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PubMed2004

Recursive penalized least squares solution for dynamical inverse problems of EEG generation.

In the dynamical inverse problem of electroencephalogram (EEG) generation where a specific dynamics for the electrical current distribution is assumed, we can impose general spatiotemporal constraints onto the solution by casting the problem into a state space representation and assuming a specific class of parametric models for the dynamics. The Akaike Bayesian Information Criterion (ABIC), which is based on the Type II likelihood, was used to estimate the parameters and evaluate the model. In addition, dynamic low-resolution brain electromagnetic tomography (LORETA), a new approach for estimating the current distribution is introduced. A recursive penalized least squares (RPLS) step forms the main element of our implementation. To obtain improved inverse solutions, dynamic LORETA exploits both spatial and temporal information, whereas LORETA uses only spatial information. A considerable improvement in performance compared to LORETA was found when dynamic LORETA was applied to simulated EEG data, and the new method was applied also to clinical EEG data.

Brain↗

PubMed2007

An automated tracking system to measure the dynamic properties of vesicles in living cells.

Recent technological improvements have made it possible to examine the dynamics of individual vesicles at a very high temporal and spatial resolution. Quantification of the dynamic properties of secretory vesicles is labor-intensive and therefore it is crucial to develop software to automate the process of analyzing vesicle dynamics. Dual-threshold and binary image conversion were applied to enhance images and define the areas of objects of interest that were to be tracked. The movements, changes in fluorescence intensity, and changes in the area of each tracked object were measured using a new software system named the Protein Tracking system (PTrack). Simulations revealed that the system accurately recognized tracked objects and measured their dynamic properties. Comparison of the results from tracking real time-lapsed images manually with those automatically obtained using PTrack revealed similar patterns for changes in fluorescence intensity and a high accuracy (<89%). According to tracking results, PTrack can distinguish different vesicular organelles that are similar in shape, based on their unique dynamic properties. In conclusion, the novel tracking system, PTrack, should facilitate automated quantification of the dynamic properties of vesicles that are important when classifying vesicular protein locations.

Animals↗

PubMedDate not supplied

High-affinity rat anti-fluorescein monoclonal antibody with unique fine specificity properties including differential recognition of dynamic ligand analogues.

The ability of antibodies to specifically select and stabilize through binding one or more isomers of highly dynamic ligands remains a relatively unexplored immunochemical problem. The experimental strategy employed in this study was to elicit homogeneous antibodies to polyaromatic fluorescein which exists in one isomeric form. The binding properties of a monoclonal rat antifluorescein antibody specific to a given isomer were quantitatively studied to determine the capacity to bind dynamic analogues of fluorescein which exists in multiple isomers. To generate monoclonal anti-fluorescein antibodies that reacted with specific dynamic analogues of fluorescein possessing unconjugated aromatic ring systems, immune spleenocytes from Lou/M rats immunized with FITC(I)-KLH were fused with Balb/c SP2/0-Ag14 murine myeloma cells forming rat-mouse hybridomas. Cell line P2A12-1-C8 was selected for further characterization from the original 23 stable rat hybrids, since it produced a monoclonal antibody with a binding affinity 2.0 x 10(10)/M for fluorescein based on dissociation rate measurements. P2A12-1-C8 exhibited significant reactivity with HPF and phenol red, which are dynamic structural analogues of the homologous fluorescein ligand. No reactivity was demonstrated with phenolphthalein, which based on relative chemical structures was expected to be more reactive than phenol red. Computer-based molecular modeling and energy minimization studies of fluorescein, HPF, phenol red, and phenolphthalein showed that in terms of the most energetically favorable orientation of the three aromatic rings, phenol red more closely simulated fluorescein than phenolphthalein. The results were analyzed in terms of the mechanisms of dynamic ligand stabilization and binding involving accommodation of specific ligand isomers by energetically permissible conformational states exhibited by an antibody active site. Thus, antibody reactivity of an anti-fluorescein antibody with phenol red and phenolphthalein was dictated more by ligand dynamics and aromatic orientation than by chemical structure similarities.

Absorption↗

PubMedDate not supplied

Dynamic spin-echo imaging: theoretical assessment and implementation.

