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PubMed1994

Changes of insulin in plasma and receptor for insulin in various tissues after the exposure of rats to space flights and hypokinesia.

The explanation of the mechanism of the response to gravity changes is of great importance for the determination of the capacity of human subjects to adapt to the load of gravitational stress. Therefore several studies were performed to investigate the activity of endocrine system, since the hormones are involved in the regulation of physiological functions and metabolic processes. However the studies of endocrine system activity during altered gravity conditions, especially during the weightlessness are influenced by the several interventions in biomedical observations due to operational program of astronauts, wide variability in individual response and tolerance, use of extensive countermeasures, differences in the type of space missions and in the studies after landing also a hypergravity effect at landing and variability in postflight readaptation process. The significant changes of plasma insulin and glucose levels were observed in astronauts during space flights and in the first days of recovery period. In the first inflight period plasma insulin levels were increased, unchanged or decreased however after 4-5 weeks of exposure to weightlessness a decrease of insulin plasma levels were noted. After space flights an increase of plasma insulin levels were demonstrated in experimental animals and in human subjects. Since plasma insulin level is considered as most important factor involved in the regulation for insulin receptors in target tissues, an investigation of insulin receptors in various tissues was performed in rats exposed to space flight or to hypokinesia (model used for simulation of some effects of microgravity).

Adipose Tissue↗

PubMedDate not supplied

Power of QTL detection by either fixed or random models in half-sib designs.

The aim of this study was to compare the variance component approach for QTL linkage mapping in half-sib designs to the simple regression method. Empirical power was determined by Monte Carlo simulation in granddaughter designs. The factors studied (base values in parentheses) included the number of sires (5) and sons per sire (80), ratio of QTL variance to total genetic variance (lambda= 0.1), marker spacing (10 cM), and QTL allele frequency (0.5). A single bi-allelic QTL and six equally spaced markers with six alleles each were simulated. Empirical power using the regression method was 0.80, 0.92 and 0.98 for 5, 10, and 20 sires, respectively, versus 0.88, 0.98 and 0.99 using the variance component method. Power was 0.74, 0.80, 0.93, and 0.95 using regression versus 0.77, 0.88, 0.94, and 0.97 using the variance component method for QTL variance ratios (lambda) of 0.05, 0.1, 0.2, and 0.3, respectively. Power was 0.79, 0.85, 0.80 and 0.87 using regression versus 0.80, 0.86, 0.88, and 0.85 using the variance component method for QTL allele frequencies of 0.1, 0.3, 0.5, and 0.8, respectively. The log10 of type I error profiles were quite flat at close marker spacing (1 cM), confirming the inability to fine-map QTL by linkage analysis in half-sib designs. The variance component method showed slightly more potential than the regression method in QTL mapping.

Alleles↗

PubMed2007

Design and simulation of a neutron facility.

State and other regulatory entities require that for any facility housing a particle accelerator the surrounding areas must be restricted to public access unless the dose equivalent rate is less than 0.02 mSv h at 5 cm from any accessible wall surrounding the facility under conditions of maximum radiation output. A Monte Carlo radiation transport simulation code, MCNP5, was used to design a proposed facility to shield two D-T neutron generators and one D-D neutron generator. A number of different designs were simulated, but due to cost and space issues a small concrete cave proved to be the best solution for the shielding problem. With this design, all of the neutron generators could be used and all of the rooms surrounding the neutron facility could be considered unrestricted to public access. To prevent unauthorized access into the restricted area of the neutron facility, light curtains, warning lights, door interlocks, and rope barriers will be built into the facility.

Computer Simulation↗

PubMed1996

Toward an exhaustive sampling of the configurational spaces of the two forms of the peptide hormone guanylin.

The recently introduced Essential Dynamics sampling method is extended such that an exhaustive sampling of the available (backbone) configurational space can be achieved. From an initial Molecular Dynamics simulation an approximated definition of the essential subspace is obtained. This subspace is used to direct subsequent simulations by means of constraint forces. The method is applied to the peptide hormone guanylin, solvated in water, of which the structure was determined recently. The peptide exists in two forms and for both forms, an extensive sampling was produced. The sampling algorithm fills the available space (of the essential coordinates used in the procedure) at a rate that is approximately six to seven times larger than that for traditional Molecular Dynamics. The procedure does not cause any significant perturbation, which is indicated by the fact that free Molecular Dynamics simulations started at several places in the space defined by the Essential Dynamics sample that complete space. Moreover, analyses of the average free Molecular Dynamics step have shown that nowhere except close to the edge of the available space, there are regions where the system shows a drift in a particular direction. This result also shows that in principle, the essential subspace is a constant free energy surface, with well-defined and steep borders, in which the system moves diffusively. In addition, a comparison between two independent essential dynamics sampling runs, of one form of the peptide, shows that the obtained essential subspaces are virtually identical.

