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PubMed2005

Real-time observation of molecular motion on a surface.

The laser-induced movement of CO molecules over a platinum surface was followed in real time by means of ultrafast vibrational spectroscopy. Because the CO molecules bound on different surface sites exhibit different C-O stretch vibrational frequencies, the site-to-site hopping, triggered by excitation with a laser pulse, can be determined from subpicosecond changes in the vibrational spectra. The unexpectedly fast motion--characterized by a 500-femtosecond time constant--reveals that a rotational motion of the CO molecules, rather than pure translation, is required for this diffusion process. This conclusion is corroborated by density functional theory calculations.

Journal Article↗
PubMed2006

Formation and positioning of nucleosomes: effect of sequence-dependent long-range correlated structural disorder.

The understanding of the long-range correlations (LRC) observed in DNA sequences is still an open and very challenging problem. In this paper, we start reviewing recent results obtained when exploring the scaling properties of eucaryotic, eubacterial and archaeal genomic sequences using the space-scale decomposition provided by the wavelet transform (WT). These results suggest that the existence of LRC up to distances approximately 20-30 kbp is the signature of the nucleosomal structure and dynamics of the chromatin fiber. Actually the LRC are mainly observed in the DNA bending profiles obtained when using some structural coding of the DNA sequences that accounts for the fluctuations of the local double-helix curvature within the nucleosome complex. Because of the approximate planarity of nucleosomal DNA loops, we then study the influence of the LRC structural disorder on the thermodynamical properties of 2D elastic chains submitted locally to mechanical/topological constraint as loops. The equilibrium properties of the one-loop system are derived numerically and analytically in the quite realistic weak-disorder limit. The LRC are shown to favor the spontaneous formation of small loops, the larger the LRC, the smaller the size of the loop. We further investigate the dynamical behavior of such a loop using the mean first passage time (MFPT) formalism. We show that the typical short-time loop dynamics is superdiffusive in the presence of LRC. For displacements larger than the loop size, we use large-deviation theory to derive a LRC-dependent anomalous-diffusion rule that accounts for the lack of disorder self-averaging. Potential biological implications on DNA loops involved in nucleosome positioning and dynamics in eucaryotic chromatin are discussed.

Base Sequence↗
PubMed1995

Brain stem integration of vocalization: role of the nucleus retroambigualis.

1. The descending pathways that mediate the periaqueductal gray (PAG)-evoked coordination of respiratory, laryngeal, and orofacial activity for vocalization have yet to be delineated. Two hypotheses have been offered. One theory is that this activity is mediated by a diffuse descending projection to parvocellular reticular interneurons, adjacent to the relevant laryngeal and orofacial motoneuronal pools. The second hypothesis is that the motor activity for vocalization is integrated via a projection from the PAG to a caudal medullary column of neurons, the nucleus retroambigualis (NRA). These hypotheses were tested with the use of a series of medullary transections combined with PAG stimulation. Transections that eliminated, in a series of caudal-to-rostral steps, the NRA, also eliminated the PAG-evoked cricothyroid and most of the thyroarytenoid laryngeal motor activity. These results indicate that the final common pathway for much of the laryngeal activity in PAG-evoked vocalization includes un initial synapse in the caudal medulla, presumably in the NRA. 2. The electromyographic changes evoked by microinjection of D,L-homocysteic acid (DLH) in the NRA of the unanesthetized, precollicular decerebrate cat were analyzed in order to delineate the NRA contribution to the coordinated respiratory, laryngeal, and oral muscle changes in vocalization. A total of 415 DLH injection sites were located at or caudal to the level of the obex. Vocalization was evoked at 46 of these sites, which were all confined to a restricted region of the ventrolateral medulla 1-3 mm caudal to the obex. This region corresponded to the rostral half of the NRA and the immediately adjacent medullary tegmentum. 3. In all experiments evidence was obtained that variable muscle activation, rather than functional and integrated muscle patterns, was represented within the NRA. Vocalization evoked by DLH microinjection in the NRA was usually associated with excitation of the cricothyroid, thyroarytenoid, external oblique, internal oblique, internal intercostal, and diaphragm muscles that occurred in a different manner from site to site. That is, injection at sites separated by 0.3-0.5 mm evoked quite different responses. 4. NRA-evoked vocalization was compared with PAG-evoked vocalization using small injections (1.5-4.5 nl) into each region. As well, larger microinjections (15-120 nl) into NRA were made for comparison with previous results from the PAG using similar doses. Within the PAG, stereotyped and relatively "fixed" patterns of muscle activity are represented, whereas within the NRA there was no representation of specific muscle patterns, but rather a partial topographic separation of "premotor neurons" regulating different muscles. Correspondingly, stereotyped vocalizations were never evoked from the NRA. Further, most NRA-evoked vocalizations were unusual in quality and would not be identified generally as feline. 5. Evidence was obtained for a separation of pathways from the PAG regulating sound production and orofacial modulation of that sound. In contrast to the results from the PAG, excitation of NRA neurons rarely evoked activity in the oral muscles (genioglossus or anterior belly of digastric) or orofacial modulation of sound production. 6. Our finding suggests that the NRA serves as an important substrate for the generation of respiratory pressure and larynges adduction, which are two essential aspects of not only vocalization but also several behaviors involving Valsava maneuvers such as coughing, vomiting, and defecation.

