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At least 811 records · Page 45Linked to original sources

PubMed1996

Quasisteady behavior of pulsatile, confined, counterflowing jets: implications for the assessment of mitral and tricuspid regurgitation.

Mitral and tricuspid regurgitation create turbulent jets within the atria. Clinically, for the purpose of estimating regurgitant severity, jet size is assumed to be proportional to peak jet flow rate and regurgitant volume. Unfortunately, the relationship is more complex because the determinants of jet size include interactions between jet pulsatility, jet momentum, atrial width, and the velocity of ambient atrial counterflows. These effects on fluorescent jet penetration were measured using an in vitro simulation. Both steady and pulsatile jets were driven into an opposing counterflow velocity field peak jet length (Ljp) measurements made as a function of (1) peak orifice velocity (Ujp), (2) the time required for the jet to accelerate from zero to peak velocity and begin to decelerate (Tjp), (3) jet orifice diameter (Dj), (4) counterflow velocity (Uc), and (5) counterflow tube diameter (Dc). A compact mathematical description was developed using dimensional analysis. Results showed that peak jet length was a function of the counterflow tube diameter, the ratio of peak jet to counterflow momentum, (Mjp/Mc) = (U2jpD2j)/(U2cD2c), and a previously undescribed jet pulsatility parameter, the pulsatility index (PI), PI = D2c/(TjpUjpDj). For the same jet orifice flow conditions, jet penetration decreased as chamber diameter decreased, as the jet PI increased, and as the momentum ratio decreased. These interactions provide insight into why regurgitant jet size is not always a good estimate of regurgitant severity.

Blood Flow Velocity↗

PubMed2004

Wavelength division multiplexing based on apodized planar holographic Bragg reflectors.

We report wavelength division multiplexing based on lithographically fabricated slab-waveguide-contained planar holographic Bragg reflectors (HBRs). Partial HBR diffractive contour writing and contour displacement are successfully demonstrated to enable precise bandpass engineering of multiplexer transfer functions and make possible compact-footprint devices based on hologram overlay. Four- and eight-channel multiplexers with channel spacings of approximately 50 and approximately 100 GHz, improved sidelobe suppression, and flattop passbands are demonstrated. When a second-order apodization effect, comprising effective waveguide refractive-index variation with written contour fraction, and the effect of hologram overlap on the hologram reflective amplitude are included in the simulation, excellent agreement between predicted and observed spectral passband profiles is obtained. With demonstrated simulation capability, the ability to fabricate general desired passband profiles becomes tractable.

Journal Article↗

PubMed1980

Pulsatile prosthetic valve flows.

The laser Doppler system has been established as a useful tool for eliciting the properties of simulated cardiovascular flows, and thus for comparative studies of flow properties of prosthetic valves. Significant differences among valve types and between models of one type have been documented. The complex variations of velocity profiles with time show that comparisons must be made for unsteady pulsatile rather than steady flow, despite the volume and complexity of the data required. Future studies will include methods of compacting the data presentation and improving the details of the experimental stimulation.

Blood Flow Velocity↗

PubMed2006

A note on removal of the compaction effect for the 210Pb method.

The compaction effect may significantly flatten an excess (210)Pb depth profile near the sediment-water interface, resulting in erroneous (210)Pb dating. There are three mathematical approaches to correct for the compaction effect. In the present paper, some further deductions have been done to make the procedure of approach calculations more clearly and practically. Meanwhile, the three approaches are also compared using a case study selected from the literature.

Algorithms↗

PubMed1998

Neutron-scattering studies reveal further details of the Ca2+/calmodulin-dependent activation mechanism of myosin light chain kinase.

Previously, we utilized small-angle X-ray scattering and neutron scattering with contrast variation to obtain the first low-resolution structure of 4Ca2+.calmodulin (CaM) complexed with a functional enzyme, an enzymatically active truncation mutant of skeletal muscle myosin light chain kinase (MLCK). These experiments showed that, upon binding to MLCK, CaM undergoes a conformational collapse identical to that observed when CaM binds to the isolated peptide corresponding to the CaM binding sequence of MLCK. CaM thereby was shown to release the inhibition of the kinase by inducing a significant movement of its CaM binding and autoinhibitory sequences away from the surface of the catalytic core [Krueger, J. K., Olah, G. A., Rokop, S. E., Zhi, G., Stull, J. T., and Trewhella, J. (1997) Biochemistry 36, 6017-6023]. We report here similar scattering experiments on the CaM.MLCK complex with the addition of substrates; a nonhydrolyzable analogue of adenosine-triphosphate, AMPPNP, and a peptide substrate for MLCK, a phosphorylation sequence from myosin regulatory light chain (pRLC). These substrates are shown to induce an overall compaction of the complex. The separation of the centers-of-mass of the CaM and MLCK components is shortened (by approximately 12 A), thus bringing CaM closer to the catalytic site compared to the complex without substrates. In addition, there appears to be a reorientation of CaM with respect to the kinase upon substrate binding that results in interactions between the N-terminal sequence of CaM and the kinase that were not observed in the complex without substrates. Finally, the kinase itself becomes more compact in the CaM.MLCK.pRLC.AMPPNP complex compared to the complex without substrates. This observed compaction of MLCK upon substrate binding is similar to that arising from the closure of the catalytic cleft in cAMP-dependent protein kinase upon binding pseudosubstrate.

