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PubMed1996

Fast dynamic imaging using two reference images.

This paper presents a fast dynamic imaging method which is characterized by the acquisition of two high-resolution reference images and a sequence of low-resolution dynamic data sets. Image reconstruction is accomplished using a generalized series based algorithm. Experimental results demonstrate that dynamic images with high temporal resolution can be obtained while maintaining excellent spatial resolution. This method will be useful for a variety of dynamic imaging applications including contrast-enhanced dynamic imaging and functional brain studies.

Algorithms↗
PubMed2005

Dynamic dephasing changes in developing ischemic cerebral infarction in rats studied by Carr-Purcell T2 magnetic resonance imaging.

Carr-Purcell (CP) T(2) MRI with adiabatic pulses, acquired with varying interecho interval (tau(CP)), was used to study the time course of T(2) and relative dynamic-dephasing contrast in the rat brain. Exposure to 30 min of middle cerebral artery occlusion (MCAo) resulted in an irreversible increase in absolute CP-T(2) relaxation times. This was not associated with signal change in the relative dynamic-dephasing images, as computed by subtracting short tau(CP) CP-T(2) images from long tau(CP) images and normalizing for long tau(CP) images. A day after MCAo strong CP-T(2) hyperintensity and low apparent diffusion coefficient were evident in the striatum with a decline in relative dynamic-dephasing contrast. Low dynamic dephasing contrast prevailed in striatum until day 5 post-MCAo, returning to control levels with similar time course to normalizing T(2) and diffusion. The present results show a novel behavior of dynamic-dephasing contrast in poststroke brain tissue, providing data to assess the age of infarction in association to T(2) images.

Animals↗
PubMed2004

Dynamic behavior of respiratory system during nasal continuous positive airway pressure in spontaneously breathing premature newborn infants.

The end-expiratory lung-volume level of premature newborn infants is maintained above passive resting volume during active breathing, through the combination of reduced time constant and high respiratory rate. To determine whether nasal continuous positive airway pressure (NCPAP) alters this characteristic dynamic breathing pattern, we studied the effects of various NCPAP levels on the dynamic elevation of end-expiratory lung volume level (DeltaEELV) in spontaneously breathing premature newborn infants, using respiratory inductive plethysmography (RIP). Eleven premature newborn infants with moderate respiratory failure were included. NCPAP levels were set in a random order to 0, 2, 4, and 6 cm H2O. Tidal volume (Vt), rib-cage contribution to Vt (%RC), phase angle between abdominal and thoracic motions (theta), respiratory rate (RR), and inspiratory and expiratory times (Ti and Te) were continuously recorded by RIP. The slope of the linear part of the expiratory flow-volume relation was extrapolated up to zero flow level to evaluate the dynamic elevation of the functional residual capacity (FRC) (DeltaEELV). The time-constant of the respiratory system (tauRS) was calculated as the slope of the linear part of the expiratory flow-volume loop. At NCPAP = 6 cm H2O, DeltaEELV reached 0.6 +/- 0.2 times the Vt at NCPAP = 0 cm H2O. An increase in NCPAP level resulted in a significant decrease in DeltaEELV (P < 0.01). A decrease in DeltaEELV during NCPAP was associated with a significant increase in Te from 0.62 +/- 0.13 sec at NCPAP = 0 cm H2O to 0.80 +/- 0.07 sec at NCPAP = 6 cm H2O (P < 0.05), and a decrease in tauRS from 0.4 +/- 0.1 sec at NCPAP = 0 cm H2O to 0.24 +/- 0.04 sec at NCPAP = 6 cm H2O (P < 0.01). These results indicate that the characteristic spontaneous breathing pattern causing a dynamic elevation of FRC is abolished by NCPAP. We speculate that the dynamic volume-preserving mechanisms resulting from expiratory flow braking are no longer required during NCPAP, as the constant pressure may passively elevate FRC.

Female↗
PubMed1994

Response of dynamic structure to removal of a disulfide bond: normal mode refinement of C77A/C95A mutant of human lysozyme.

