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PubMed2004

Structural characterization of an intermolecular RNA-RNA interaction involved in the transcription regulation element of a bipartite plant virus.

The 34-nucleotide trans-activator (TA) located within the RNA-2 of Red clover necrotic mosaic virus folds into a simple hairpin. The eight-nucleotide TA loop base pairs with eight complementary nucleotides in the TA binding sequence (TABS) of the capsid protein subgenomic promoter on RNA-1 and trans-activates subgenomic RNA synthesis. Short synthetic oligoribonucleotide mimics of the RNA-1 TABS and the RNA-2 TA form a weak 1:1 bimolecular complex in vitro with a K(a) of 5.3 x 10(4) M(-1). K(a) determination for a series of RNA-1 and RNA-2 mimic variants indicated optimum stability is obtained with seven-base complementarity. Thermal denaturation and NMR show that the RNA-1 TABS 8mers are weakly ordered in solution while RNA-2 TA oligomers form the predicted hairpin. NMR diffusion studies confirmed RNA-1 and RNA-2 oligomer complex formation in vitro. MC-Sym generated structural models suggest that the bimolecular complex is composed of two stacked helices, one being the stem of the RNA-2 TA hairpin and the other formed by the intermolecular base pairing between RNA-1 and RNA-2. The RCNMV TA structural model is similar to those for the Simian retrovirus frameshifting element and the Human immunodeficiency virus-1 dimerization kissing hairpins, suggesting a conservation of form and function.

Base Pairing↗
PubMed2001

Kinetic theory of point vortices: diffusion coefficient and systematic drift.

We develop a kinetic theory for point vortices in two-dimensional hydrodynamics. Using standard projection operator techniques, we derive a Fokker-Planck equation describing the relaxation of a "test" vortex in a bath of "field" vortices at statistical equilibrium. The relaxation is due to the combined effect of a diffusion and a drift. The drift is shown to be responsible for the organization of point vortices at negative temperatures. A description that goes beyond the thermal bath approximation is attempted. A new kinetic equation is obtained which respects all conservation laws of the point vortex system and satisfies a H theorem. Close to equilibrium, this equation reduces to the ordinary Fokker-Planck equation.

Journal Article↗
PubMed2005

Crystallization and preliminary X-ray diffraction analysis of a cold-adapted catalase from Vibrio salmonicida.

Catalase (EC 1.11.1.6) catalyses the breakdown of hydrogen peroxide to water and molecular oxygen. Recombinant Vibrio salmonicida catalase (VSC) possesses typical cold-adapted features, with higher catalytic efficiency, lower thermal stability and a lower temperature optimum than its mesophilic counterpart from Proteus mirabilis. Crystals of VSC were produced by the hanging-drop vapour-diffusion method using ammonium sulfate as precipitant. The crystals belong to the monoclinic space group P2(1), with unit-cell parameters a = 98.15, b = 217.76, c = 99.28 A, beta = 110.48 degrees. Data were collected to 1.96 A and a molecular-replacement solution was found with eight molecules in the asymmetric unit.

Adaptation, Biological↗
PubMedDate not supplied

Visual simulation of heat shimmering and mirage.

We provide a physically-based framework for simulating the natural phenomena related to heat interaction between objects and the surrounding air. We introduce a heat transfer model between the heat source objects and the ambient flow environment, which includes conduction, convection, and radiation. The heat distribution of the objects is represented by a novel temperature texture. We simulate the thermal flow dynamics that models the air flow interacting with the heat by a hybrid thermal lattice Boltzmann model (HTLBM). The computational approach couples a multiple-relaxation-time LBM (MRTLBM) with a finite difference discretization of a standard advection-diffusion equation for temperature. In heat shimmering and mirage, the changes in the index of refraction of the surrounding air are attributed to temperature variation. A nonlinear ray tracing method is used for rendering. Interactive performance is achieved by accelerating the computation of both the MRTLBM and the heat transfer, as well as the rendering on contemporary graphics hardware (GPU).

Algorithms↗
PubMed1970

Bacteriocin Typing of Vibrio cholerae.

Bacteriocins of Vibrio cholerae have been demonstrated against enterobacterial and vibrio indicator organisms by conventional techniques. Abundant bacteriocin production took place on casein hydrolysate-yeast extract, tryptic soy, digest broth, proteose-peptone, and neopeptone agars. Essential factors were a citrate-phosphate buffer concentration of 0.5 to 0.7%, at pH 7.5 to 7.6, and cold shock. Thermal treatment of indicator organisms at 45 C for 12 min increased the percentage of typable strains. The bacteriocins of V. cholerae appeared to be powerful diffusible bactericidal agents. By using 8 indicator strains, 11 bacteriocin types have been recognized among 425 strains, of which 87% are typable at present.