A spin-echo method for obtaining dynamic magnetic resonance (MR) images is described. The method combines the RARE (rapid acquisition with relaxation enhancement) pulse sequence with a data acquisition scheme in which only a centric fraction of the raw data is sampled to increase the time resolution of the dynamic images. The missing high-resolution data are supplied from reference images. By these means, an effective time resolution of about 10 seconds per image is achieved, which is suitable for diagnostic assessment of contrast enhancement procedures. A promising clinical application is contrast-enhanced MR imaging of the pituitary. Although the resolution of small objects in this size range is potentially degraded, this shortcoming is compensated for with use of variable refocusing flip angles. In the context of pituitary imaging, the centric 30%-40% of the raw data is shown to be the optimal fraction to acquire for the low-resolution dynamic images. Ten patients with previous history of pituitary disease have been imaged with dynamic and conventional spin-echo techniques. In six of these patients, an equivalent diagnosis was reached with dynamic and conventional images, while in two, only the dynamic images showed the lesion; in the final two patients, only the conventional images showed the lesion.

Adenoma↗

PubMed2004

Three-dimensional dynamic liver MR imaging using sensitivity encoding for detection of hepatocellular carcinomas: comparison with superparamagnetic iron oxide-enhanced mr imaging.

PURPOSE: To assess the diagnostic performance of three-dimensional dynamic liver imaging with sensitivity encoding (SENSE), including double arterial phase images and increased resolution, by comparing it to superparamagnetic iron oxide (SPIO)-enhanced magnetic resonance (MR) imaging for the detection of hypervascular hepatocellular carcinoma (HCC). MATERIALS AND METHODS: Twenty-seven consecutive patients with 50 HCCs underwent Gd-BOPTA-enhanced dynamic imaging using SENSE and SPIO-enhanced MR imaging with at least a 24-hour interval between examinations. Using a three-dimensional gradient-echo technique applying SENSE, dynamic imaging consisting of double arterial phase-, portal phase- and delayed phase-images, was obtained. Using T2-weighted turbo spin-echo and T2*-weighted fast imaging with steady-state precession sequence, SPIO-enhanced MR imaging was obtained. For qualitative analysis, the diagnostic accuracy of both MR examinations for detecting the 50 HCCs was evaluated using the alternative free-response receiver operating characteristic method. Sensitivity and positive predictive value were also evaluated. RESULTS: The mean sensitivity and positive predictive value of three-dimensional dynamic imaging with SENSE were 91.3% and 89.2%, respectively, and those of SPIO-enhanced imaging were 77.3% and 92.6 %, respectively. There was a significant difference in sensitivity between the two images (P <0.05). The mean Az value of three-dimensional dynamic imaging with SENSE (0.97 +/- 0.01) was significantly higher than that of SPIO-enhanced imaging (0.90 +/- 0.02) (P=0.00). CONCLUSION: Three-dimensional dynamic liver MR imaging using SENSE for acquiring double arterial phase images is more efficient than SPIO-enhanced MR imaging for detecting HCCs.

Carcinoma, Hepatocellular↗

PubMed2006

Feasibility of dynamic susceptibility contrast perfusion MR imaging at 3T using a standard quadrature head coil and eight-channel phased-array coil with and without SENSE reconstruction.

PURPOSE: To investigate changes in image and dynamic signal-to-noise ratios (SNRs) of the DeltaR2* curve, as well as magnetic susceptibility-induced artifacts between a standard quadrature head coil and an eight-channel phased-array coil with and without sensitivity-encoding (SENSE) at 3T, compared to the current clinical standard head coil acquisition at 1.5T. MATERIALS AND METHODS: Dynamic susceptibility contrast (DSC) perfusion MRI was performed on 80 brain tumor patients using a gradient-echo, echo-planar imaging (EPI) sequence. Image and dynamic SNR were compared between 1.5T and 3T field strengths, a quadrature and eight-channel phased-array coil, and a conventional vs. partially parallel EPI acquisition with SENSE reconstruction. The amount of geometric distortion and signal dropout was quantified and compared between conventional and SENSE EPI acquisitions within the same exam at 3T. RESULTS: An initial 2.6-fold elevation in dynamic SNR was observed in normal-appearing white matter when doubling the field strength (P < 0.001), with an additional 1.7-fold increase found when employing an eight-channel phased-array coil (P < 0.002). Compared to the standard 3T eight-channel coil acquisition, the implementation of SENSE reduced the number of voxels experiencing large anterior shifts in the phase-encode direction, lowered the volume of signal dropout by 2.0-11.5%, and allowed a 1.4-fold increase in slice coverage, while only decreasing the dynamic SNR by 22%. CONCLUSION: SENSE EPI at 3T yielded a significant improvement in dynamic SNR over the 1.5T acquisitions. A significant reduction in magnetic susceptibility-induced artifacts was achieved with SENSE EPI compared to the standard EPI eight-channel coil acquisition at 3T.