In order to investigate the response of dynamic structure to removal of a disulfide bond, the dynamic structure of human lysozyme has been compared to its C77A/C95A mutant. The dynamic structures of the wild type and mutant are determined by normal mode refinement of 1.5-A-resolution X-ray data. The C77A/C95A mutant shows an increase in apparent fluctuations at most residues. However, most of the change originates from an increase in the external fluctuations, reflecting the effect of the mutation on the quality of crystals. The effects of disulfide bond removal on the internal fluctuations are almost exclusively limited to the mutation site at residue 77. No significant change in the correlation of the internal fluctuations is found in either the overall or local dynamics. This indicates that the disulfide bond does not have any substantial role to play in the dynamic structure. A comparison of the wild-type and mutant coordinates suggests that the disulfide bond does not prevent the 2 domains from parting from each other. Instead, the structural changes are characteristic of a cavity-creating mutation, where atoms surrounding the mutation site move cooperatively toward the space created by the smaller alanine side chain. Although this produces tighter packing, more than half of the cavity volume remains unoccupied, thus destabilizing the native state.

Binding Sites↗
PubMed2001

Modeling of the metallo-beta-lactamase from B. fragilis: structural and dynamic effects of inhibitor binding.

The structure and dynamics of an inhibitor-bound complex of the metallo-beta-lactamase from Bacteroides fragilis are studied by using molecular dynamics. A search of the conformational space was performed to obtain three distinct models of the complex, which were then subjected to solvated molecular dynamics. A solvated molecular dynamics study of the apo protein was performed to serve as a baseline for comparison with the bound simulations. We find loop conformation changes due to binding as well as a decrease in flexibility of the protein as a whole and especially in the major loop of the beta-lactamase. We report the structural and dynamical features of the inhibitor-bound and apo models, as well as experimentally measurable quantities, which should be capable of distinguishing the two binding modes we have determined.

Apoproteins↗
PubMed1994

Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement.

A reduced variable conformational sampling strategy for macromolecules based on molecular dynamics in torsion angle space is evaluated using crystallographic refinement as a prototypical search problem. Bae and Haug's algorithm for constrained dynamics [Bae, D.S., Haug, E.J. A recursive formulation for constrained mechanical system dynamics. Mech. Struct. Mach. 15:359-382, 1987], originally developed for robotics, was used. Their formulation solves the equations of motion exactly for arbitrary holonomic constraints, and hence differs from commonly used approximation algorithms. It uses gradients calculated in Cartesian coordinates, and thus also differs from internal coordinate formulations. Molecular dynamics can be carried out at significantly higher temperatures due to the elimination of the high frequency bond and angle vibrations. The sampling strategy presented here combines high temperature torsion angle dynamics with repeated trajectories using different initial velocities. The best solutions can be identified by the free R value, or the R value if experimental phase information is appropriately included in the refinement. Applications to crystallographic refinement. Applications to crystallographic refinement show a significantly increased radius of convergence over conventional techniques. For a test system with diffraction data to 2 A resolution, slow-cooling protocols fail to converge if the backbone atom root mean square (rms) coordinate deviation from the crystal structure is greater than 1.25 A, but torsion angle refinement can correct backbone atom rms coordinate deviations up to approximately 1.7 A.

Algorithms↗
PubMed2003

Dynamic Cox modelling based on fractional polynomials: time-variations in gastric cancer prognosis.

The most popular model used for survival analysis is the proportional hazards regression model proposed by Cox. This is mainly due to its exceptional simplicity. Nevertheless the fundamental assumption of the Cox model is the proportionality of the hazards. For many applications, however, this assumption is doubtful. Proposals to extend the Cox model for non-proportional hazards to allow for dynamic effect structures usually either depend on prespecifications or require non-standard estimation techniques and are thus not favoured in application. Moreover, tests to verify the dynamic effect structures are not straightforward or lack omnibus power. In this paper we propose a flexible method for modelling dynamic effects in survival data within the Cox framework. The method is based on fractional polynomials as introduced by Royston and Altman. This allows for a transformation of the dynamic predictor which leads back to the conventional Cox model and hence fitting is straightforward using standard estimation techniques. In addition, it offers the possibility of easily verifying the existence of time-variation. We describe a model selection algorithm which selects time-varying effects only when evidence is given in the data. We illustrate the properties of the approach in a simulation study and compare it with other methods. In a survival study of gastric cancer patients, we apply the approach to analyse dynamic structures in the effects of prognostic factors.

