SEARCH · PubMed Health

Results for “Compaction simulator”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 307 records · Page 17Linked to original sources

PubMed2004

Determination of mechanical stiffness of bone by pQCT measurements: correlation with non-destructive mechanical four-point bending test data.

Mechanical tests of bone provide valuable information about material and structural properties important for understanding bone pathology in both clinical and research settings, but no previous studies have produced applicable non-invasive, quantitative estimates of bending stiffness. The goal of this study was to evaluate the effectiveness of using peripheral quantitative computed tomography (pQCT) data to accurately compute the bending stiffness of bone. Normal rabbit humeri (N=8) were scanned at their mid-diaphyses using pQCT. The average bone mineral densities and the cross-sectional moments of inertia were computed from the pQCT cross-sections. Bending stiffness was determined as a function of the elastic modulus of compact bone (based on the local bone mineral density), cross-sectional moment of inertia, and simulated quasistatic strain rate. The actual bending stiffness of the bones was determined using four-point bending tests. Comparison of the bending stiffness estimated from the pQCT data and the mechanical bending stiffness revealed excellent correlation (R2=0.96). The bending stiffness from the pQCT data was on average 103% of that obtained from the four-point bending tests. The results indicate that pQCT data can be used to accurately determine the bending stiffness of normal bone. Possible applications include temporal quantification of fracture healing and risk management of osteoporosis or other bone pathologies.

Animals↗

PubMed1999

Bioactive ceramics prepared by sintering and crystallization of calcium phosphate invert glasses.

Novel glass-ceramics were synthesized via sintering and crystallization by heating powder compacts of SiO2-free calcium phosphate invert glasses of 60CaO x 30P2O5 x 7Na2O x 3TiO2 or 60CaO x 30P2O5 x 7Na2O x 3MgO at 800-850 degrees C in air. The glass-ceramics were relatively dense materials consisting of crystalline phases such as beta-Ca3(PO4)2 and beta-Ca2P2O7 with glassy phases. The compacts were densified by the viscous flow of the glassy phases while heating. By soaking in simulated body fluid at 37 degrees C, a calcium phosphate phase was formed newly on the surface of the glass-ceramic derived from 60CaO x 30P2O5 x 7Na2O x 3TiO2 glass, while the phase was not formed on that derived from 60CaO x 30P2O5 x 7Na2O x 3MgO glass: the former was implied to show bioactivity. Composition of the glassy phase as the matrix varies with the additives such as TiO2 and MgO, and the chemical properties of the phase influence the bioactivity of the glass-ceramics. The glass-ceramic derived from 60CaO x 30P2O5 x 7Na2O x 3TiO2 glass has relatively high fracture toughness of K(IC) approximately 2 MPa m(0.5) and bending strength of 100-120 MPa.

Calcium Compounds↗

PubMed1995

Solution structure of the MutT enzyme, a nucleoside triphosphate pyrophosphohydrolase.

The MutT enzyme (129 residues) catalyzes the hydrolysis of normal and mutagenic nucleoside triphosphates, such as 8-oxo-dGTP, by substitution at the rarely attacked beta-P, to yield NMP and pyrophosphate. Previous heteronuclear NMR studies of MutT have shown the secondary structure to consist of a five-stranded mixed beta-sheet connected by the loop I-alpha-helix I--loop II motif, by two tight turns, and by loop III, and terminated by loop IV--alpha-helix II [Abeygunawardana et al. (1993) Biochemistry 32, 13071-13080; Weber et al. (1993) Biochemistry 32, 13081-13087). Complete side-chain assignments of 1H and 13C resonances have now been made by 3D C(CO)NH and HCCH-TOCSY experiments. A total of 1461 interproton proximities (11 per residue), obtained by 3D 15N-resolved NOESY-HSQC and 3D 13C-resolved NOESY-HSQC spectra, including 372 long-range NOEs, as well as 65 dihedral angle (phi) restraints and 34 backbone hydrogen bond restraints were used to determine the tertiary structure of MutT by distance geometry, simulated annealing, and energy minimization with the program X-PLOR. The structure is globular and compact with the parallel portion of the beta-sheet sandwiched between the two alpha-helices, forming an alpha+beta fold. The essential divalent cation has previously been shown to bind near residues Gly-37, Gly-38, Lys-39, and Glu-57, and nucleotides have been shown to bind near residues Leu-54 and Val-58 by NMR relaxation methods [Frick et al. (1995) Biochemistry 34, 5577-5586].(ABSTRACT TRUNCATED AT 250 WORDS)

Bacterial Proteins↗

PubMed2005

Less is more: towards an optimal universal description of protein folds.