Animals↗
PubMed2003

Splenic lymphoma arising in a patient with Gaucher disease. A case report and review of the literature.

Patients with Gaucher disease have an increased risk of malignancies, especially the lymphoreticular type. To our knowledge, this is the first reported case of Gaucher disease diagnosed during the workup and diagnosis of a splenic marginal-zone lymphoma with progression to diffuse large B-cell lymphoma. There are several theories as to how Gaucher disease leads to malignancies. The accumulated glucocerebroside in the reticuloendothelial organs, histologically visible as Gaucher cells, is thought to provide chronic antigenic stimulus to the immune system. Polyclonal hypergammaglobulinemia develops, and monoclonal populations of lymphocytes and plasma cells may arise from this premalignant proliferative state. How Gaucher disease is related to nonlymphoid malignancies remains unclear.

Aged↗
PubMed2005

[Vibrational spectra of thymine calculated from DFT and their comparison with experimental results].

The vibrational spectra of thymine were predicted by density functional theory (DFT). In the calculation B3LYP complex function, and diffuse function and polarization function were added to heavy atoms and light atoms. Taking the effects of H-bonds into consideration, the authors added two water molecules in our calculation and simulated the case of forming H-bonds in crystal thymine. Whilst the Raman and infrared spectra of thymine were recorded, and the spectra of thymine calculated from DFT agree with the experimental results. The calculation results in the present paper are more approximate to the experimental data than ever reported. The vibrational modes of thymine were assigned.

Crystallization↗
PubMed1985

Identification and its vicissitudes.

The treatment of 'identification' in the American literature is conveniently divided into three eras: (1) The Pioneers (1915-1945). (2) The Synthesizers (1945-1975). (3) Current Commentators (1975-1985). For the Pioneers, concepts and terminology were diffuse, reflecting the diversity of clinical material, methodology and theories accompanying the rapid expansion in analytic experience over a half century. The achievement of an integrated survey by Otto Fenichel in 1945 marked the transition from a fragmentary to a synthesizing approach to identification and its inherent aspects of incorporation and ejection, introjection and projection, internalization and externalization. The Synthesizers brought to the force developmental and adaptive viewpoints which traced along longitudinal lines the processes of maturation from the earliest mother--child unit to later phases of life. The differentiation of the self (one's own person) from systemic functioning within the Freudian ego (Hartmann) and a corresponding importance accorded to reciprocal self-object relationships, proved eventful for the conceptualization of identification. A broadening of traditional analytic frameworks with respect to both normal and abnormal forms of behaviour was a correlated achievement in placing identificatory processes between the inner and outer worlds. The Commentators extended the synthesizing trends, reviewed historical perspectives accordingly, and selected such areas as individual and group identify, the correlation of direct observation with analytic reconstructions and the personal and professional functioning of the analyst himself for special study.

History, 20th Century↗
PubMed1977

The effect of Candida albicans on the isolation of N. gonorrhoeae.