Adenylyl Imidodiphosphate↗

PubMed1996

DNA topological context affects access to eukaryotic DNA topoisomerase I.

We have analyzed the reactivity of a 217 base pair segment of the intrinsically curved Crithidia fasciculata kinetoplast DNA towards eukaryotic DNA topoisomerase I. The substrates were open [linear fragment and nicked circle] and closed minidomains [closed relaxed circle and circles with linking differences of -1 and -2]. We interpreted the results with the aid of a model that was used to predict the structures of the topoisomers. The modelling shows that the delta Lk(-1) form is unusually compact because of the curvature in the DNA. To determine the role of sequence-directed curvature in both the experimental and modeling studies, controls were examined in which the curved Crithidia sequence was replaced by an uncurved sequence obtained from the plasmid pBR322. Reactivity of the Crithidia DNA [as analyzed both by the cleavage and topoisomerization reactions] markedly varied among the DNA forms: (i) the hierarchy of overall reactivity observed is: linear fragment > nicked circular, closed circular [delta Lk(0)], interwound [delta Lk(-2)] > bent interwound [delta Lk(-1)]; (ii) the intensity of several cleavage positions differs among DNA forms. The results show that eukaryotic DNA topoisomerase I is very sensitive to the conformation of the substrates and that its reactivity is modulated by the variation of the compactness of the DNA molecule. The C. fasciculata sequence contains a highly curved segment that determines the conformation of the closed circle in a complex way.

Animals↗

PubMed1995

Proposals for the angiotensin II receptor-bound conformation by comparative computer modeling of AII and cyclic analogs.

A conformational search using high-temperature molecular dynamics on angiotensin II(AII) and on two cyclic S-S bridged analogs, namely [Hcy3,5]AII and [Cys3,5]AII, in conjunction with a cluster analysis based on the similarities of the three-dimensional patterns of the binding and activation elements, had led to putative AII receptor-bound conformations. These conformations are characterized by a compact folded shape of the peptide backbone, and by particular relative positions of the four pharmacophore groups, namely the aromatic moieties of the Tyr4, His6 and Phe8 residues, and the C-terminal carboxyl group. This compact folded shape, arising from attractive electrostatic interactions between the desolvated N- and C-terminal groups, is similar to the crystallographically determined conformation of AII bound to the antibody Fab receptor.

Angiotensin II↗

PubMed1991

Effects of limited input distance constraints upon the distance geometry algorithm.

In this paper we examine the distance geometry (DG) algorithm in the form used to determine the structure of proteins. We focus on three aspects of the algorithm: bound smoothing with the triangle inequality, the random selection of distances within the bounds, and the number of distances needed to specify a structure. Computational experiments are performed using simulated and real data for basic pancreatic trypsin inhibitor (BPTI) from nmr and crystallographic measurements. We find that the upper bounds determined by bound smoothing to be a linear function of the true crystal distance. A simple model that describes the results obtained with randomly selected trial distances is proposed. Using this representation of the trial distances, we show that BPTI DG structures are more compact than the true crystal structure. We also show that the DG-generated structures no longer resemble test structures when the number of these interresidue distance constraints is less than the number of degrees of freedom of the protein backbone. While the actual model will be sensitive the way distances are chosen, our conclusions are likely to apply to other versions of the DG algorithm.

Algorithms↗

PubMed2002

The dilemma of the selfish herd: the search for a realistic movement rule.

The selfish herd hypothesis predicts that aggregations form because individuals move toward one another to minimize their own predation risk. The "dilemma of the selfish herd" is that movement rules that are easy for individuals to follow, fail to produce true aggregations, while rules that produce aggregations require individual behavior so complex that one may doubt most animals can follow them. If natural selection at the individual level is responsible for herding behavior, a solution to the dilemma must exist. Using computer simulations, we examined four different movement rules. Relative predation risk was different for all four movement rules (p<0.05). We defined three criteria for measuring the quality of a movement rule. A good movement rule should (a) be statistically likely to benefit an individual that follows it, (b) be something we can imagine most animals are capable of following, and (c) result in a centrally compact flock. The local crowded horizon rule, which allowed individuals to take the positions of many flock-mates into account, but decreased the influence of flock-mates with distance, best satisfied these criteria. The local crowded horizon rule was very sensitive to the animal's perceptive ability. Therefore, the animal's ability to detect its neighbors is an important factor in the dynamics of group formation.