Adult↗

PubMed1985

Studies of powder flow using a recording powder flowmeter and measurement of the dynamic angle of repose.

This paper describes the utility of the dynamic measurement of the angle of repose for pharmaceutical systems, using a variable rotating cylinder to quantify powder flow. The dynamic angle of repose of sodium chloride powder sieve fractions was evaluated using a variable rotating cylinder. The relationship between the static and the dynamic angle of repose is discussed. The dynamic angle of repose of six lots of a multivitamin preparation were compared for inter- and intralot variation. In both cases, no significant differences (p greater than 0.05) were observed. In the multivitamin formulation, lubricants at lower concentration levels did not show a significant effect (p greater than 0.05) on the dynamic angle of repose when compared with flow rates. The effect of different hopper sizes and geometry has been evaluated using the recording powder flowmeter. The results indicate that although different hoppers affect the quantitative nature of the results, the same general trends are apparent. Thus, it appears possible to use a recording powder flowmeter with small quantities of material to predict the effect of formulation and processing variables on the flow of production scale quantities. This paper does not describe a comprehensive evaluation of the pharmaceutical utility of measuring the dynamic angle of repose. However, the results discussed are not encouraging and suggest that the recording powder flowmeter is more sensitive to the effects of formulation and production variables on powder flow.

Chemistry, Pharmaceutical↗

PubMed2004

Dynamics of chelation-supercritical fluid extraction from wood fibers.

The dynamics of supercritical fluid extraction (SFE) of the metal content of wood fibers chelated with lithium bis(trifluoroethyl) dithiocarbamate (FDDC) by supercritical (SF) CO2 was investigated experimentally by monitoring the spectra of the eluted metal complex as a function of time. The characteristic shape of the dynamic SFE curve was determined mainly by the flow conditions in the extraction vessel, the mass transfer resistance in the SF phase, and the solubility. High extraction yields of metal content were obtained in two-stage extraction including static (batch) and dynamic (semi-batch) stages. Increasing the length of the static stage increased the rate of dynamic elution of metal complex until it approached the dynamics of fluid displacement for a continuous stirred tank reactor (CSTR). In such cases, increasing the flow rate had no effect on the dynamic extraction curve when it was plotted using dimensionless time. Efficient chelation-SFE from wood fibers was obtained at a pressure of 20.3 MPa and with a static time of 30 min.

Carbon Dioxide↗

PubMed2001

Dynamic balance function in phasic cervical dystonia following Botulinum toxin therapy.

Previous research by our group revealed normal dynamic balance function in pure tonic cervical dystonia (CD) with impaired equilibrium in phasic CD patients investigated at least 3 months following Botulinum toxin (BtxA) treatment. The current study was performed to determine whether impaired dynamic equilibrium in phasic CD is influenced by symptomatic treatment with BtxA. Dynamic balance was tested in 20 patients with phasic CD on a dynamic platform with a cylindrical curved base (stabilometer) 4 weeks following BtxA treatment. Balance was assessed by the linear displacement of the platform and the maximum amplitude of platform displacement with open and closed eyes and compared with pre-BtxA data. Despite a clinically significant BtxA-induced reduction of phasic head movements, none of the platform measures improved significantly. In addition, there was no correlation between the BtxA-induced clinical improvement and changes in any of the dynamic balance measures pre- vs. post-BtxA. In conclusion, the persistent dynamic balance impairment after effective BtxA therapy may indicate that disequilibrium in phasic CD does not simply reflect disturbed vestibular input from repetitive head oscillations, but argues in favour of different sensorimotor processing in tonic and phasic CD.

Adult↗

PubMed1993

Investigations of the thermostability of rubredoxin models using molecular dynamics simulations.

