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At least 973 records · Page 54Linked to original sources
PubMed2002

Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water?

The folding free energy landscape of the C-terminal beta-hairpin of protein G is explored using the surface-generalized Born (SGB) implicit solvent model, and the results are compared with the landscape from an earlier study with explicit solvent model. The OPLSAA force field is used for the beta-hairpin in both implicit and explicit solvent simulations, and the conformational space sampling is carried out with a highly parallel replica-exchange method. Surprisingly, we find from exhaustive conformation space sampling that the free energy landscape from the implicit solvent model is quite different from that of the explicit solvent model. In the implicit solvent model some nonnative states are heavily overweighted, and more importantly, the lowest free energy state is no longer the native beta-strand structure. An overly strong salt-bridge effect between charged residues (E42, D46, D47, E56, and K50) is found to be responsible for this behavior in the implicit solvent model. Despite this, we find that the OPLSAA/SGB energies of all the nonnative structures are higher than that of the native structure; thus the OPLSAA/SGB energy is still a good scoring function for structure prediction for this beta-hairpin. Furthermore, the beta-hairpin population at 282 K is found to be less than 40% from the implicit solvent model, which is much smaller than the 72% from the explicit solvent model and approximately equal 80% from experiment. On the other hand, both implicit and explicit solvent simulations with the OPLSAA force field exhibit no meaningful helical content during the folding process, which is in contrast to some very recent studies using other force fields.

Animals↗
PubMed2005

Linkage disequilibrium mapping via cladistic analysis of phase-unknown genotypes and inferred haplotypes in the Genetic Analysis Workshop 14 simulated data.

We recently described a method for linkage disequilibrium (LD) mapping, using cladistic analysis of phased single-nucleotide polymorphism (SNP) haplotypes in a logistic regression framework. However, haplotypes are often not available and cannot be deduced with certainty from the unphased genotypes. One possible two-stage approach is to infer the phase of multilocus genotype data and analyze the resulting haplotypes as if known. Here, haplotypes are inferred using the expectation-maximization (EM) algorithm and the best-guess phase assignment for each individual analyzed. However, inferring haplotypes from phase-unknown data is prone to error and this should be taken into account in the subsequent analysis. An alternative approach is to analyze the phase-unknown multilocus genotypes themselves. Here we present a generalization of the method for phase-known haplotype data to the case of unphased SNP genotypes. Our approach is designed for high-density SNP data, so we opted to analyze the simulated dataset. The marker spacing in the initial screen was too large for our method to be effective, so we used the answers provided to request further data in regions around the disease loci and in null regions. Power to detect the disease loci, accuracy in localizing the true site of the locus, and false-positive error rates are reported for the inferred-haplotype and unphased genotype methods. For this data, analyzing inferred haplotypes outperforms analysis of genotypes. As expected, our results suggest that when there is little or no LD between a disease locus and the flanking region, there will be no chance of detecting it unless the disease variant itself is genotyped.

Chromosome Mapping↗
PubMed2004

Fuzzy logic simulation of the testosterone effect on sex differences in Vandenberg-Kuse mental rotation scores.

The relationship between testosterone level and mental rotation was modeled using a fuzzy logical simulation. The fuzzy model of men's and women's testosterone levels and MR scores mapped the input "space" of testosterone to the output "space" of mental rotation. The simulation showed that a single variable (testosterone) can produce a significant difference in output. The model typifies sex difference in distribution of mental rotation scores previously observed experimentally.

Female↗
PubMed2003

A whole-body mathematical model for intracranial pressure dynamics.

Most attempts to study intracranial pressure using lumped-parameter models have adopted the classical "Kellie-Monro Doctrine," which considers the intracranial space to be a closed system that is confined within the nearly-rigid skull, conserves mass, and has equal inflow and outflow. The present work revokes this Doctrine and develops a mathematical model for the dynamics of intracranial pressures, volumes, and flows that embeds the intracranial system in extensive whole-body physiology. The new model consistently introduces compartments representing the tissues and vasculature of the extradural portions of the body, including both the thoracic region and the lower extremities. In addition to vascular connections, a spinal-subarachnoid cerebrospinal fluid (CSF) compartment bridges intracranial and extracranial physiology allowing explict buffering of intracranial pressure fluctuations by the spinal theca. The model contains cerebrovascular autoregulation, regulation of systemic vascular pressures by the sympathetic nervous system, regulation of CSF production in the choroid plexus, a lymphatic system, colloid osmotic pressure effects, and realistic descriptions of cardiac output. To validate the model in situations involving normal physiology, the model's response to a realistic pulsatile cardiac output is examined. A well-known experimentally-derived intracranial pressure-volume relationship is recovered by using the model to simulate CSF infusion tests, and the effect on cerebral blood flow of a change in body position is also examined. Cardiac arrest and hemorrhagic shock are simulated to demonstrate the predictive capabilities of the model in pathological conditions.