Journal Article↗
PubMed2004

Formation of novel rare-gas molecules in low-temperature matrices.

Progress in the study of a new class of chemically bound compounds of noble-gas atoms is reviewed. The focus is on rare-gas molecules of the form HNgY, where Ng is a noble-gas atom and Y is an electronegative group, prepared by photolysis of HY in the rare-gas matrix. Other related types of new molecules of noble-gas atoms are discussed as well. Topics discussed in this review include: (a) The nature of bonding and the energetic stability of the compounds. (b) The vibrational spectroscopy of the molecules, and its role in identification of the species. (c) The mechanism and dynamics of photochemical formation of HNgY in the matrix, and the pathways for thermal and infrared (IR)-induced decomposition. Specifically, attention is given to the issue of "direct" formation following photolysis of HY versus "delayed" formation involving H atom diffusion. (d) Molecules of the lighter rare gases Ar, Ne, and He, focusing on the experimentally prepared HArF and on theoretical predictions suggesting the existence of other molecules. (e) The most-recently discovered photochemically induced insertion compounds of Ng into hydrocarbons, such as HXeCCH. (f) Clusters of HNgY with other molecules. The possible existence of neat aggregates and crystals of HNgY. The reviewed state-of-the-art suggests this field is at an early stage of development with major open questions bearing on the surprising properties of the molecules and on the formation mechanisms. These are part of the challenge for the future.

Journal Article↗
PubMed1994

Improved ventilatory function in burn patients using volumetric diffusive respiration.

BACKGROUND: Volumetric diffusive respiration (VDR) offers theoretical advantages over conventional mechanical ventilation (CV) by using lower airway pressures, recruiting alveoli, and mobilizing secretions. STUDY DESIGN: Forty-eight thermally injured pediatric patients with failing respiratory status were changed from CV to VDR. Data were obtained just before transition for CV and after stabilization on VDR, within six hours of transition. RESULTS: Both ventilation and oxygenation were significantly improved with PaCO2 decreasing from 47 +/- 3 to 39 +/- 11 mm Hg and PaO2 increasing from 105 +/- 8 to 171 +/- 12 mm Hg after transition to VDR. Treatment with the VDR ventilator also resulted in a significant decrease in peak inspiratory pressures (PIP) from 52 +/- 2 to 38 +/- 2 cm H2O. The PaO2 to FiO2 ratio increased from 189 +/- 16 using CV, to 329 +/- 21 using VDR, suggesting an improvement in the ventilation and perfusion matching. Ventilatory efficiency, measured by the PaO2/FiO2/PIP ratio, greatly improved after transition from CV to VDR with fraction of inspired oxygen increasing from 3.9 +/- 0.4 to 10.3 +/- 1.0. Hemodynamic function (blood pressure and pulse rate) were not adversely affected by VDR. CONCLUSIONS: The VDR ventilator is more effective than conventional ventilation for maintaining optimal gas exchange at lower airway pressures in thermally injured pediatric patients.

Adolescent↗
PubMed1990

[Diffusion bonding of hydroxyapatite ceramics and biometals].

To improve the mechanical characteristics of hydroxyapatite (HAP) ceramics, a metal-ceramic composite formed by a solid state direct diffusion bonding system was studied. The joining treatment was carried out of a high vacuum and high temperature, for the bioactive ceramics (HAP) and the following biometals; platinum, gold-platinum alloy, titanium and titanium alloys, zirconium, niobium and aluminium alloy. The effects of the variations of thermal expansion mismatch and the interactive reactions at the interface were investigated by fractographic observation (SEM), X-ray diffraction method and EPMA analysis. On some of these joining combinations, the bonding strength had the same bonding strength as the adhesive materials. The results of interface observations showed that the bonding strength is affected by the interface reactions and the diffusion phenomena.

Adhesiveness↗
PubMed2004

Adsorption, diffusion, and recombination of hydrogen on pure and boron-doped graphite surfaces.