MOTIVATION: Identification and characterization of protein structure regularities can reveal the mechanisms governing protein structure, function and evolution. Here we focus on an intermediate level of regularity. We have developed automated methods to systematically construct a dictionary of supersecondary structures that can be used as 'protein parts' to describe fold-sized structures. RESULTS: The dictionary was constructed by aligning representative structures of all known folds, clustering similar substructures and selecting the most descriptive substructures in a minimum description length fashion. We show that the dictionary is compact and descriptive, capable of describing a substantial fraction of all known protein folds. We performed simulations using independent sets of training and testing folds. Dictionaries generated using the training set had high coverage over the folds in the testing set, suggesting that dictionary entries reflect general features of protein structures and should be capable of describing novel protein folds.

Algorithms↗

PubMed1991

Mathematical model of geometry and fibrous structure of the heart.

We developed a mathematical representation of ventricular geometry and muscle fiber organization using three-dimensional finite elements referred to a prolate spheroid coordinate system. Within elements, fields are approximated using basis functions with associated parameters defined at the element nodes. Four parameters per node are used to describe ventricular geometry. The radial coordinate is interpolated using cubic Hermite basis functions that preserve slope continuity, while the angular coordinates are interpolated linearly. Two further nodal parameters describe the orientation of myocardial fibers. The orientation of fibers within coordinate planes bounded by epicardial and endocardial surfaces is interpolated linearly, with transmural variation given by cubic Hermite basis functions. Left and right ventricular geometry and myocardial fiber orientations were characterized for a canine heart arrested in diastole and fixed at zero transmural pressure. The geometry was represented by a 24-element ensemble with 41 nodes. Nodal parameters fitted using least squares provided a realistic description of ventricular epicardial [root mean square (RMS) error less than 0.9 mm] and endocardial (RMS error less than 2.6 mm) surfaces. Measured fiber fields were also fitted (RMS error less than 17 degrees) with a 60-element, 99-node mesh obtained by subdividing the 24-element mesh. These methods provide a compact and accurate anatomic description of the ventricles suitable for use in finite element stress analysis, simulation of cardiac electrical activation, and other cardiac field modeling problems.

Animals↗

PubMed2001

[The Baxter AS 50 syringe pump: a comparison with propofol-specific syringe pumps].

We used a Baxter AS 50 syringe pump for intravenous anesthesia with propofol, and compared it with a Grasby 3500 and a Terumo STC-525 X pumps, which are specifically designed for propofol infusion. The AS 50 pump is a programmable syringe infusion pump, which allows us to register up to 70 drug names in 10 categories and various infusion modes for drugs. There are 14 types of continuous infusion mode, a custom dilution mode, and three types of time infusion modes. The continuous infusion mode in mg.kg-1.h-1 is available for propofol anesthesia. Operation of this pump is simple and user-friendly, as with for the other propofol-specific pumps. Although the AS 50 pump is limited to a maximum bolus rate of 438 ml.h-1, this restriction is not a serious problem in clinical practice. The AS 50 pump is also equipped with an RS-232 C digital interface port to allow external remote monitoring or automated control. On-line simulation of blood propofol concentration is possible with a simulation program such as Propofol-Mon. Our impression is that the AS 50 pump is compact, easy to use, accurate and reliable for propofol anesthesia.

Anesthesia, Intravenous↗

PubMed1992

Insect motion perception.