Algorithms↗

PubMed1997

Practical problems of determining the dimensions of heart rate data.

The practical problems are explored of determining the dimension of the phase space set generated from real, experimental and simulated data of the times between consecutive heartbeats in normal and diseased rabbits. It is determined how different measures of dimension have depended on the procedures used to construct the phase space set and on such properties of the data as the amount of data, noise, long-term trends and stationarity. Reproducible estimates of the dimensions of different physiological states are found to require considerable amounts of data recorded under stationary conditions.

Anesthesia, General↗

PubMed2000

Simulating the oxygen K-edge spectrum from grain boundaries in ceramic oxides using the multiple scattering methodology

In this paper we demonstrate the use of the multiple scattering methodology to interpret oxygen K-edge spectra from both the bulk and grain boundaries in a variety of ceramic oxides. The experimental electron energy loss spectra (EELS) used in this study, were obtained from a dedicated scanning transmission electron microscope (STEM). Using the STEM to obtain the spectra has the advantage that each spectrum can be acquired with atomic spatial resolution. While the energy resolution is limited to approximately 0.8 eV, and the angular integration in the microscope apertures precludes momentum resolved spectroscopy, this unprecedented spatial resolution allows the electronic structure at individual defect sites to be determined. Additionally, as the microscope can also provide an atomic resolution image of the defect, the relationship between the atomic structure of the defect and its local electronic structure can be determined. In practice, this is achieved by using the structure observed in the image to build the real space atomic cluster for multiple scattering simulations. Detailed interpretation of the simulations of oxygen K-edge spectra from bulk MgO, CaO, SrTiO3, TiO2, MnO2, Mn3O4, Mn2O3 and MnO are presented. In addition, the simulations from grain boundaries in TiO2 (undoped) and SrTiO3 (undoped and Mn doped) are discussed in relation to quantifying the changes in the local electronic structure that are a direct consequence of the defect structure. The simulations are used to make interpretations of the structure-property relationships at these grain boundaries.

Journal Article↗

PubMed1995

Interpretation of 'quantal' peaks in distributions of evoked synaptic transmission at central synapses.

At some synaptic connections in the central nervous system, amplitude distributions of evoked synaptic currents exhibit surprisingly sharp and regularly spaced peaks. At these connections, detailed analysis of the peaks has led to the proposal that the 'quantal' synaptic current displays very little variability, not only at a release site, but also between release sites. In this study the latter hypothesis has been tested using simulations of evoked transmission. In contrast with previous conclusions, these simulations demonstrate that the experimental observation of regularly spaced peaks in amplitude distributions of synaptic currents is compatible with large underlying differences in the synaptic current amplitudes between release sites. The simulations also reveal that quantal analysis based entirely on the observation and analysis of regularly spaced peaks in evoked synaptic current amplitude distributions, cannot be used with confidence to estimate presynaptic release probabilities, 'quantal' current amplitudes at each release site, or the total number of available release sites. This problem may be a confounding factor in determining whether pre- or postsynaptic changes underlie alterations in synaptic efficacy, such as occurs during long term potentiation.

Animals↗

PubMedDate not supplied

Closed-loop, estimator-based model of human posture following reduced gravity exposure.

A computational and experimental method is employed to provide an understanding of a critical human space flight problem, posture control following reduced gravity exposure. In the case of an emergency egress, astronauts' postural stability could be life saving. It is hypothesized that muscular gains are lowered during reduced gravity exposure, causing a feeling of heavy legs, or a perceived feeling of muscular weakness, upon return to Earth's 1 g environment. We developed an estimator-based model that is verified by replicating spatial and temporal characteristics of human posture and incorporates an inverted pendulum plant in series with a Hill-type muscle model, two feedback pathways, a central nervous system estimator, and variable gains. Results obtained by lowering the variable muscle gain in the model support the hypothesis. Experimentally, subjects were exposed to partial gravity (3/8 g) simulation on a suspension apparatus, then performed exercises postulated to expedite recovery and alleviate the heavy legs phenomenon. Results show that the rms position of the center of pressure increases significantly after reduced gravity exposure. Closed-loop system behavior is revealed, and posture is divided into a short-term period that exhibits higher stochastic activity and persistent trends and a long-term period that shows relatively low stochastic activity and antipersistent trends.

Adult↗

PubMedDate not supplied

French research program on the physiological problems caused by weightlessness. Use of the primate model.