Recently, several studies have reported that strains of Candida albicans and perhaps other noraml bacterial flora are capable of inhibiting the growth of Neisseria gonorrhoeae in vitro, and it is possible that this may occur in vivo as well. This possible antagonism between N. gonorrhoeae and normal flora microorganisms poses many questions regarding the reliable laboratory diagnosis of gonorrhea. Mixed cultures of C. albicans and N. gonorrhoeae were grown together on GC base agar plates with varying concentrations of nystatin. Recovery of N. gonorrhoeae was improved as nystatin concentration was increased to 25 IU/ml, while growth of C. albicans was effectively inhibited. At concentrations of 50 and 100 IU/ml nystatin also began to inhibit N. gonorrhoeae. There was a noticeable decrease of nystatin bioactivity against C. albicans when the GC plates were stored at 4 C, thus making it more difficult to isolate N. gonorrhoeae. Growth curves of C. albicans and N. gonorrhoeae grown together in liquid medium did not significantly differ from growth curves of the individual organisms. Statistical analysis of our findings does not support the theory that strains of C. albicans produce a soluble diffusible factor that is inhibitory to N. gonorrhoeae.

Amphotericin B↗
PubMed1980

[Critical considerations on psychoanalysis, in relation to its possible introduction in the National Health Service].

The Author points out that the psycho-analysis and the psychotherapy of analytical type have been objects of severe criticisms, not always objective and often contradictory. The medical world opposed or ignored at the beginning the Freudian theories and those from them deriving. At present the diffusion of the psychotherapy finds obstacles both in the resistances offered by the medical and social context to which it is addressed, and in the dogmatism and in the scarce flexibility of some psychotherrapeutic schools and currents. Above all the A. focuses on this last aspect, works a review of the shrewdest and most documented criticisms aroused to psycho-analysis and enunciates, lastly, the postulates required in order to have any psychotherapeutic method considered as scientifically trustworthy. This last requisite is indispensable to the introduction of the psychotherapy into the National Health Service.

Attitude of Health Personnel↗
PubMed1997

Molecular characterisation of Lyme disease borreliae using RAPD analysis and 16S rDNA sequencing.

Here we report the use of random amplified polymorphic DNAs (RAPDs) and sequence analysis of the genes encoding for the small subunit ribosomal RNA (16S rDNA) for the characterisation of Borrelia burgdorferi sensu lato strains recovered from Ixodes ricinus and from Lyme disease patients. All strains examined were assigned to the species Borrelia garinii. However, both RAPDs and 16S rDNAs revealed a level of genetic variation among the strains which appears higher than expected for a bacterial species. In addition, the data obtained agree with the clonal theory applied to Borrelia burgdorferi s.l. for explaining some traits of its epidemiology. According to this theory, particular strains should spread rapidly, leading to the diffusion of bacteria with a particular chromosomal genotype. Our results reveal high genetic variation even among strains isolated in the same period from a restricted geographic area. Moreover, the data here reported indicate that clonal diffusion of antigenic characteristics could also occur.

Borrelia↗
PubMed2002

Non-invasive neuroimaging using near-infrared light.

This article reviews diffuse optical brain imaging, a technique that employs near-infrared light to non-invasively probe the brain for changes in parameters relating to brain function. We describe the general methodology, including types of measurements and instrumentation (including the tradeoffs inherent in the various instrument components), and the basic theory required to interpret the recorded data. A brief review of diffuse optical applications is included, with an emphasis on research that has been done with psychiatric populations. Finally, we discuss some practical issues and limitations that are relevant when conducting diffuse optical experiments. We find that, while diffuse optics can provide substantial advantages to the psychiatric researcher relative to the alternative brain imaging methods, the method remains substantially underutilized in this field.

Brain↗
PubMed2000

Reaction-controlled diffusion

The dynamics of a coupled two-component nonequilibrium system is examined by means of continuum field theory representing the corresponding master equation. Particles of species A may perform hopping processes only when particles of different type B are present in their environment. Species B is subject to diffusion-limited reactions. If the density of B particles attains a finite asymptotic value (active state), the A species displays normal diffusion. On the other hand, if the B density decays algebraically approximately t(-alpha) at long times (inactive state), the effective attractive A-B interaction is weakened. The combination of B decay and activated A hopping processes gives rise to anomalous diffusion, with mean-square displacement (A)(t)(2)> approximately t(1-alpha) for alpha<1. Such algebraic subdiffusive behavior ensues for nth-order B annihilation reactions (nB-->) with n>/=3, and n=2 for d<2. The mean-square displacement of the A particles grows only logarithmically with time in the case of B pair annihilation (n=2) and d>/=2 dimensions. For radioactive B decay (n=1), the A particles remain localized. If the A particles may hop spontaneously as well, or if additional random forces are present, the A-B coupling becomes irrelevant, and conventional diffusion is recovered in the long-time limit.