Blood Pressure↗
PubMed1994

Orthostatic hypotension in patients, bed rest subjects, and astronauts.

Orthostatic hypotension after even short space flights has affected a significant number of astronauts. Given the need for astronauts to function at a high level of efficiency during and after their return from space, the application of pharmacologic and other treatments is strongly indicated. This report addresses the clinical problem of orthostatic hypotension and its treatments to ascertain whether pharmacologic or physiologic treatment may be useful in the prevention of orthostatic hypotension associated with space flight. Treatment of orthostatic hypotension in patients now includes increasing intravascular volume with high sodium intake and mineralocorticoids, or increasing vascular resistance through the use of drugs to stimulate alpha or block beta vascular receptors. Earlier treatment used oral sympathomimetic ephedrine hydrochloride alone or with "head-up" bed rest. Then long-acting adrenocortical steroid desoxycorticosterone preparations with high-salt diets were used to expand volume. Fludrocortisone was shown to prevent the orthostatic drop in blood pressure. The combination of the sympathomimetic amine hydroxyamphetamine and a monoamine oxidase inhibitor tranylcypromine has been used, as has indomethacin alone. Davies et al. used mineralocorticoids at low doses concomitantly with alpha-agonists to increase vasoconstrictor action. Schirger et al used tranylcypromine and methylphenidate with or without a Jobst elastic leotard garment or the alpha-adrenergic agonist midodrine (which stimulates both arterial and venous systems without direct central nervous system or cardiac effects). Vernikos et al established that the combination of fludrocortisone, dextroamphetamine, and atropine exhibited a beneficial effect on orthostatic hypotension induced by 7-day 6 degrees head-down bed rest (a model used to simulate the weightlessness of space flight). Thus, there are numerous drugs that, in combination with mechanical techniques, including lower body negative pressure to elevate transmural pressure, could be studied to treat orthostatic hypotension after space flight.

Animals↗
PubMed2005

Selective sweep mapping of genes with large phenotypic effects.

Many domestic dog breeds have originated through fixation of discrete mutations by intense artificial selection. As a result of this process, markers in the proximity of genes influencing breed-defining traits will have reduced variation (a selective sweep) and will show divergence in allele frequency. Consequently, low-resolution genomic scans can potentially be used to identify regions containing genes that have a major influence on breed-defining traits. We model the process of breed formation and show that the probability of two or three adjacent marker loci showing a spurious signal of selection within at least one breed (i.e., Type I error or false-positive rate) is low if highly variable and moderately spaced markers are utilized. We also use simulations with selection to demonstrate that even a moderately spaced set of highly polymorphic markers (e.g., one every 0.8 cM) has high power to detect regions targeted by strong artificial selection in dogs. Further, we show that a gene responsible for black coat color in the Large Munsterlander has a 40-Mb region surrounding the gene that is very low in heterozygosity for microsatellite markers. Similarly, we survey 302 microsatellite markers in the Dachshund and find three linked monomorphic microsatellite markers all within a 10-Mb region on chromosome 3. This region contains the FGFR3 gene, which is responsible for achondroplasia in humans, but not in dogs. Consequently, our results suggest that the causative mutation is a gene or regulatory region closely linked to FGFR3.

Animals↗
PubMed2006

3D source localization of interictal spikes in epilepsy patients with MRI lesions.