The need to acquire a better knowledge of the main biological problems induced by microgravity implies--in addition to human experimentation--the use of animal models, and primates seem to be particularly well adapted to this type of research. The major areas of investigation to be considered are the phospho-calcium metabolism and the metabolism of supporting tissues, the hydroelectrolytic metabolism, the cardiovascular function, awakeness, sleep-awakeness cycles, the physiology of equilibrium and the pathophysiology of space sickness. Considering this program, the Centre d'Etudes et de Recherches de Medecine Aerospatiale, under the sponsorship of the Centre National d'Etudes Spatiales, developed both a program of research on restrained primates for the French-U.S. space cooperation (Spacelab program) and for the French-Soviet space cooperation (Bio-cosmos program), and simulation of the effects of microgravity by head-down bedrest. Its major characteristics are discussed in the study.

Adaptation, Physiological↗

PubMed1994

Acute effects of simulated microgravity on heart rate variability.

Microgravity is known to stress the heart and blood vessels and to perturb the normal neural regulation of the cardiovascular system. In an effort to gain greater insight into the adjustments of neural control of the cardiovascular system in space, we have used a model of simulated microgravity, the -6 degrees head-down tilt body position (HDT). As a common method for the description of the functional state of the cardiovascular system the power spectral analysis of the heart rate can be used. The following working hypotheses were postulated: 1. HDT causes an acute activation of the parasympathetic nerve traffic to the heart, which is detectable by a reduction in heart rate and by the spectral power distribution of the heart rate variability. 2. HDT induces changes in the autonomic nervous response to upright posture which can be detected after a 45-minute period of head-down tilt.

Adult↗

PubMed1993

Simulations of washout experiments in postmortem rat lungs.

We developed a rat lung model to simulate single-breath and multiple-breath washout experiments performed by Verbanck et al. (J. Appl. Physiol. 71: 847-854, 1991) and González Mangado et al. (J. Appl. Physiol. 71: 855-862, 1991). The multi-branch-point rat lung model is based on anatomic data of the rat airway tree as obtained by Rodriguez et al. (Am. J. Anat. 180: 143-155, 1987). We simulated single- and multiple-breath washout maneuvers and computed the slope of the alveolar plateaus and Fowler and Bohr dead spaces. In general, the comparison between experiments and simulations shows a good agreement, suggesting that the mechanism of diffusion-convection interaction in an asymmetric structure entirely accounts for the ventilation maldistribution in the rat lung. In particular, it is shown that the marked asymmetry of the rat lung structure is responsible for the fact that He slopes are larger than SF6 slopes in rat lungs, as opposed to what is observed in other species.

Animals↗

PubMed1996

Conformational sampling by NMR solution structures calculated with the program DIANA evaluated by comparison with long-time molecular dynamics calculations in explicit water.

The NMR solution structure of bovine pancreatic trypsin inhibitor (BPTI) obtained by distance geometry calculations with the program DIANA is compared with groups of conformers generated by molecular dynamics (MD) simulations in explicit water at ambient temperature and pressure. The MD simulations started from a single conformer and were free or restrained either by the experimental NOE distance restraints or by time-averaged restraints; the groups of conformers were collected either in 10 ps intervals during 200 ps periods of simulation, or in 50 ps intervals during a 1 ns period of simulation. Overall, these comparisons show that the standard protein structure determination protocol with the program DIANA provides a picture of the protein structure that is in agreement with MD simulations using "realistic" potential functions over a nanosecond timescale. For well-constrained molecular regions there is a trend in the free MD simulation of duration 1 ns that the sampling of the conformation space is slightly increased relative to the DIANA calculations. In contrast, for surface-exposed side-chains that are less extensively constrained by the NMR data, the DIANA conformers tend to sample larger regions of conformational space than conformers selected from any of the MD trajectories. Additional insights into the behavior of surface side-chains come from comparison of the MD runs of 200 ps or 1 ns duration. In this time range the sampling of conformation space by the protein surface depends strongly on the length of the simulation, which indicates that significant side-chain transitions occur on the nanosecond timescale and that much longer simulations will be needed to obtain statistically significant data on side-chain dynamics.

Amino Acid Sequence↗

PubMedDate not supplied

Frequency-domain simulation of MR tagging.

Simulation of MR images is a useful tool for offline sequence development and as an aid to understanding image formation. One particular application of simulation is MR tagging, which is used for tracking myocardial motion. Simple spatial-domain methods cannot adequately represent effects common in these images, such as motion artifact and signal wrap. An existing frequency-domain model is shown to be inappropriate for tagged images, and an extension based on the Bloch equations and Fourier shift theorem is described to correct this. Software incorporating the new model is used to generate ideal tag intensity profiles and to accurately simulate tagged images. The shifted k-space patterns associated with tagged images, and their dependence on the order of the binomial tagging sequence, are explained. An application of the Fourier shift theorem is suggested that allows more rapid simulation of static tagged images.

Computer Simulation↗

PubMed2002

An experimental study on mandibular expansion: increases in arch width and perimeter.