Boron inserted as impurity by substitution of carbon atoms in graphite is known to modify the reactivity of the surface in interaction with hydrogen. Boron induces a better H retention capability in graphite while it makes easier the recombination into molecular hydrogen under heating in thermal-desorption experimental conditions. It has already been calculated that boron modifies the electronic structure of the surface, which results in an increase of the adsorption energy for H. This result seems in good agreement with the better retention for H in doped graphite, but contradictory with the easier recombination observed. The aim of this work is to dismiss this contradiction by elucidating the modifications induced by boron in the recombination mechanism. We studied the diffusion of H on pure and boron-doped graphite in the density functional theory framework. We determined a diffusionlike mechanism leading to molecular hydrogen formation. Finally, we have shown the fundamental modifications induced by boron on the [0001] graphite surface reactivity. From these calculations it stands out that recombination is the result of desorption on pure graphite and diffusion on B-doped surfaces, while the activation energy for the rate limiting step is half reduced by boron. The results are compared to experimental observations. The connection between the cluster and periodic quantum modes for graphite is also discussed.

Journal Article↗
PubMed1986

Involvement of the dorsolateral funiculus in the descending spinal projections responsible for diffuse noxious inhibitory controls in the rat.

Recordings were made from convergent neurons in the lumbar dorsal horn of the spinal cord of the rat. These neurons were activated by both innocuous and noxious mechanical stimuli applied to their excitatory receptive fields located on the extremity of the hindpaw. Transcutaneous application of suprathreshold 2-ms square-wave electrical stimuli to the center of the excitatory field, resulted in responses to C-fiber activation being observed. This type of response was inhibited by applying a noxious thermal conditioning stimulus on the muzzle. The immersion of the muzzle in a 52 degrees C waterbath resulted in a strong reduction of the response during the application of the noxious conditioning stimulus and this was followed by long lasting poststimulus effects. Such inhibitory processes have been termed diffuse noxious inhibitory controls (DNIC). The effects on these inhibitions of lesions including the dorsolateral funiculus (DLF) were investigated in acute experiments: tests were performed before and at least 30 min after the DLF lesion. A lesion including the DLF ipsilateral to the neuron under study completely abolished the inhibitory processes triggered from the muzzle. Concomitantly, a facilitation of C-fiber responses was observed. Nevertheless, DNIC was still impaired even using a juxtathreshold current to elicit a weak C-fiber response. To ascertain further the main, if not entire, participation of the ipsilateral DLF in the descending projections responsible for the heterotopic inhibitory processes, the effects of a lesion of the contralateral DLF were investigated. Neither the inhibitory processes nor the unconditioned C-fiber responses were altered by this procedure. Again, a second lesion including the ipsilateral DLF induced a blockade of DNIC. It is concluded that the descending projections involved in the triggering of DNIC are mainly, if not entirely, confined to the DLF ipsilateral to the neuron under study. The contralateral DLF did not appear to play a role in these processes.

Animals↗
PubMed2000

Magnetic resonance temperature imaging for guidance of thermotherapy.

Continuous thermometry during a hyperthermic procedure may help to correct for local differences in heat conduction and energy absorption, and thus allow optimization of the thermal therapy. Noninvasive, three-dimensional mapping of temperature changes is feasible with magnetic resonance (MR) and may be based on the relaxation time T(1), the diffusion coefficient (D), or proton resonance frequency (PRF) of tissue water. The use of temperature-sensitive contrast agents and proton spectroscopic imaging can provide absolute temperature measurements. The principles and performance of these methods are reviewed in this paper. The excellent linearity and near-independence with respect to tissue type, together with good temperature sensitivity, make PRF-based temperature MRI the preferred choice for many applications at mid to high field strength (>/= 1 T). The PRF methods employ radiofrequency spoiled gradient-echo imaging methods. A standard deviation of less than 1 degrees C, for a temporal resolution below 1 second and a spatial resolution of about 2 mm, is feasible for a single slice for immobile tissues. Corrections should be made for temperature-induced susceptibility effects in the PRF method. If spin-echo methods are preferred, for example when field homogeneity is poor due to small ferromagnetic parts in the needle, the D- and T(1)-based methods may give better results. The sensitivity of the D method is higher that that of the T(1) methods provided that motion artifacts are avoided and the trace of D is evaluated. Fat suppression is necessary for most tissues when T(1), D, or PRF methods are employed. The latter three methods require excellent registration to correct for displacements between scans.

Animals↗
PubMed2006

Effect of poloxamers on nifedipine microparticles prepared by Hot Air Coating technique.