Adult↗
PubMed2002

High-sensitivity analyses of metabolites in biological samples by capillary electrophoresis using dynamic pH junction-sweeping.

Emerging fields of biochemical research, such as metabolomics, present challenges to current separation technologies because of the large number of metabolites present in a cell and their often low (submicromolar) concentration. Although capillary electrophoresis (CE) holds great promise as the method of choice for high-resolution separations of biological samples, it suffers from poor concentration sensitivity, especially with the use of UV detection. In CE, sweeping and dynamic pH junction represent two complementary on-line focusing techniques that have been used for sensitivity enhancement of hydrophobic and weakly acidic analytes, respectively. However, the application of either the sweeping or dynamic pH junction technique alone might, in some cases, be less effective for the analysis of certain sample mixtures. Recent work in the development of a hyphenated dynamic pH junction-sweeping technique is presented as an effective on-line method of preconcentration suitable for both hydrophilic (anionic) and hydrophobic (neutral) analytes. Sensitive analyses of flavin metabolites by CE with laser-induced fluorescence (LIF) detection is demonstrated in various biological matrixes, including cell extracts of Bacillus subtilis, pooled human plasma, as well as heat-deproteinized flavoenzymes. Enhanced analyte band narrowing and improved sensitivity is achieved for flavins using dynamic pH junction-sweeping compared to either sweeping or dynamic pH junction alone. This results in over a 1200-fold improvement in sensitivity relative to conventional injection methods, giving a limit of detection (LOD, defined as S/N = 3) of about 4.0 x 10(-12) M. Strategies for sensitive and more comprehensive analyses of other cell metabolites, including nucleotides, coenzymes, and steroids, are also discussed when using on-line focusing techniques in conjunction with multiplexed CE and UV detection.

Bacillus subtilis↗
PubMed2004

Dynamic cervical change during real-time ultrasound: prospective characterization and comparison in patients with and without symptoms of preterm labor.

OBJECTIVES: To compare the incidence of dynamic cervical change (spontaneous real-time cervical shortening) in singleton patients with and without symptoms of preterm labor (PTL). METHODS: A total of 109 patients between 23 and 34 weeks' gestation with and without PTL symptoms underwent cervical length ultrasound and contraction monitoring over a 10-min period. Cervical length measurements were taken at 1-min intervals. Exclusion criteria included ruptured membranes, dilation > 3 cm or cerclage. Following the examination, the sonographer made a subjective assessment as to whether noticeable dynamic cervical change had occurred. A measurement was then made during the application of fundal pressure. The initial cervical length, shortest length, maximum change in length and incidence of dynamic change were compared between patients with and without PTL symptoms. The shortest cervical length was compared to the presence and timing of uterine contractions and the measurement during the application of fundal pressure. RESULTS: A total of 43 asymptomatic patients and 66 symptomatic patients were studied. Compared to asymptomatic patients, patients with PTL symptoms had shorter initial lengths, nadir lengths and mean lengths over time as well as a greater amount of maximum change. Dynamic cervical change was more frequently seen in symptomatic patients (48% vs. 9%, P < 0.001) and was associated with uterine contractions (odds ratio 4.6, 95% CI 1.9-10.8). Fundal pressure was not able to reproduce the shortest cervical length that occurred spontaneously during the observation period. CONCLUSIONS: Dynamic cervical change (real-time cervical shortening) is common in patients with PTL symptoms and is associated with uterine contractions. Whether this finding enhances the ability to predict preterm delivery remains to be elucidated.

Adult↗
PubMed1998

A computer model of intracranial dynamics integrated to a full-scale patient simulator.