The purpose of this study was to estimate the increase in arch perimeter associated with mandibular lateral expansion. The mandibular expansion was simulated using a three-dimensional (3D) finite element method (FEM) and a computer graphics technique (3D simulation). The centre of rotation of molars during movement accompanied by lateral expansion was calculated using 3D FEM. The geometry of the model was determined using the mandibular bone of an East Indian skeletal specimen and 1 mm computer tomogram (CT) slices. The 3D set-up simulation was then conducted using 3D computer graphics instead of performing a manual set-up. Rotational movement was induced in the buccal segment, from the first premolar to second molar, in the 3D set-up model around the location of the centre of rotation (4.5 mm below the root apex of the first molar) derived from the FEM. According to 3D simulation, the model showed an opening space of 1.43 mm between the canine and first premolar, and thus a change in arch perimeter of 2.86 mm. The tip of the mesio-lingual cusp of the first molar moved 3.88 mm laterally, resulting in a change in inter-molar width of 7.76 mm. These values mean that a 1 mm increase in arch width resulted in an increase in arch perimeter of 0.37 mm. This result would be of value clinically for prediction of the effects of mandibular expansion.

Biomechanical Phenomena↗

PubMed1992

On the interpretation of biochemical data by molecular dynamics computer simulation.

The application of computer simulation to molecular systems of biochemical interest is reviewed. It is shown that computer simulation is a tool complementary to experimental methods, which can be used to access atomic details inaccessible to experimental probes. Examples are given in which computer simulation augments the experimental information by providing an atomic picture of high resolution with respect to space, energy or time. The usefulness of a computer simulation largely depends on its quality. The most important factors that limit the accuracy of simulated results are discussed. The accuracy of different simulation studies can differ by orders of magnitude. The accuracy will depend on the type of biomolecular system and process studied. It will also depend on the choice of force field, the simulation set-up and the protocol that is used. A list of quality-determining factors is given, which may be useful when interpreting simulation studies appearing in the literature.

Biochemical Phenomena↗

PubMed2005

Ion funnels for the masses: experiments and simulations with a simplified ion funnel.

A modified ion funnel is described. Counterintuitively, increased spacing between electrodes results in enhanced "focusing" of the ions through the funnel. Consequently, the internal diameter (i.d.) of the funnel need not decrease to the conductance limit (as in previous designs). A simple dc-only lens, which also serves as the conductance limit, combined with the natural flow of gas is used to extract the ions from the funnel. Ions with mass to charge ratios varying between 75 and 3000 m/z are passed through the funnel with no apparent discrimination. The funnel can be operated under mild conditions that preserve weakly bound noncovalent complexes. After testing several designs, a thin closely spaced dc lens was found to be the best solution for extracting ions. A simple method for simulating ion trajectories at nonzero pressures based on ion mobility and explicit diffusion is described. This theoretical approach was used to design and calculate ion trajectories for the modified funnel presented here. Finally, the increased spacing between electrodes in the current funnel significantly relaxes machining constraints, reduces cost, and enhances ease of use versus previous funnel designs.

Computer Simulation↗

PubMed2001

Bimanual haptic workstation for laparoscopic surgery simulation.

Realistic laparoscopic surgical simulators will require real-time graphic imaging and tactile feedback. Our research objective is to develop a cost-effective haptic workstation for the simulation of laparoscopic procedures for training and treatment planning. The physical station consists of a custom-built frame into which laparoscopic trocars and surgical tools may be attached/inserted and which are continuously adjustable to various positions and orientations to simulate multiple laparoscopic surgical approaches. Instruments inserted through the trocars are attached to end effectors of two haptic devices and interfaced to a high speed PC with fast graphics capability. The haptic device transduces 3D motion of the two manually operated surgical instruments into slave maneuvers in virtual space. The slave instrument tips probe the simulated organ. Simulations currently in progress include: 1) Surface-only renderings, deformation, and haptic interactions with elements in the gall gladder surgical field; 2) Voxel-based simulations of the bulk manipulation of tissue; 3) laparoscopic herniorrhaphy. This system provides force feed-forward from the grasped tools to the contact tissue in virtual space, with deformation of the tissue by the virtual probe, and force feedback from the deformed tissue to the operator's hands.

Computer Graphics↗

PubMed2001

A basal area model responsive to thinning for a plantation forest.

The Tarawera Valley spacing and thinning trial data were used to develop a dynamical model for basal area prediction that is responsive to both spacing and thinning. The model is a 'critically damped' second-order model, i.e., it simulates a sigmoidal response, before and after thinning. It has a scalar spacing variable, which makes the model responsive to different spacing trials. It also has a vector 'reductor' term, which enables simulation over different productivity sites, although this still needs to be validated with measured data. The dynamical model has the potential of being applied across a forest estate with different productivity sites, if data are available for all sites.

Conservation of Natural Resources↗