The Hot Air Coating (HAC) technique was used to prepare microparticles consisting of 30% nifedipine coated with different lipid mixtures. Cetearyl alcohol or cetearyl alcohol and 5% or 15% of a poloxamer (Pluronic F68 or Pluronic F127) were used as excipients. HAC products were analyzed in terms of morphology, flowability, thermal properties and nifedipine release behaviour, in order to elucidate the role played by the Pluronics on the physico-chemical and pharmaceutical characteristics of microparticles. HAC particles were spherical and their surface appeared scale-worked; thermal studies demonstrated the existence of relevant interactions among the system components and the dissolution experiments led to the hypothesis that the drug is released primarily by diffusion through the lipid coating: the poloxamer and its concentration have a significant influence on the pharmaceutical properties of the dosage form, as shown by the a parameter of Weibull model.

Algorithms↗
PubMed2006

Evidence that amorphous water below 160 K is not a fragile liquid.

We have examined transport mechanisms in amorphous solid water (ASW) by studying thermal desorption of layered nanoscale films of CCl4 and labeled ASW. The interlayer mixing observed near T approximately 150-160 K is inconsistent with a mechanism involving diffusion through a dense phase. Instead, intermixing occurs via vapor-phase transport through an interconnected porous network created within the film during crystallization. As a consequence, the self-diffusivity of ASW is significantly smaller than previously thought, indicating that water undergoes either a glass transition or a fragile-to-strong transition at a temperature above 160 K.

Letter↗
PubMed2003

Kinetics of the superficial perfusion and temperature in connection with photodynamic therapy of basal cell carcinomas using esterified and non-esterified 5-aminolaevulinic acid.

BACKGROUND: Photodynamic therapy (PDT) is a local treatment modality with increasing indications for various malignant and non malignant diseases. The treatment parameters have not yet been optimized as there is a need for a better understanding of the process. The skin is an important target and serves as a good model for monitoring and evaluating the interaction of light with biological tissue. OBJECTIVES: The tissue perfusion and the temperature of basal cell carcinomas were measured in connection with PDT in order to investigate the biological mechanisms involved. METHODS: An infrared camera was used during the treatment to measure skin temperature and a laser Doppler perfusion imaging device was used to image the superficial perfusion before and after treatment. Six hours after topical application of 5-aminolaevulinic acid (ALA) or methyl esterified ALA (ALA-ME), 38 basal cell carcinomas were treated using light from a diode laser at 633 nm. RESULTS: In the lesions, the perfusion immediately after PDT was similar to that before PDT. One hour after the treatment the perfusion in the lesion was increased 50% compared with before PDT. However, in the skin surrounding the lesions the perfusion was doubled immediately after PDT and was still increasing 1 h after treatment. A temperature increase in the lesions of about 1-3 degrees C was observed for light fluence rates of 100-150 mW cm-2. In all patients treated, a diffuse temperature increase was visible outside the lesions. In some of the patients, the outlines of the blood vessels surrounding the treated lesions became visible in the thermal images. Measurements of temperature on healthy volunteers not administered photosensitizer, but illuminated with light of the same fluence rate, showed a similar increase in temperature in the illuminated spots. However, no temperature increase was observed outside the illuminated area. No statistically significant differences were found between the measurements on patients treated with ALA and ALA-ME. CONCLUSIONS: The increased perfusion in the area surrounding the lesions after PDT, as seen by perfusion and temperature measurements, is the result of an inflammatory reaction to the PDT process. However, directly after PDT the perfusion in the lesions was the same as before irradiation. The combination of these observations suggests the presence of local blood stasis during and immediately after the treatment. The temperature measurements showed that the increased temperature was well below the temperature limit of hyperthermal damage. Furthermore, the measurements indicate that the increase in temperature was primarily a consequence of the heat absorbed in the tissue.

Adult↗
PubMed2005

Static and dynamical properties of heavy water at ambient conditions from first-principles molecular dynamics.

The static and dynamical properties of heavy water have been studied at ambient conditions with extensive Car-Parrinello molecular-dynamics simulations in the canonical ensemble, with temperatures ranging between 325 and 400 K. Density-functional theory, paired with a modern exchange-correlation functional (Perdew-Burke-Ernzerhof), provides an excellent agreement for the structural properties and binding energy of the water monomer and dimer. On the other hand, the structural and dynamical properties of the bulk liquid show a clear enhancement of the local structure compared to experimental results; a distinctive transition to liquidlike diffusion occurs in the simulations only at the elevated temperature of 400 K. Extensive runs of up to 50 ps are needed to obtain well-converged thermal averages; the use of ultrasoft or norm-conserving pseudopotentials and the larger plane-wave sets associated with the latter choice had, as expected, only negligible effects on the final result. Finite-size effects in the liquid state are found to be mostly negligible for systems as small as 32 molecules per unit cell.