The first step in this work of reconstruction of a theory of insect vision was to demonstrate that visual behaviour relies on scanning by self-motion and apparently involves measurement of angular velocities of contrasts moving across the eye. The next step was to demonstrate that parallax is also significant as a way of segmenting the visual scene into separate objects. There followed a series of experiments to rule out the existing theory that motion perception depends on autocorrelation, and at the same time an alternative theory was developed. The new theory assumes that at the level of the optic medulla there are numerous parallel channels on each visual axis, representing different neurons, all looking out for their specific combination of signals. The combinations are formed by positive, negative or no-change temporal contrasts at two adjacent visual axes at two successive times, forming 3(4) = 81 possible templates. Simulation of this highly parallel system shows that it can represent the moving image in a compact form that would be adequate to explain what is known for motion and form vision (but not colour vision) in insects. Form, like colour, would be seen as the ratio of numbers of responses of particular templates, in the same way that colours are seen as ratios of responses of receptors for different wavelengths.(ABSTRACT TRUNCATED AT 250 WORDS)

Algorithms↗

PubMed2001

Identification and ab initio simulations of early folding units in proteins.

The location of protein subunits that form early during folding, constituted of consecutive secondary structure elements with some intrinsic stability and favorable tertiary interactions, is predicted using a combination of threading algorithms and local structure prediction methods. Two folding units are selected among the candidates identified in a database of known protein structures: the fragment 15-55 of 434 cro, an all-alpha protein, and the fragment 1-35 of ubiquitin, an alpha/beta protein. These units are further analyzed by means of Monte Carlo simulated annealing using several database-derived potentials describing different types of interactions. Our results suggest that the local interactions along the chain dominate in the first folding steps of both fragments, and that the formation of some of the secondary structures necessarily occurs before structure compaction. These findings led us to define a prediction protocol, which is efficient to improve the accuracy of the predicted structures. It involves a first simulation with a local interaction potential only, whose final conformation is used as a starting structure of a second simulation that uses a combination of local interaction and distance potentials. The root mean square deviations between the coordinates of predicted and native structures are as low as 2-4 A in most trials. The possibility of extending this protocol to the prediction of full proteins is discussed. Proteins 2001;42:164-176.

Amino Acid Sequence↗

PubMed2005

Solution structure and internal dynamics of NSCP, a compact calcium-binding protein.

The solution structure of Nereis diversicolor sarcoplasmic calcium-binding protein (NSCP) in the calcium-bound form was determined by NMR spectroscopy, distance geometry and simulated annealing. Based on 1859 NOE restraints and 262 angular restraints, 17 structures were generated with a rmsd of 0.87 A from the mean structure. The solution structure, which is highly similar to the structure obtained by X-ray crystallography, includes two open EF-hand domains, which are in close contact through their hydrophobic surfaces. The internal dynamics of the protein backbone were determined by studying amide hydrogen/deuterium exchange rates and 15N nuclear relaxation. The two methods revealed a highly compact and rigid structure, with greatly restricted mobility at the two termini. For most of the amide protons, the free energy of exchange-compatible structural opening is similar to the free energy of structural stability, suggesting that isotope exchange of these protons takes place through global unfolding of the protein. Enhanced conformational flexibility was noted in the unoccupied Ca2+-binding site II, as well as the neighbouring helices. Analysis of the experimental nuclear relaxation and the molecular dynamics simulations give very similar profiles for the backbone generalized order parameter (S2), a parameter related to the amplitude of fast (picosecond to nanosecond) movements of N(H)-H vectors. We also noted a significant correlation between this parameter, the exchange rate, and the crystallographic B factor along the sequence.

Amides↗

PubMed2003

A simulation study of the error in dipole source localization for EEG spikes with a realistic head model.