The ability to visualize intracranial dynamics during simulated clinical scenarios is a valuable tool for teaching brain physiology and the consequences of different medical interventions on the brain. Studies have isolated physiologic variables and shown their effects on brain dynamics. However, no studies have shown the combined effects of these variables on intracranial dynamics. This brain model offers one approach that brings all these relationships together and shows how they affect the dynamics of the brain. The brain model obtains its physiologic inputs from a full-scale patient simulator which responds to clinical interventions. This integration allows individuals working on the patient simulator to see the effects of their actions on brain dynamics. The brain model gives a real-time display of intracranial events (cerebral metabolic rate, cerebral blood flow, cerebral blood volume, cerebral perfusion pressure, and intracranial pressure) and responds to changes in the pulmonary and cardiovascular condition of the patient simulator.

Blood Volume↗
PubMed1997

Dynamic Film and Interfacial Tensions in Emulsion and Foam Systems

In concentrated fluid dispersions the liquid films are under dynamic conditions during film rupture or drainage. Aqueous foam films stabilized with sodium decylsulfonate and aqueous emulsion films stabilized with the nonionic Brij 58 surfactant were formed at the tip of a capillary and the film tension was measured under static and dynamic conditions. In the stress relaxation experiments the response of the film tension to a sudden film area expansion was studied. These experiments also allowed the direct measurement of the Gibbs film elasticity. In the dynamic film tension experiments, the film area was continuously increased by a constant rate and the dynamic film tension was monitored. The measured film tensions were compared with the interfacial tensions of the respective single air/water and oil/water interfaces, which were measured using the same radius of curvature, relative expansion, and expansion rate as in the film studies. It was found that under dynamic conditions the film tension is higher than twice the single interfacial tension (IFT) and a mechanism was suggested to explain the difference. When the film, initially at equilibrium, is expanded and the interfacial area increases, a substantial surfactant depletion occurs inside the film. As a result, the surfactant can be supplied only from the adjoining meniscus (Plateau border) by surface diffusion, and the film tension is controlled by the diffusion and adsorption of surfactant in the meniscus. The results have important implications for the stability and rheology of foams and emulsions with high dispersed phase ratios (polyhedral structure).

Journal Article↗
PubMed1997

The Interpretation of Dynamic Contact Angles Measured by the Wilhelmy Plate Method

We present an analysis for properly interpreting apparent dynamic contact angles measured using the Wilhelmy plate method at low capillary numbers, Ca. This analysis removes the ambiguity in current dynamic measurements which interpret data with the same formula as static measurements. We properly account for all forces, including viscous forces, acting on the plate as it moves into or out of a liquid bath. Our main result, valid at O(1) as Ca --> 0, relates the apparent dynamic contact angle to material-dependent, geometry-independent parameters necessary for describing dynamic wetting of a system. The special case of the apparent contact angle = pi/2 was solved to O(Ca). This O(Ca) solution can guide numerical work necessary for higher Ca's and arbitrary values of the apparent contact angle. These results make the Wilhelmy plate a viable method for determining material parameters for dynamic spreading.

Journal Article↗
PubMed1999

A Novel Fast Technique for Measuring Dynamic Surface and Interfacial Tension of Surfactant Solutions at Constant Interfacial Area.

A novel, fast formed drop technique is developed for measuring dynamic surface and interfacial tension of surfactant solutions. It employs the basis of the capillary pressure methods. A new way of formation of a fresh interface is the key point in the proposed technique. It is based on the fact that a jet of liquid flowing out of a capillary breaks very fast after a sudden stop of the flow, but a small drop with a fresh interface remains at the capillary tip. Once the drop is formed, its size (and thereby its area) remains constant, while the capillary pressure is measured with a pressure transducer. The dynamic surface (or interfacial) tension is calculated by means of the Laplace equation for capillarity. In this way, measurements under constant interfacial area in a time domain from about 50 ms up to several minutes or more can be made. The measurements with pure liquids give constant values of the dynamic surface and interfacial tension equal to the corresponding equilibrium values reported in literature. The dynamic surface tension of Triton X 100 and Triton X 405 solutions measured by the new technique are in a good agreement with those obtained by the static drop weight method. The applicability of the new technique for measuring the dynamic interfacial tension is demonstrated. Copyright 1999 Academic Press.