Journal Article↗
PubMed2002

Self-diffusion and collective diffusion in a model viscoelastic system.

We use dynamic light scattering (DLS) and fluorescence recovery after pattern photobleaching (FRAPP) to investigate the dynamics of a model transient network made of an oil-in-water droplet microemulsion to which small amounts of a telechelic polymer are added. The DLS correlation functions exhibit three relaxation modes. The two first modes can be interpreted quantitatively in the frame of the classical De Gennes-Brochard theory of DLS in viscoelastic system. The third, slower mode is diffusive and arises from the ternary character (droplets, polymers, and water) of the system. By contrast, the pattern relaxation in FRAPP exhibits a single-, slow-exponential decay with a characteristic time proportional to the squared inverse scattering vector: the corresponding self-diffusion coefficient of the droplets is found to be close to the diffusion coefficient characterizing the third mode in DLS. We interpret these results in terms of the coupled relaxation of the concentration fluctuations of the polymers and the droplets.

Journal Article↗
PubMed1999

Translational diffusion of flexible lipid chains in a Langmuir monolayer: a dynamic Monte Carlo study.

We report a computer simulation study of the lateral diffusion of conformationally disordered lipid molecules in a monolayer structure. The simulations were carried out with dynamic Monte Carlo methods, employing two different representations of the internal motions of the lipid chains. The classical Cohen-Turnbull theory is found to provide a good description of the simulated lateral diffusion coefficients at moderate densities. The substantial deviations found at low densities are attributed to the small density fluctuations needed to create the free volume required for the lateral diffusion process.

Computer Simulation↗
PubMed2002

A lattice kinetic scheme for incompressible viscous flows with heat transfer.

A lattice kinetic scheme for incompressible viscous flows with heat transfer is developed based on the lattice Boltzmann method. In the new scheme, macroscopic variables are calculated without velocity distribution functions. Thus, the scheme can save computer memory because there is no need to store the velocity distribution functions. Governing equations for the macroscopic variables are obtained by applying the asymptotic theory. The continuity equation, the Navier-Stokes equations, and the convection-diffusion equation for fluid temperature are obtained with relative errors of O(epsilon2), where epsilon is a small parameter that is of the same order as a lattice spacing and is related to a relaxation parameter. In order to verify the accuracy of the scheme, natural convection flows in a square cavity are simulated, and the calculated results are in good agreement with available standard results.

Colloids↗
PubMed2006

Application of Fokker-Planck-Kramers equation treatment for short-time dynamics of diffusion-controlled reaction in supercritical Lennard-Jones fluids over a wide density range.

The validity of a Fokker-Planck-Kramers equation (FPKE) treatment of the rate of diffusion-controlled reaction at short times [K. Ibuki and M. Ueno, J. Chem. Phys. 119, 7054 (2003)] is tested in a supercritical Lennard-Jones fluid over a wide density range by comparing it with the Langevin dynamics and molecular dynamics simulations and other theories. The density n range studied is 0.323n(c)< or =n< or =2.58n(c) and the temperature 1.52T(c), where n(c) and T(c) are the critical density and temperature, respectively. For the rate of bimolecular reactions, the transition between the collision-limited and diffusion-limited regimes is expected to take place in this density range. The simulations show that the rate constant decays with time extensively at high densities, and that the magnitude of decay decreases gradually with decreasing density. The decay profiles of the rate constants obtained by the simulations are reproduced reasonably well by the FPKE treatment in the whole density range studied if a continuous velocity distribution is used in solving the FPKE approximately. If a discontinuous velocity distribution is used instead of the continuous one, the FPKE treatment leads to a rate constant much larger than the simulation results at medium and low densities. The rate constants calculated from the Smoluchowski-Collins-Kimball (SCK) theory based on the diffusion equation are somewhat smaller than the simulation results in medium and low densities when the intrinsic rate constant is chosen to adjust the steady state rate constant in the low density limit to that derived by the kinetic collision theory. The discrepancy is relatively small, so that the SCK theory provides a useful guideline for a qualitative discussion of the density effect on the rate constant.