The present study aims to accurately localize epileptogenic regions which are responsible for epileptic activities in epilepsy patients by means of a new subspace source localization approach, i.e. first principle vectors (FINE), using scalp EEG recordings. Computer simulations were first performed to assess source localization accuracy of FINE in the clinical electrode set-up. The source localization results from FINE were compared with the results from a classic subspace source localization approach, i.e. MUSIC, and their differences were tested statistically using the paired t-test. Other factors influencing the source localization accuracy were assessed statistically by ANOVA. The interictal epileptiform spike data from three adult epilepsy patients with medically intractable partial epilepsy and well-defined symptomatic MRI lesions were then studied using both FINE and MUSIC. The comparison between the electrical sources estimated by the subspace source localization approaches and MRI lesions was made through the coregistration between the EEG recordings and MRI scans. The accuracy of estimations made by FINE and MUSIC was also evaluated and compared by R(2) statistic, which was used to indicate the goodness-of-fit of the estimated sources to the scalp EEG recordings. The three-concentric-spheres head volume conductor model was built for each patient with three spheres of different radii which takes the individual head size and skull thickness into consideration. The results from computer simulations indicate that the improvement of source spatial resolvability and localization accuracy of FINE as compared with MUSIC is significant when simulated sources are closely spaced, deep, or signal-to-noise ratio is low in a clinical electrode set-up. The interictal electrical generators estimated by FINE and MUSIC are in concordance with the patients' structural abnormality, i.e. MRI lesions, in all three patients. The higher R(2) values achieved by FINE than MUSIC indicate that FINE provides a more satisfactory fitting of the scalp potential measurements than MUSIC in all patients. The present results suggest that FINE provides a useful brain source imaging technique, from clinical EEG recordings, for identifying and localizing epileptogenic regions in epilepsy patients with focal partial seizures. The present study may lead to the establishment of a high-resolution source localization technique from scalp-recorded EEGs for aiding presurgical planning in epilepsy patients.

Action Potentials↗
PubMedDate not supplied

Experimental study on HASTE sequences: impacts of parameters on liver imaging.

This study investigates the impacts of effective TE (TEeff), echo spacing and echo train lengths (ETLs) on the imaging quality of HASTE sequences for liver imaging through a slit and a liver phantom. The HASTE sequence with a short echo spacing demonstrated higher CNR for a phantom simulating hepatocellular carcinoma (HCC) than that with long echo spacing. With a long echo spacing, the HASTE sequence showed higher spatial resolution for hemangiomas and metastasis. The improvement of spatial resolution along with the increase in ETLs (imaging matrix) was more prominent for hemangioma than for HCC.

Carcinoma, Hepatocellular↗
PubMed2005

Using a photon phase-space source for convolution/superposition dose calculations in radiation therapy.

For a given linac design, the dosimetric characteristics of a photon beam are determined uniquely by the energy and radial distributions of the electron beam striking the x-ray target. However, in the usual commissioning of a beam from measured data, a large number of variables can be independently tuned, making it difficult to derive a unique and self-consistent beam model. For example, the measured dosimetric penumbra in water may be attributed in various proportions to the lateral secondary electron range, the focal spot size and the transmission through the tips of a non-divergent collimator; the head-scatter component in the tails of the transverse profiles may not be easy to resolve from phantom scatter and head leakage; and the head-scatter tails corresponding to a certain extra-focal source model may not agree self-consistently with in-air output factors measured on the central axis. To reduce the number of adjustable variables in beam modelling, we replace the focal and extra-focal sources with a single phase-space plane scored just above the highest adjustable collimator in a EGS/BEAM simulation of the linac. The phase-space plane is then used as photon source in a stochastic convolution/superposition dose engine. A photon sampled from the uncollimated phase-space plane is first propagated through an arbitrary collimator arrangement and then interacted in the simulation phantom. Energy deposition kernel rays are then randomly issued from the interaction points and dose is deposited along these rays. The electrons in the phase-space file are used to account for electron contamination. 6 MV and 18 MV photon beams from an Elekta SL linac are used as representative examples. Except for small corrections for monitor backscatter and collimator forward scatter for large field sizes (<0.5% with <20 x 20 cm2 field size), we found that the use of a single phase-space photon source provides accurate and self-consistent results for both relative and absolute dose calculations.

Algorithms↗
PubMed2001

Prediction of total genetic value using genome-wide dense marker maps.

Recent advances in molecular genetic techniques will make dense marker maps available and genotyping many individuals for these markers feasible. Here we attempted to estimate the effects of approximately 50,000 marker haplotypes simultaneously from a limited number of phenotypic records. A genome of 1000 cM was simulated with a marker spacing of 1 cM. The markers surrounding every 1-cM region were combined into marker haplotypes. Due to finite population size N(e) = 100, the marker haplotypes were in linkage disequilibrium with the QTL located between the markers. Using least squares, all haplotype effects could not be estimated simultaneously. When only the biggest effects were included, they were overestimated and the accuracy of predicting genetic values of the offspring of the recorded animals was only 0.32. Best linear unbiased prediction of haplotype effects assumed equal variances associated to each 1-cM chromosomal segment, which yielded an accuracy of 0.73, although this assumption was far from true. Bayesian methods that assumed a prior distribution of the variance associated with each chromosome segment increased this accuracy to 0.85, even when the prior was not correct. It was concluded that selection on genetic values predicted from markers could substantially increase the rate of genetic gain in animals and plants, especially if combined with reproductive techniques to shorten the generation interval.