Journal Article↗
PubMed1996

Main-chain dynamics of a partially folded protein: 15N NMR relaxation measurements of hen egg white lysozyme denatured in trifluoroethanol.

15N NMR relaxation measurements have been used to study the dynamic behaviour of the main-chain of hen lysozyme in a partially folded state, formed in a 70% (v/v) trifluoroethanol (TFE)/30% water mixture at 37 degrees C and pH 2. This state is characterised by helical secondary structure in the absence of extensive tertiary interactions. The NMR relaxation data were interpreted by mapping of spectral density functions and by derivation of segmental as well as global order parameters. The results imply that the dynamics of lysozyme in TFE can, at least for the great majority of residues, be adequately described by internal motions which are superimposed on all overall isotropic tumbling of the molecule. Although the dynamic behaviour shows substantial variations along the polypeptide chain, it correlates well with the conformational preferences identified in the TFE state by other NMR parameters. Segments of the polypeptide chain which are part of persistent helical structures are highly restricted in their motion (S2 > 0.8 , with effective internal correlation times tau(e) < 200 ps) but are also found to experience conformational exchange on a millisecond timescale. Regions which are stabilised in less persistent helical structure possess greater flexibility (0.6 < S2 < 0.8, 200 ps < tau(e) < 1 ns) and those which lack defined conformational preferences are highly flexible (S2 < 0.6, tau(e) approximately 1 ns). The dynamic behaviour of the main-chain was found to be correlated with other local features of the polypeptide chain, including hydrophobicity and the position of the disulphide bridges. Despite the absence of extensive tertiary interactions, preferential stabilisation of native-like secondary structure by TFE results in a pattern of main-chain dynamics which is similar to that of the native state.

Animals↗
PubMed2000

How do substrates enter and products exit the buried active site of cytochrome P450cam? 1. Random expulsion molecular dynamics investigation of ligand access channels and mechanisms.

Cytochrome P450s form a ubiquitous protein family with functions including the synthesis and degradation of many physiologically important compounds and the degradation of xenobiotics. Cytochrome P450cam from Pseudomonas putida has provided a paradigm for the structural understanding of cytochrome P450s. However, the mechanism by which camphor, the natural substrate of cytochrome P450cam, accesses the buried active site is a long-standing puzzle. While there is recent crystallographic and simulation evidence for opening of a substrate-access channel in cytochrome P450BM-3, for cytochrome P450cam, no such conformational changes have been observed either in different crystal structures or by standard molecular dynamics simulations. Here, a novel simulation method, random expulsion molecular dynamics, is presented, in which substrate-exit channels from the buried active site are found by imposing an artificial randomly oriented force on the substrate, in addition to the standard molecular dynamics force field. The random expulsion molecular dynamics method was tested in simulations of the substrate-bound structure of cytochrome P450BM-3, and then applied to complexes of cytochrome P450cam with different substrates and with product. Three pathways were identified, one of which corresponds to a channel proposed earlier on the basis of crystallographic and site-directed mutagenesis data. Exit via the water-filled channel, which was previously suggested to be a product exit channel, was not observed. The pathways obtained by the random expulsion molecular dynamics method match well with thermal motion pathways obtained by an analysis of crystallographic B-factors. In contrast to large backbone motions (up to 4 A) observed in cytochrome P450BM-3 for the exit of palmitoleic acid, passage of camphor through cytochrome P450cam only requires small backbone motions (less than 2.4 A) in conjunction with side-chain rotations. Concomitantly, in almost all the exit trajectories, salt-links that have been proposed to act as ionic tethers between secondary structure elements of the protein, are perturbed.

Bacterial Proteins↗
PubMed2001

Relationship of DNA structure to internal dynamics: correlation of helical parameters from NOE-based NMR solution structures of d(GCGTACGC)(2) and d(CGCTAGCG)(2) with (13)C order parameters implies conformational coupling in dinucleotide units.