OBJECTIVE: We tried to determine the error range of dipole modeling for EEG spikes originating from various clinically important sources by a simulation study employing a realistic head model. The computed error range was also compared with the degree of disturbance of dipole modeling caused by adding background activity to the spike. METHODS: The scalp fields generated by temporal, frontal and rolandic epileptic sources with spatial extent were simulated, and the corresponding 3-dimensional maps of residual variance (RV) were built by computing the RV for a single dipole at each point on a fine imaginary grid in the brain. Single dipole modeling was also performed for the simulated scalp fields after adding real background activity. RESULTS: The brain volume corresponding to a small RV was compact for the frontal sources and the lateral and baso-mesial temporal sources, and large for the anterior and baso-lateral temporal sources. The distribution of dipoles estimated for spikes contaminated with background corresponded to that of the volume of small RV and to spike-amplitude. Estimates were improved by employing inferior temporal electrodes. CONCLUSIONS: When evaluating dipole models of epileptic spikes, error ranges can be estimated and they vary considerably from region to region. SIGNIFICANCE: This study illustrates the variability of the error in dipole modeling of epileptic spikes. This variability is important when considering the clinical interpretation of modeling results.

Brain Mapping↗

PubMed1997

A finite element solution for the anisotropic biphasic theory of tissue-equivalent mechanics: the effect of contact guidance on isometric cell traction measurement.

We present a method for solving the governing equations from our anisotropic biphasic theory of tissue-equivalent mechanics (Barocas and Tranquillo, 1997) for axisymmetric problems. A mixed finite element method is used for discretization of the spatial derivatives, and the DASPK subroutine (Brown et al., 1994) is used to solve the resulting differential-algebraic equation system. The preconditioned GMRES algorithm, using a preconditioner based on an extension of Dembo's (1994) adaptation of the Uzawa algorithm for viscous flows, provides an efficient and scaleable solution method, with the finite element method discretization being first-order accurate in space. In the cylindrical isometric cell traction assay, the chosen test problem, a cylindrical tissue equivalent is adherent at either end to fixed circular platens. As the cells exert traction on the collagen fibrils, the force required to maintain constant sample length, or load, is measured. However, radial compaction occurs during the course of the assay, so that the cell and network concentrations increase and collagen fibrils become aligned along the axis of the cylinder, leading to cell alignment along the axis. Our simulations predict that cell contact guidance leads to an increase in the load measured in the assay, but this effect is diminished by the tendency of contact guidance to inhibit radial compaction of the sample, which in turn reduces concentrations and hence the measured load.

Algorithms↗

PubMed2005

A grid layout algorithm for automatic drawing of biochemical networks.

MOTIVATION: Visualization is indispensable in the research of complex biochemical networks. Available graph layout algorithms are not adequate for satisfactorily drawing such networks. New methods are required to visualize automatically the topological architectures and facilitate the understanding of the functions of the networks. RESULTS: We propose a novel layout algorithm to draw complex biochemical networks. A network is modeled as a system of interacting nodes on squared grids. A discrete cost function between each node pair is designed based on the topological relation and the geometric positions of the two nodes. The layouts are produced by minimizing the total cost. We design a fast algorithm to minimize the discrete cost function, by which candidate layouts can be produced efficiently. A simulated annealing procedure is used to choose better candidates. Our algorithm demonstrates its ability to exhibit cluster structures clearly in relatively compact layout areas without any prior knowledge. We developed Windows software to implement the algorithm for CADLIVE. AVAILABILITY: All materials can be freely downloaded from http://kurata21.bio.kyutech.ac.jp/grid/grid_layout.htm; http://www.cadlive.jp/ SUPPLEMENTARY INFORMATION: http://kurata21.bio.kyutech.ac.jp/grid/grid_layout.htm; http://www.cadlive.jp/

Algorithms↗

PubMed2004

Importance of chirality and reduced flexibility of protein side chains: a study with square and tetrahedral lattice models.