Animals↗

PubMed1995

A diagnostic-quality electronic portal imaging system.

Initial clinical experience is presented, on the use of a prototype portal imaging system which is designed to provide diagnostic-quality images on-line at the accelerator. The system comprises a compact diagnostic X-ray unit mounted on the accelerator head, with its source in the isocentric plane exactly 37 degrees around from the therapy source. The image detector is an image intensifier with digital image storage/processing facilities. Images were taken at the accelerator of treatment fields in seven patients (pelvic, head and neck, chest fields) and these images were comparable in anatomical contrast to simulator radiographs. Two techniques for marking the therapy field onto the portal images were successfully demonstrated. One was to mark relevant corners or edges of the therapy light field on the skin using small Pb markers which become clearly visible in the 'diagnostic' portal image. The other was to record a separate 'therapy' image and through the software, extract and superimpose the field edges on to the 'diagnostic' image. The system and method proved fundamentally sound on criteria of image quality, geometric precision of rotation between therapy and imaging conditions, and its potential for development as a practical clinical tool.

Female↗

PubMed2004

A new correlation effect in the Helmholtz and surface potentials of the electrical double layer.

The restricted primitive model of an electrical double layer around a spherical macroparticle is studied by using integral equation theories and Monte Carlo simulations. The resulting theoretical curves for the Helmholtz and surface potentials versus the macroparticle charge show an unexpected positive curvature when the ionic size of uni- and divalent electrolyte species is increased. This is a novel effect that is confirmed here by computer experiments. An explanation of this phenomenon is advanced in terms of the adsorption and layering of the electrolytic species and of the compactness of the diffuse double layer. It is claimed that the interplay between electrostatic and ionic size correlation effects, absent in the classical Poisson-Boltzmann view, is responsible for this singularity.

Journal Article↗

PubMed2000

Smoluchowski dynamics of the vnd/NK-2 homeodomain from Drosophila melanogaster: second-order maximum correlation approximation.

The mode coupling diffusion theory is applied to the derivation of local dynamics in proteins in solution. The rotational dynamics of the bonds along the protein sequence are calculated and compared to the experimentally measured nmr (15)N spin-lattice relaxation time T(1), at 36.5, 60.8, and 81.1 MHz of the vnd/NK-2 homeodomain from Drosophila melanogaster. The starting point for the calculations is the experimental three-dimensional solution structure of the homeodomain determined by multidimensional nmr spectroscopy. The higher order mode-coupling computations are compared also with the recently published first-order approximation calculations. The more accurate calculations improve substantially the first-order ORZLD calculations and show that the role of the strength of the hydrodynamic interactions becomes crucial to fix the order of magnitude of the rotational dynanics for these very compact molecules characterized by partial screening of the internal atoms to water. However, the relative mobility of the bonds along the sequence and the differential fluctuations depend only weakly on the hydrodynamic strength but strongly on the geometry of the three-dimensional structure and on the statistics incorporated into the theory. Both rigid and fluctuating dynamic models are examined, with fluctuations evaluated using molecular dynamics simulations. The comparison with nmr data shows that mode coupling diffusion accounts for the T(1) relaxation pattern at low frequency where the rotational tumbling dominates. An important contribution of internal motions in the nanosecond time scale is seen at high frequencies and is discussed in terms of diffusive concepts.

Animals↗

PubMed1992

The nature of folded states of globular proteins.

We suggest, using dynamical simulations of a simple heteropolymer modelling the alpha-carbon sequence in a protein, that generically the folded states of globular proteins correspond to statistically well-defined metastable states. This hypothesis, called the metastability hypothesis, states that there are several free energy minima separated by barriers of various heights such that the folded conformations of a polypeptide chain in each of the minima have similar structural characteristics but have different energies from one another. The calculated structural characteristics, such as bond angle and dihedral angle distribution functions, are assumed to arise from only those configurations belonging to a given minimum. The validity of this hypothesis is illustrated by simulations of a continuum model of a heteropolymer whose low temperature state is a well-defined beta-barrel structure. The simulations were done using a molecular dynamics algorithm (referred to as the "noisy" molecular dynamics method) containing both friction and noise terms. It is shown that for this model there are several distinct metastable minima in which the structural features are similar. Several new methods of analyzing fluctuations in structures belonging to two distinct minima are introduced. The most notable one is a dynamic measure of compactness that can in principle provide the time required for maximal compactness to be achieved. The analysis shows that for a given metastable state in which the protein has a well-defined folded structure the transition to a state of higher compactness occurs very slowly, lending credence to the notion that the system encounters a late barrier in the process of folding to the most compact structure. The examination of the fluctuations in the structures near the unfolding----folding transition temperature indicates that the transition state for the unfolding to folding process occurs closer to the folded state.