The affects of differences in amino acid sequence on the temperature stability of the three-dimensional structure of the small beta-sheet protein, rubredoxin (Rd), was revealed when a set of homology models was subjected to molecular dynamics simulations at relatively high temperatures. Models of Rd from the hyperthermophile, Pyrococcus furiosus (Pf), an organism that grows optimally at 100 degrees C, were compared to three mesophilic Rds of known X-ray crystal structure. Simulations covering the limits of known Rd thermostabilities were carried out at temperatures of 300 K, 343 K, 373 K, and 413 K. They suggest that Rd stability is correlated with structural dynamics. Because the dynamic behavior of three Pf Rd models was consistently different from the dynamic behavior of the three mesophilic Rd structures, detailed analysis of the temperature-dependent dynamic behavior was carried out. The major differences between the models of the protein from the hyperthermophile and the others were: (1) an obvious temperature-dependent transition in the mesophilic structures not seen with the Pf Rd models, (2) consistent AMBER energy for the Pf Rd due to differences in nonbonded interaction terms, (3) less variation in the average conformations for the Pf Rd models with temperature, and (4) the presence of more extensive secondary structure for the Pf Rd models. These unsolvated dynamics simulations support a simple, general hypothesis to explain the hyperthermostability of Pf Rd. Its structure simplifies the conformational space to give a single minimum accessible over an extreme range of temperatures, whereas the mesophilic proteins sample a more complex conformational space with two or more minima over the same temperature range.

Computer Simulation↗

PubMed1996

Dynamics of ribonuclease A and ribonuclease S: computational and experimental studies.

RNase S is a complex consisting of two proteolytic fragments of RNase A: the S peptide (residues 1-20) and S protein (residues 21-124). RNase S and RNase A have very similar X-ray structures and enzymatic activities. Previous experiments have shown increased rates of hydrogen exchange and greater sensitivity to tryptic cleavage for RNase S relative to RNase A. It has therefore been asserted that the RNase S complex is considerably more dynamically flexible than RNase A. In the present study we examine the differences in the dynamics of RNase S and RNase A computationally, by MD simulations, and experimentally, using trypsin cleavage as a probe of dynamics. The fluctuations around the average solution structure during the simulation were analyzed by measuring the RMS deviation in coordinates. No significant differences between RNase S and RNase A dynamics were observed in the simulations. We were able to account for the apparent discrepancy between simulation and experiment by a simple model. According to this model, the experimentally observed differences in dynamics can be quantitatively explained by the small amounts of free S peptide and S protein that are present in equilibrium with the RNase S complex. Thus, folded RNase A and the RNase S complex have identical dynamic behavior, despite the presence of a break in polypeptide chain between residues 20 and 21 in the latter molecule. This is in contrast to what has been widely believed for over 30 years about this important fragment complementation system.

Computer Simulation↗

PubMed2003

Dynamic effects of mutations within two loops of cytochrome c551 from Pseudomonas aeruginosa.

In this work, we investigated the structural and dynamic consequences of two substitutions, P58A and G36P, located in two different solvent-exposed loops of cytochrome c551. The results show that both mutations affect regions that are distant from the site of mutation. Here, the two loops appear to be dynamically coupled to each other, because the substitution at one site affects the structure and the dynamics of the other site. However, the substitutions at Gly-36 and Pro-58 presented substantial differences, which were related to the mechanical (rigidity and deformability) properties of the site surrounding the mutation. Although the P58A mutant conserved a significant dynamic similarity to the wild-type protein as the immediate surroundings of position 58 became more rigid, the G36P mutant, which had deformed its flexible surroundings, presented a dynamic behavior that was markedly different from that of the wild-type protein. These results suggest that perturbation of sterically isolated and flexible regions, such as solvent-exposed loops, can have strong dynamic consequences on the protein as a whole, raising the possibility that these effects could in turn affect the stability or the function of the protein.

Amino Acid Substitution↗

PubMed2005

Structural dynamics of nucleosome core particle: comparison with nucleosomes containing histone variants.

