of our results. In addition, we discuss the semiquantitative extension of this theory to finite cores and pinpoint mathematical subtleties related to the thin interface limit of singly diffusive reaction-diffusion models.

Journal Article↗
PubMed2006

Detection of correlated dynamics on multiple timescales by measurement of the differential relaxation of zero- and double-quantum coherences involving sidechain methyl groups in proteins.

Multiple effects may lead to significant differences between the relaxation rates of zero-quantum coherences (ZQC) and double-quantum coherences (DQC) generated between a pair of nuclei in solution. These include the interference between the anisotropic chemical shifts of the two nuclei participating in formation of the ZQC or DQC, the individual dipolar interactions of each of the two nuclei with the same proton, and the slow modulation of the isotropic chemical shifts of the two nuclei due to conformational exchange. Motional events that occur on a timescale much faster than the rotational correlation time (ps-ns) influence the first two effects, while the third results from processes that occur on a far slower timescale (mus-ms). An analysis of the differential relaxation of ZQC and DQC is thus informative about dynamics on the fast as well as the slow timescales. We present here an experiment that probes the differential relaxation of ZQC and DQC involving methyl groups in protein sidechains as an extension to our recently proposed experiments for the protein backbone. We have applied the methodology to (15)N, (13)C-labeled ubiquitin and used a detailed analysis of the measured relaxation rates using a simple single-axis diffusion model to probe the motional restriction of the C(next)H(next) bond vector where C(next) is the carbon that is directly bonded to a sidechain methyl carbon (C(methyl)). Comparison of the present results with the motional restriction of the C(next)C(methyl) bond (S(axis)(2)) reveals that the single-axis diffusion model, while valid in the fringes of the protein and for shorter chain amino acids, proves inadequate in the central protein core for long chain, asymmetrically branched amino acids where more complex motional models are necessary, as is the inclusion of the possibility of correlation between multiple motional modes. In addition, the present measurements report on the modulation of isotropic chemical shifts due to motion on the mus-ms timescale. Three Leu residues (8, 50, and 56) are found to display these effects. These residues lie in regions where chemical shift modulation had been detected previously both in the backbone and sidechain regions of ubiquitin.

Anisotropy↗
PubMed2002

Studies on rifampicin release from ethylcellulose coated nonpareil beads.

The rifampicin release studies from ethylcellulose coated nonpareil beads were studied. Propylene glycol and Castor oil were used as plasticizers. The in vitro dissolution studies revealed that the release rate is inversely proportional to percent of coating thickness. The release rate also depends on the type of plasticizer used in the coating polymer. The mechanism of drug release follows Higuchi diffusion model. Water vapour permeation studies indicated that the water vapour transport rate through free films is directly related to the drug release rate. DSC thermograms and IR spectras revealed that there is no interaction between rifampicin and other additives. SEM photographs of coated beads, before dissolution and after dissolution, also indicates that the drug release mechanism follows diffusion model.

Cellulose↗
PubMed1985

Vapour and liquid diffusion of model penetrants through human skin; correlation with thermodynamic activity.

This work investigates vapour and liquid permeation through human skin of model penetrants benzyl alcohol, benzaldehyde, aniline, anisole and 2-phenylethanol applied in model vehicles butanol, butyl acetate, isophorone, isopropyl myristate, propylene carbonate, toluene, n-heptane and water. Vapour permeation was a linear function of thermodynamic activity as measured by headspace gas chromatography, except when the vehicle was n-heptane. Liquid permeation did not always follow simple thermodynamic predictions, e.g. for the penetrant, benzyl alcohol, when the vehicle damaged the skin (toluene, n-heptane) or when propylene carbonate produced low fluxes and isopropyl myristate, high values. At comparable thermodynamic activities, liquid fluxes were often ten-fold higher than vapour fluxes, and these differences were reflected by the partition coefficients and the amount of penetrant entering the stratum corneum membrane. The conclusion was that liquid fluxes were membrane controlled, whereas an interfacial effect probably contributed to low vapour permeation.

Benzyl Alcohol↗
PubMed2003

Clarithromycin inhibits overproduction of muc5ac core protein in murine model of diffuse panbronchiolitis.