Side chains of amino acid residues are the determining factor that distinguishes proteins from other unstable chain polymers. In simple models they are often represented implicitly (e.g., by spin states) or simplified as one atom. Here we study side chain effects using two-dimensional square lattice and three-dimensional tetrahedral lattice models, with explicitly constructed side chains formed by two atoms of different chirality and flexibility. We distinguish effects due to chirality and effects due to side chain flexibilities, since residues in proteins are L residues, and their side chains adopt different rotameric states. For short chains, we enumerate exhaustively all possible conformations. For long chains, we sample effectively rare events such as compact conformations and obtain complete pictures of ensemble properties of conformations of these models at all compactness region. This is made possible by using sequential Monte Carlo techniques based on chain growth method. Our results show that both chirality and reduced side chain flexibility lower the folding entropy significantly for globally compact conformations, suggesting that they are important properties of residues to ensure fast folding and stable native structure. This corresponds well with our finding that natural amino acid residues have reduced effective flexibility, as evidenced by statistical analysis of rotamer libraries and side chain rotatable bonds. We further develop a method calculating the exact side chain entropy for a given backbone structure. We show that simple rotamer counting underestimates side chain entropy significantly for both extended and near maximally compact conformations. We find that side chain entropy does not always correlate well with main chain packing. With explicit side chains, extended backbones do not have the largest side chain entropy. Among compact backbones with maximum side chain entropy, helical structures emerge as the dominating configurations. Our results suggest that side chain entropy may be an important factor contributing to the formation of alpha helices for compact conformations.

Computer Simulation↗

PubMed2003

Models of coral growth: spontaneous branching, compactification and the Laplacian growth assumption.

In stony corals it is often observed that specimens collected from a sheltered growth site have more open and more thinly branched growth forms than specimens of the same species from more exposed growth sites, where stronger water currents are found. This observation was explained using an abiotic computational model inspired by coral growth, in which the growth velocity depended locally on the absorption of a resource dispersed by advection and diffusion (Kaandorp and Sloot, J. Theor. Biol 209 (2001) 257). In that model a morphological range was found; as the Péclet-number (indicating the relative importance of advective and diffusive nutrient transport) was increased, more compact and spherical growth forms were found. Two unsatisfactory items have remained in this model, which we address in the present paper. First, an explicit curvature rule was responsible for branching. In this work we show that the curvature rule is not needed: the model exhibits spontaneous branching, provided that the resource field is computed with enough precision. Second, previously no explanation was given for the morphological range found in the simulations. Here we show that such an explanation is given by the conditions under which spontaneous branching occurs in our model, in which the compactness of the growth forms depends on the ratio of the rates of growth and nutrient transport. We did not find an effect of flow. This suggests that the computational evidence that hydrodynamics influences the compactness of corals in laminar flows may not be conclusive. The applicability of the Laplacian growth paradigm to understand coral growth is discussed.

Absorption↗

PubMed1987

Point mutations as an optimal search process in biological evolution.

Point mutations are pictured as jumps in a phase space representing the sequences of amino acids or nucleotides as discrete points. It is shown that this space can be given a natural metric by quantifying common physical and chemical properties of amino acid constituents in terms of a natural measure. Evolution through point mutations is simulated by the search for points in the phase space representing amino acid sequences of high survival fitness. Due to the local compactness of the distribution of these functionally allowed points in phase space any successful search procedure has characteristics qualitatively different from those in the case of a random distribution. This is demonstrated by model calculations. A specified distribution of allowed points is generated with subsequent evaluation of the success of the retrieval process as a function of the jump probabilities between lattice sites. The results of such simulations are compared with data obtained from the analysis of the DNA or mRNA sequences coding related proteins. By counting silent and expressed nucleotide replacement frequencies one can draw conclusions as to the efficacy of the natural evolutionary search processes in the phase space of amino acid sequences. There are cases, where the highest possible information gain of one bit per accepted point mutation is achieved. In general the information gain is found to be somewhat sub-maximal due to functional requirements.

Amino Acid Sequence↗

PubMed1987

Design of a new pulse duplicator system for prosthetic heart valves.

This paper discusses results of a computer simulation for designing a new pulse duplicator system for mechanical heart valves. The design objective of the system is to obtain a compact, efficient pulse duplicator system capable of accurately measuring the volume flow rate across a valve. The volume flow rate is determined as the derivative of the volume displacement of an actuator piston which directly drives the fluid. The system does not need any circulatory loop, since the piston is controlled on-line to follow command signals representing an aortic impedance. The results of the computer simulation show: the designed PI-controllers of the actuator can precisely control valve motion to follow given command signals, the eigenvalues of the controllers have to be carefully chosen to prevent unstable behaviors of a valve in diastole, and the dimensions of the actuator is optimized by minimizing a cost function of the total efficiency of the system.