The present study provides insights on the dominant mechanisms of motions of the nucleosome core particle and the changes in its functional dynamics in response to histone variants. Comparative analysis of the global dynamics of nucleosomes with native and variant H2A histones, using normal mode analysis revealed that the dynamics of the nucleosome is highly symmetric, and its interaction with the nucleosomal DNA plays a vital role in its regulation. The collective dynamics of nucleosomes are predicted to be dominated by two types of large-scale motions: (1) a global stretching-compression of nucleosome along the dyad axis by which the nucleosome undergoes a breathing motion with a massive distortion of nucleosomal DNA, modulated by histone-DNA interactions; and (2) the flipping (or bending) of both the sides of the nucleosome in an out-of-plane fashion with respect to the dyad axis, originated by the highly dynamic N-termini of H3 and (H2A.Z-H2B) dimer in agreement with the experimentally observed perturbed dynamics of the particular N-terminus under physiological conditions. In general, the nucleosomes with variant histones exhibit higher mobilities and weaker correlations between internal motions compared to the nucleosome containing ordinary histones. The differences are more pronounced at the L1 and L2 loops of the respective monomers H2B and H2A, and at the N-termini of the monomers H3 and H4, all of which closely interact with the wrapping DNA.

Amino Acid Motifs↗

PubMed2006

Molecular dynamics study of a calmodulin-like protein with an IQ peptide: spontaneous refolding of the protein around the peptide.

The Calmodulin (CaM) is a small (16.7 kDa), highly acidic protein that is crucial to all eukaryotes by serving as a prototypical calcium sensor. In the present study, we investigated, through molecular dynamics simulations, the dynamics of a complex between the Mlc1p protein, which is a CaM-like protein, and the IQ4 peptide. This protein-peptide interaction is of high importance because IQ motifs are widely distributed among different kinds of CaM-binding proteins. The Mlc1p-IQ4 complex, which had been resolved by crystallography to 2.1 A, confers to a Ca(+2)-independent stable structure. During the simulations, the complex undergoes a complicated modulation process, which involves bending of the angles between the alpha-helices of the protein, breaking of the alpha-helical structure of the IQ4 peptide into two sections, and formation of new contact points between the protein and the peptide. The dynamics of the process consist of fast sub picosecond events and much slower ones that take a few nanoseconds to completion. Our study expands the information embedded in the crystal structure of the Mlc1p-IQ4 complex by describing its dynamic behavior as it evolves from the crystal structure to a form stable in solution. The article shows that careful application of molecular dynamics simulations can be used for extending the structural information presented by the crystal structure, thereby revealing the dynamic configuration of the protein in its physiological environment.

Algorithms↗

PubMed1999

Real-time PC-based system for dynamic beat-to-beat QT-RR analysis.

A real-time analysis (RTA) system, based on a personal computer with a digital signal processor card (DSP) was developed. The system extracts and saves the QT and RR intervals from an incoming ECG signal sampled at 1 kHz. The method of defining the QT and RR intervals is based on performing multiple cross-correlations that enables rejection of artifacts from the analysis. The relationship between the RR and the QT intervals is found using the following general formula QT(i) cRR(i)(i-1). Linear regression is performed on the logarithms of QT and RR measurements obtained to estimate a constant (a = logc) and a slope (b), reflecting the dynamic change of the QT intervals. Having these two values, the dynamic QT extrapolated to a heart period of 1 s (QTcd) was calculated. The system also performs spectral analysis of the intervals and dynamic QT-RR relation analysis. The system was evaluated on recordings from 10 infants aged 4 to 24 weeks. The QT/RR computerized measuring device used in the present study answers to the requirements for precise dynamic beat-to-beat QT measurement. Its sampling rate is high and can achieve a real millisecond-precision without the need of interpolation methods. The measurements are performed on-line, at the time of the actual recording. Results appear immediately and a measure of dynamic QT behavior can be easily obtained within minutes. The computerized system with the dynamic QT-RR measurements may provide a simple and accurate tool for testing drug treatment and effects of other interventions for cardiac disorders and arrhythmia risk.

Electrocardiography↗

PubMed1999

Dynamic Surface Elasticity of Micellar and Nonmicellar Solutions of Dodecyldimethyl Phosphine Oxide. Longitudinal Wave Study.