Long-term treatment of macrolide antibiotics is considered an effective treatment for diffuse panbronchiolitis (DPB). Although hypersecretion is a common feature of this disease, and it is known that macrolides inhibit mucin production, the mechanism of the effect on mucin production is unclear. The aim of our study was to determine the production of muc5ac core protein, a major core protein of mucin in airway secretion, and the effect of clarithromycin treatment on such production in a mouse model mimicking DPB. Alcian blue-periodic acid-Schiff-positive cells were detected in the lungs of Pseudomonas aeruginosa-infected mice. Western blots of these mice showed muc5ac glycoprotein at day 1 and increased progressively from day 4 to day 14 after inoculation of bacteria. Clarithromycin (10 mg. kg-1. day-1 for 7 days) significantly reduced the muc5ac expression at both the mRNA and protein levels. To investigate the role of molecules upstream in muc5ac regulation, we examined the role of mitogen-activated protein kinase. Extracellular signal-regulated kinase 1/2 phosphorylation increased in the infected lung and decreased after treatment. Our results suggest that overproduction of muc5ac plays an important role in the pathogenesis of DPB and that clinical improvement following macrolide therapy seems to involve, at least in part, its inhibition of mucin overproduction, through modulation of intracellular signal transduction.

Animals↗
PubMed2007

Macromolecular transport in heart valves. II. Theoretical models.

This paper proposes a new, two-dimensional convection-diffusion model for macromolecular transport in heart valves based on horseradish peroxidase (HRP) experiments on rats presented in the first of the papers in this series (Part I; Zeng Z, Yin Y, Huang AL, Jan KM, Rumschitzki DS. Am J Physiol Heart Circ Physiol 292: H2664-H2670, 2007). Experiments require two valvular intimae, one underneath each endothelium. Tompkins et al. (Tompkins RG, Schnitzer JJ, Yarmush ML. Circ Res 64: 1213-1223, 1989) found large variations in shape and magnitude in transvalvular (125)I-labeled low-density lipoprotein (LDL) profiles from identical experiments on four squirrel monkeys. Their one-dimensional, uniform-medium diffusion-only model fit three parameters independently for each profile; data variability resulted in large parameter spreads. Our theory aims to explain their data with one parameter set. It uses measured parameters and some aortic values but fits the endothelial mass transfer coefficient (k(a)=k(v)=1.63 x 10(-8) cm/s, where subscripts a and v indicate aortic aspect and ventricular aspect, respectively) and middle layer permeability (K(p(2))=2.28 x 10(-16)cm(2)) and LDL diffusion coefficient [D(2)(LDL)=5.93 x 10(-9) cm(2)/s], using one of Tompkins et al.'s profiles, and fixes them throughout. It accurately predicts Part I's rapid localized HRP leakage spot growth rate in rat leaflets that results from the intima's much sparser structure, dictating its far larger transport parameters [K(p(1))= 1.10 x 10(-12)cm(2), D(1)(LDL/HRP)=1.02/4.09 x 10(-7)cm(2)/s] than the middle layer. This contrasts with large arteries with similarly large HRP spots, since the valve has no internal elastic lamina. The model quantitatively explains all of Tompkins et al.'s monkey profiles with these same parameters. Different numbers and locations of isolated macromolecular leaks on both aspects and different section-leak(s) distances yield all profiles.

Animals↗
PubMed2000

Development and dissipation of Ca(2+) gradients in adrenal chromaffin cells.

We used pulsed laser imaging to measure the development and dissipation of Ca(2+) gradients evoked by the activation of voltage-sensitive Ca(2+) channels in adrenal chromaffin cells. Ca(2+) gradients appeared rapidly (<5 ms) upon membrane depolarization and dissipated over several hundred milliseconds after membrane repolarization. Dissipation occurred with an initial fast phase, as the steep gradient near the membrane collapsed, and a slower phase as the remaining shallow gradient dispersed. Inhibition of active Ca(2+) uptake by the endoplasmic reticulum (thapsigargin) and mitochondria (carbonylcyanide p-trifluoro-methoxyphenylhydrazone/oligomycin) had no effect on the size of Ca(2+) changes or the rate of gradient dissipation, suggesting that passive endogenous Ca(2+) buffers are responsible for the slow Ca(2+) redistribution. We used a radial diffusion model incorporating Ca(2+) diffusion and binding to intracellular Ca(2+) buffers to simulate Ca(2+) gradients. We included a 3D optical sectioning model, simulating the effects of out-of-focus light, to allow comparison with the measured gradients. Introduction of a high-capacity immobile Ca(2+) buffer, with a buffer capacity on the order of 1000 and appropriate affinity and kinetics, approximated the size of the Ca(2+) increases and rate of dissipation of the measured gradients. Finally, simulations without exogenous buffer suggest that the Ca(2+) signal due to Ca(2+) channel activation is restricted by the endogenous buffer to a space less than 1 microm from the cell membrane.

Adenosine Triphosphate↗