Biomechanical Phenomena↗

PubMed2006

[Quality assured ultrasound simulation training for the detection of fetal malformations--can a training benefit be evidenced?].

INTRODUCTION: The factual sonographic training in obstetrics differs in Germany in a broad range. In this context, a tendency towards minimalistic dealings with this issue prevails. In contrast to this, the provisions of the German maternity guidelines relating to ultrasound clearly define quality oriented requirements serving altogether as a basic sonographic standard which mandatorily has to be met by all German Obstetricians. In order to close this gap between professional education and social demand, a training concept regarding obstetric ultrasound was devised by the German Association of Gynecologists utilizing the ultrasound simulator system. The aim of this study was to evaluate the usefulness and the effectiveness of this method and its potential role and benefit in structured sonographic training. MATERIAL AND METHODS: Between October 2004 and August 2005, 74 obstetric ultrasound training courses according to the ultrasound simulator concept of the Medical School of Hanover were realized in nine federal states of Germany by the German Academy of Gynecology. The aim of these courses was it to procure ultrasound knowledge regarding the structured sonographic exclusion of fetal malformations in a compact manner. As a measure of quality assurance, a standardized questionnaire was issued before and after the courses in order to analyze the benefit of these simulator-based ultrasound courses. RESULTS: The concept found prevailing approval (90 %) at the level of principle, practical implementation and clinical usefulness. 88,2 % of the participants estimated their subjective training effect as being good. The analysis of the questionnaire showed a statistically significant improvement of sonographic knowledge. On average, 74.1 % of the questions were answered correctly by the end of the course as opposed to a mere 46.3 % at the beginning. CONCLUSION: Structured ultrasound training courses based on the ultrasound simulator system seem to be able to define a basic quality of training and significantly improves examiners' skills in prenatal medicine possible independent of local or structural factors. Hence they seem to be a suitable instrument to close the gap between the sonographic education worthy of improvement and the existing social demand for efficiacy of obstetric sonography.

Congenital Abnormalities↗

PubMed2000

A simulation study of the consistency of oscillometric blood pressure measurements with and without artefacts.

BACKGROUND: Oscillometric pressure is measured by analysing, in relation to the cuff pressure, low-amplitude cuff-pressure pulsations generated by each arterial pulse. The cuff pressure is sampled at the pulse rate, introducing measurement variations, which are compounded by artefactual pulses. OBJECTIVE: To study the consistency of measurements with and without artefacts using simulated waveforms. METHODS: The Propaq Smartcuf (with and without electrocardiographic synchronization), the Welch Allyn 52 000 (before and after its software had been upgraded), the Critikon DINAMAP 8100 and Compact TS and the Criticare 507 NJC were evaluated. Each monitor recorded 15 determinations at 120/80 (93) mmHg without and with either low-frequency or high-frequency artefacts generated by the Bio-Tek BP-Pump simulator. Consistency of measurements was defined as SD of less than 2 mmHg for at least two of the systolic, diastolic and mean arterial pressures with all less than 3 mmHg. RESULTS: All monitors except the Critikon 8100 satisfied the consistency criteria without artefacts with most SD less than 1 mmHg. Several satisfied the criteria with a severe low-frequency artefact (all recorded SD were less than 6 mmHg). None satisfied the criteria with a severe high-frequency artefact. High systolic blood pressures were typically recorded with a severe tremor artefact, though the Criticare device, which measures during cuff inflation, recorded lower systolic blood pressures. The Propaq device with electrocardiographic synchronization had the lowest variability, with synchronization increasing determination time. CONCLUSION: Oscillometric monitors are more sensitive to a high-frequency artefact than they are to a low-frequency artefact. Signal-processing techniques can improve consistency of measurements. Simulators can evaluate a monitor's consistency with and without artefacts.

Blood Pressure Determination↗