Journal Article↗
PubMed1999

Late stage kinetics of a phase separation induced by a cw laser wave in binary liquid mixtures.

cw laser waves can be used to locally induce phase transitions. We investigate experimentally and theoretically a laser-driven liquid-liquid phase separation in a micellar phase of microemulsion and analyze its late stage kinetics. The medium is optically quenched in composition in the metastable region of the phase diagram. Two processes can lead to these concentration variations: electrostriction and thermodiffusion. The first originates from induced dipolar couplings in a field gradient. The second corresponds to a variation in concentration driven by a small thermal gradient. Since the nucleated droplets are optically trapped by the beam, we show that it becomes possible to experimentally analyze an academic situation, i.e., the diffusion-driven growth of a single droplet in compensated gravity. The late stage of this kinetics can be divided into two parts, a bulk behavior and a regime controlled by the finite transverse size of the beam. The bulk regime is totally analogous to that observed in classical situations (R proportional, variant t(1/3), where R is the droplet radius and t the time), and the scaling of the amplitudes in terms of reduced length and time scales is in total agreement with the expected behaviors for fluids belonging to the same Ising universality class. Moreover, the Gaussian beam behaves as an optical bottle with "soft walls" in which the absence of rigid boundaries, and thus of wetting couplings, allows an intrinsic description of the influence of finite-size effects on the kinetics. The beam size breaks the dynamic universality when the growing domains start to feel it. We experimentally investigate the resulting slowing down, and a diffusion-driven model of the growth inside a laser wave is built for comparison. The good agreement observed for the bulk regime and during its modification induced by finite-size effects opens a promising field for the development of this new application of laser waves to control out-of-equilibrium liquid mixtures.

Journal Article↗
PubMed2001

Heat transfer and convection onset in a compressible fluid: 3He near the critical point.

Heat transport in 3He above its critical temperature Tc was studied along the critical isochore in a flat Rayleigh-Bénard cell (height h=1 mm, diameter D=57 mm). The range of the reduced temperature epsilon was 5 x 10(-4)< or = epsilon < or =2 x 10(-1). The temperature difference deltaT(t) across the fluid layer as a function of the time t was measured for different values of the heat current q until steady state was reached. The crossover was observed from the regime dominated by the Rayleigh criterion for the convection onset to that controlled by the adiabatic temperature gradient (ATG), or "Schwarzschild criterion," in good quantitative agreement with predictions. The slope of the convective heat current versus the reduced Rayleigh number was found to be independent of compressibility and the same as for still less compressible fluids. Plots of Nu versus Ra, both corrected for the ATG effect, are presented for early-stage convective turbulence (1 x 10(5)<Ra<5 x 10(8)), with unexpected results for the highest values of Pr approximately 590. The evolution of the transients deltaT(t) upon turning q on and off are described. In the nonconvective regime, the observed transient relaxation curve agrees quantitatively with predictions. In the convective regime, the shape of deltaT(t) changes qualitatively with increasing q and with epsilon. In the Appendix, new data for the thermal conductivity are presented, the impact of the "piston effect" on the temperature profiles inside the fluid is described, and the derivation for deltaT(t) in the diffusive regime is outlined.

Journal Article↗
PubMed2002

Dangling bond deflection model: growth of gel network with loop structure.

It has been shown that the closed-loop structure in the model gel networks is responsible for their stiffness. However, the creation of loops has been underestimated in most of the existing kinetic aggregation models [e.g., DLCA (diffusion-limited cluster-cluster aggregation) and derivatives]. A dangling bond deflection (DEF) mechanism is proposed to model the fluctuation of dangling branches or dead ends under thermal excitation. The random deflections of the dangling branches can create loops in the network by forming intracluster bonds, and proceed during both the gelling and aging processes. The resulting DLCADEF networks have extensive loop structure with a negligible number of dangling branches. Its growth kinetics and fractal behavior resemble those of real gels, including volume-invariant gel time and fractal dimension of about 2. The DLCADEF model is the first attempt to model the gel growth with loop formation by the physically realistic fluctuation mechanism. The mechanical properties of the resulting networks will be studied and verified by comparison with real gels.

Journal Article↗