Measurements of the dynamic surface properties are used for the first time for the determination of the mean aggregation number of micelles. An approximate expression for the dilational dynamic surface elasticity of micellar solutions in the concentration region near the CMC is obtained on the basis of the more general theory which has been developed several years ago (B. A. Noskov, Izv. Akad. Nauk SSSR. Mekh Zydkasty i gaza N2, 105 (1989)). If the reverse frequency of external perturbations does not exceed the characteristic time of the slow step of the micellization process, the only properties of micelles which determine the dynamic surface elasticity are the mean aggregation number and the mean diffusion coefficient. The method of longitudinal surface waves has been applied to determine the dynamic surface elasticity of solutions of dodecyldimethyl phosphine oxide in the frequency range from 0.2 to 1.8 Hz. Both the real and the imaginary components of the dynamic surface elasticity depend nonmonotonically on the concentration below the CMC. All the experimental data agree reasonably well with the pure diffusional adsorption mechanism. Above the CMC both components of the surface elasticity decrease faster with the surfactant concentration. This fact can be explained by the contribution of micelles to the mass exchange between the surface layer and the bulk phase. Application of the theory of dynamic surface properties of micellar solutions to experimental data allows us to obtain an estimation of the mean aggregation number of micelles of dodecyldimethyl phosphine oxide. Copyright 1999 Academic Press.

Journal Article↗

PubMed2001

Dynamic Surface Tension Behavior of a Mixed Insoluble/Soluble Surfactant Dispersion at Pulsating Air/Liquid Interfaces: Roles of the Soluble Surfactant.

The influence of tyloxapol on the dynamic surface tension response of dipalmitoyl phosphatidylcholine (DPPC) dispersions at pulsating air/liquid interfaces was investigated. For a 1000 ppm DPPC dispersion prepared by sonication with a larger particle size, the dynamic surface activity of DPPC was strongly affected by the addition of 100 ppm tyloxapol. With a longer sonication time or smaller particle size, the DPPC inactivation was still observed but was somewhat less significant, resulting in slightly lower dynamic surface tensions. If a DPPC dispersion was sonicated in the presence of tyloxapol, the particle size of DPPC was greatly reduced by tyloxapol and the inhibitory effect of tyloxapol on the dynamic adsorption of DPPC may be significantly diminished. The results suggest that the competitive adsorption of tyloxapol may have a detrimental effect on the dynamic surface tension lowering ability of a DPPC dispersion with the extent depending on the DPPC dispersion state. Nevertheless, the dynamic surface activity of DPPC may be enhanced through the improved dispersion by tyloxapol if an appropriate preparation protocol is applied, and the inhibitory effect of tyloxapol may be reduced or overcome. Copyright 2001 Academic Press.

Journal Article↗

PubMed1994

The high-resolution structure of the histidine-containing phosphocarrier protein HPr from Escherichia coli determined by restrained molecular dynamics from nuclear magnetic resonance nuclear Overhauser effect data.

The solution structure of the histidine-containing phosphocarrier protein HPr from Escherichia coli has been determined by NMR in combination with distance geometry and restrained molecular dynamics. The structure is based on 1520 experimental restraints identified from both three-dimensional 1H-1H-13C and 1H-1H-15N nuclear Overhauser effect multiple-quantum coherence spectroscopy and two-dimensional 1H-1H nuclear Overhauser effect spectra. Thirty-two four-dimensional coordinate frames were produced by metric matrix distance geometry, subjected to distance bounds driven dynamics, projected into three-dimensional space and again subjected to distance-bounds driven dynamics. These 32 distance geometry structures were refined further by restrained molecular dynamics (40 ps) in the GROMOS in vacuo force field. All 32 structures reached acceptable energy minima while satisfying the imposed restraints. Two of these structures were subjected to a further 200 ps of molecular dynamics simulation in water, using time-dependent distance restraining, followed by a 200 ps free simulation without any distance restraining. The resulting structure is very similar to the X-ray structure of Bacillus subtilis HPr, but differs mainly in the position of the two loops containing the active site histidine residue 15 and residues 53 to 57 relative to the rest of the structure. The unfavorable phi torsion angle that was found for residue 16 in the active center of unphosphorylated Streptococcus faecalis HPr was proposed to play a role in the activity of the protein. Although present at the early stages of the structure calculations, this torsion-angle strain disappeared in the final model obtained from molecular dynamics simulations in water using time-averaged distance restraining and upon releasing the distance restraints. This suggests that the strain may be an artifact of crystallization conditions instead of an essential element in the phosphorylation/dephosphorylation process.

Bacterial Proteins↗