Journal Article↗
PubMed2005

Multifractality in intracellular enzymatic reactions.

Enzymatic kinetics adjust well to the Michaelis-Menten paradigm in homogeneous media with dilute, perfectly mixed reactants. These conditions are quite different from the highly structured cell plasm, so applications of the classic kinetics theory to this environment are rather limited. Cytoplasmic structure produces molecular crowding and anomalous diffusion of substances, modifying the mass action kinetic laws. The reaction coefficients are no longer constant but time-variant, as stated in the fractal kinetics theory. Fractal kinetics assumes that enzymatic reactions on such heterogeneous media occur within a non-Euclidian space characterized by a certain fractal dimension, this fractal dimension gives the dependence on time of the kinetic coefficients. In this work, stochastic simulations of enzymatic reactions under molecular crowding have been completed, and kinetic coefficients for the reactions, including the Michaelis-Menten parameter KM, were calculated. The simulations results led us to confirm the time dependence of michaelian kinetic parameter for the enzymatic catalysis. Besides, other chaos related phenomena were pointed out from the obtained KM time series, such as the emergence of strange attractors and multifractality.

Animals↗
PubMedDate not supplied

The effect of ultrafiltration on dialysance. Mathematical theory and experimental verification.

It is known that convective transport (ultrafiltration, QF) augments diffusive transport. This augmentation achieves great importance as solute molecular weight increases. Previous mathematical treatments of dialysance (D) have provided the relationship between D and blood flow rate (QB), dialysate flow rate (QD), and dialyzer membrane surface area permeability product (KoA), in the limit of QF = 0. The authors derived the relationship between D (defined as D') and QB, QD, and KoA for the general case of QF greater than or equal to 0: D' = X-Y/In X/Y . [(1-ó) QF + KoA] for X = X(D', QF, QD) = 1 - [D'/QD + QF] Y = Y(D', QF, QB) = D'-QB/QF-QB ó = the Staverman reflection coefficient. This equation demonstrates an approximate linear increase in D' as QF increases. Experimental verification is provided by in vivo studies of dialysis patients in which the dialysance of vancomycin doubles as QF is increased from 0 to 50. Because D' varies linearly with QF, this allows for the determination of KoA and ó. Using the Cobe 500HG Hemophan membrane, KoA for vancomycin was determined to be 6.54 and ó = 0.88.

Diffusion↗
PubMed2004

Self-diffusion in solutions of a 20 base pair oligonucleotide: effects of concentration and ionic strength.

The long-time self-diffusion coefficients of a 20 base pair duplex oligonucleotide are measured as functions of 20-mer and added NaCl salt concentrations. The self-diffusion coefficients decrease monotonically with increasing 20-mer concentrations for the high-added salt sample and display non-monotonically decreasing 20-mer concentration dependences at lower added salt concentrations. The non-monotonic behavior is attributed to the opposing effects of the tendency to increase the interactions between 20-mers as the concentration is increased and to a decrease in the extent of the Coulomb forces as counterions from the 20-mer increasingly screen them. Attempts to account for the effect of the Coulomb forces on the self-diffusion coefficients by using effective dimensions in the hard rod theory give good agreement with experiment at the highest salt concentration studied. For the lower salt concentrations there appear to be two scaling regimes--one at low polyion concentration in which the high salt scaling of the rod dimensions by adding the Debye screening to the length and diameter of the rod is appropriate and one at high polyion concentrations where the scaling of the dimensions is the addition of 1/2 the Debye screening length. Estimates of the "overlap" concentration C*=1/L(eff) indicate that the non-monotonic decrease occurs at concentrations lower than C*. Finally, the fluorescence correlation spectroscopy self-diffusion coefficients measured here are compared with the mutual diffusion coefficients measured by dynamic light scattering.

Journal Article↗