Algorithms↗

PubMed2006

A distance geometry heuristic for expanding the range of geometries sampled during conformational search.

A recent study of crystal structures of protein-ligand complexes has shown that bioactive conformations tend to be more extended than random ones (Diller and Merz, J. Comput. Aid. Mol. Des. 2002, 16, 105-112). Existing conformational sampling techniques produce molecular conformations with a distribution of geometric sizes that may not cover that of the bioactive conformations. Here, we describe a simple heuristic for biasing the conformational search toward more extended or compact conformations, while maintaining excellent sampling. The method uses a boosting strategy to generate a series of conformations, each of which is at least as extended (or compact) as the previous one. We demonstrate that this method significantly expands the range of geometric sizes generated during the search and thus increases the efficiency of sampling bioactive conformations.

Algorithms↗

PubMed2004

Lattice Monte Carlo simulations of three-dimensional charged polymer chains. II. Added salt.

The configurational properties of strongly charged polyelectrolytes accompanied by counterions and salt ions in dilute solutions are simulated using the cooperative motion algorithm on the face-centered-cubic lattice. The calculations indicate that both positive and negative ions condense on the chains at sufficiently low temperatures and their amount depends on the concentration of added salt. As the temperature decreases from high to low, the chains undergo conformational changes from neutral-like, self-avoiding polymers by more outstretched forms to compact globules. The observed extension of the chains at intermediate temperatures is also affected by the amount of salt. Furthermore, configurations with the lowest energies recorded at the lowest temperatures are aggregates of single or more entangled chains and ions of both types.

Journal Article↗

PubMed2005

Self-similarity and protein chains.

Fractal properties of 5526 different protein chains are investigated. Characteristic fractal behavior for different molecular systems is obtained from the fractal dimension analysis, which shows that the dimension is delta=2.47 . This dimension gives a measure of the protein compactness. The present finding indicates that the fractal analysis describes some structural properties of proteins and corroborates the explanation about multifractality in the energy hypersurface.

Amino Acid Sequence↗

PubMed2000

Pinpointing the putative heparin/sialic acid-binding residues in the 'sushi' domain 7 of factor H: a molecular modeling study.

Factor H, a secretory glycoprotein comprising 20 short consensus repeat (SCR) or 'sushi' domains of about 60 amino acids each, is a regulator of the complement system. The complement-regulatory functions of factor H are targeted by its binding to polyanions such as heparin/sialic acid, involving SCRs 7 and 20. Recently, the SCR 7 heparin-binding site was shown to be co-localized with the Streptococcus Group A M protein binding site on factor H (T.K. Blackmore et al., Infect. Immun. 66, 1427 (1998)). Using sequence analysis of all heparin-binding domains of factor H and its closest homologues, molecular modeling of SCRs 6 and 7, and surface electrostatic potential studies, the residues implicated in heparin/sialic acid binding to SCR 7 have been localized to four regions of sequence space containing stretches of basic as well as histidine residues. The heparin-binding site is spatially compact and lies near the interface between SCRs 6 and 7, with residues in the interdomain linker playing a significant role.

Amino Acid Sequence↗

PubMed2005

An entropy-based gene selection method for cancer classification using microarray data.

BACKGROUND: Accurate diagnosis of cancer subtypes remains a challenging problem. Building classifiers based on gene expression data is a promising approach; yet the selection of non-redundant but relevant genes is difficult. The selected gene set should be small enough to allow diagnosis even in regular clinical laboratories and ideally identify genes involved in cancer-specific regulatory pathways. Here an entropy-based method is proposed that selects genes related to the different cancer classes while at the same time reducing the redundancy among the genes. RESULTS: The present study identifies a subset of features by maximizing the relevance and minimizing the redundancy of the selected genes. A merit called normalized mutual information is employed to measure the relevance and the redundancy of the genes. In order to find a more representative subset of features, an iterative procedure is adopted that incorporates an initial clustering followed by data partitioning and the application of the algorithm to each of the partitions. A leave-one-out approach then selects the most commonly selected genes across all the different runs and the gene selection algorithm is applied again to pare down the list of selected genes until a minimal subset is obtained that gives a satisfactory accuracy of classification. The algorithm was applied to three different data sets and the results obtained were compared to work done by others using the same data sets. CONCLUSION: This study presents an entropy-based iterative algorithm for selecting genes from microarray data that are able to classify various cancer sub-types with high accuracy. In addition, the feature set obtained is very compact, that is, the redundancy between genes is reduced to a large extent. This implies that classifiers can be built with a smaller subset of genes.

Algorithms↗