The coupling between the conformational properties of double-stranded DNA and its internal dynamics has been examined. The solution structures of the isomeric DNA oligomers d(GCGTACGC)(2) (UM) and d(CGCTAGCG)(2) (CTSYM) were determined with (1)H NMR spectroscopy by utilizing distance restraints from total relaxation matrix analysis of NOESY cross-peak intensities in restrained molecular dynamics calculations. The root-mean-square deviation of the coordinates for the ensemble of structures was 0.13 A for UM and 0.49 A for CTSYM, with crystallographic equivalent R(c)=0.41 and 0.39 and sixth-root residual R(x)=0.11 and 0.10 for UM and CTSYM, respectively. Both UM and CTSYM are B-form with straight helical axes and show sequence-dependent variations in conformation. The internal dynamics of UM and CTSYM were previously determined by analysis of (13)C relaxation parameters in the context of the Lipari & Szabo model-free formalism. Helical parameters for the two DNA oligomers were examined for linear correlations with the order parameters (S(2)) of groups of (13)C spins in base-pairs and dinucleotide units of UM and CTSYM. Correlations were found for six interstrand base-pair parameters tip, y-displacement, inclination, buckle and stretch with various combinations of S(2) for atoms in Watson-Crick base-pairs and for two inter-base-pair parameters, rise and roll with various combinations of S(2) for atoms in dinucleotides. The correlations for the interstrand base-pair helical parameters indicate that the conformations of the deoxyribose residues of each strand are dynamically coupled. Also, the inter-base-pair separation has a profound effect on the local internal motions available to the DNA, supporting the idea that rise is a principal degree of freedom for DNA conformational variability. The correlations indicate collective atomic motions of spins that may represent specific motional modes in DNA, and that base sequence has a predictable effect on the relative order of groups of spins both in the bases and in the deoxyribose ring of the DNA backbone. These observations suggest that an important functional outcome of DNA base sequence is the modulation of both the conformation and dynamic behavior of the DNA backbone.

Base Pairing↗
PubMed1997

Atomic Force Sensing of Light-Induced Protein Dynamics with Microsecond Time Resolution in Bacteriorhodopsin and Photosynthetic Reaction Centers

This paper reports on experiments that have monitored protein microsecond dynamics with a cantilevered near-field optical glass fiber. In these experiments two photoactive proteins, bacteriorhodopsin (bR) and the photosynthetic reaction center (PS I), are used to demonstrate that such probes can measure light-induced microsecond protein dynamics even though the resonance frequencies of the glass cantilevers used are on the order of a few hundred kilohertz. In the case of the light-driven proton pump, bR, the light-induced atomic force sensing (AFS) signal is negative (indicating contraction) in the microsecond time domain of the L photointermediate and becomes positive (corresponding to expansion) in the subsequent M intermediate that lives for milliseconds. Double pulse experiments from M to bR show that the latter process reverses the AFS signal. Thus, the AFS structural changes are coupled with the (optical) photocycle intermediates. Light-induced contraction and expansion phenomena are also observed in the case of PS I. In both systems the time regime of the dynamic phenomena that have been measured with AFS is five orders of magnitude faster than the fastest previously recorded atomic force detection of dynamic phenomena. This advance portends a new era in dynamic imaging of protein conformational changes.

Journal Article↗
PubMed1998

Human subconscious as a p-adic dynamical system.

We propose a mathematical model of the process of thinking based on dynamical systems over a configuration space of ideas. These dynamical systems are assumed to be located in the human subconscious and are controlled by the human conscious which fixes parameters of the dynamical systems in the subconscious and transmits to the subconscious generating ideas which initiate iterations of the dynamical systems in the subconscious. Thus, we present the mathematical model which is not based on the rule of reason. Mathematically the space of ideas is described by so-called p-adic numbers. In fact, a p-adic metric on the space of ideas corresponds to the following nearness between ideas: two ideas x and y are close if they have sufficiently long common root. Already the simplest p-adic dynamical systems might describe some sides of human psychological and social behaviour.

Bipolar Disorder↗