Animals↗
PubMed1997

Transmural coupling of fluid flow in microcirculatory network and interstitium in tumors.

The growth of tumors and their response to treatment are determined by delivery of diffusible substances to cancer cells and hence by their blood supply. Relative to most normal tissues, tumor blood flow is highly heterogeneous. Several hypotheses have been postulated to explain this anomalous behavior of tumor microcirculation, but the underlying mechanisms for these heterogeneities are not fully understood. In this study we consider a potential source of nonuniformity in the blood flow: the enhanced fluid exchange between the vascular and interstitial space mediated by the high leakiness of tumor vessels which could lead to a coupling between vascular, transvascular, and interstitial fluid flow. A simple network model is presented to describe the basic features of flow through a network of permeable and compliant vessels embedded in an isotropic porous medium. Two vascular geometries are considered: a regular mesh of identical vessels and a pair of countercurrent vessels of equal diameter. In each case, the flow through each vessel of the network is described by Poiseuille's law; the transmural flow between the vessels and the external porous medium is governed by Starling's law; the fluid movement through the porous medium is described by Darcy's law; and the vessel wall is assumed to be elastic. Our results show that the behavior of microcirculation may be strongly modified as a result of vascular compliance and enhanced vascular leakiness of tumor vessels. We found not only that the vascular pressure generates the well-known, high central interstitial fluid pressure, but also that the elevated interstitial pressure in turn alters the vascular pressure distribution. These changes in vascular pressure distribution result in a modification of the blood flow pattern. As the leakiness and compliance of the vessels increase, the blood is diverted away from the center of the tumor to a more peripheral path. The clinical significance of these results is that drug delivery for chemotherapy and oxygenation needed for radiotherapy may well be hampered in the central region of the tumor, despite the presence of highly permeable vessels in these regions.

Biological Transport↗
PubMed2003

Salt bridges do not stabilize polyproline II helices.

Interactions between side chains, and in particular salt bridges, have been shown to be important in the stabilization of secondary structure. Here we investigate the contribution of a salt bridge formed between a lysine and a glutamate to the polyproline II (P(II)) helical content of proline-rich peptides. Since this structure has precisely three residues per turn, charged residues spaced three residues apart are on the same side of the helix and are best situated to interact. By contrast, computer simulations show that charged residues spaced four residues apart are both too far apart to interact strongly and are oriented such that interactions are unlikely. We have measured the P(II) content of peptides containing a lysine and glutamate pair spaced three or four residues apart using circular dichroism spectroscopy. Somewhat surprisingly we find that the P(II) content is insensitive to both the spacing and the pH. These findings indicate that i --> i + 3 salt bridges do not stabilize the P(II) helical conformation. The implications of these observations for both P(II) helix formation and denatured protein conformations are discussed.

Circular Dichroism↗
PubMed1984

Acute physiological responses of squirrel monkeys exposed to hyperdynamic environments.

This study examined the responses of small primate, the squirrel monkey, to acute exposures to hyperdynamic environments. Body temperature, heart rate, and behavior of four restrained squirrel monkeys were recorded. After baseline monitoring at 1 G, monkeys were exposed to: a) +2 Gz for 60 min, b) a hyperdynamic profile simulating the gravitational envelope of the space shuttle during launch (8 min, +2.9 Gz max), or c) a simulated shuttle re-entry profile (19 min, +1.7 Gz max). In all experiments, the colonic temperature started to fall within 10 min of the onset of centrifugation and declined by as much as 2 degrees C in some conditions. This was in contrast to the stable body temperature observed during the baseline period. Also, the heart rate showed distinct elevations during centrifugation. Heart rate subsequently declined to baseline levels during the post-centrifugation phase. Behaviorally, after the onset of centrifugation, the animals periodically appeared to become drowsy and fall asleep. On the other hand, during the control period they tended to be alert, shifting their gaze about the cage. Thus, primates are susceptible to acute exposures to hyperdynamic fields, demonstrating significant physiological and behavioral changes.

Animals↗
PubMed1995

A model for electron-beam applicator scatter.

Applicators (or cones), used in conjunction with patient specific cutouts in electron-beam radiotherapy, may interact with the primary electron beam to produce a secondary beam component (applicator scatter). This component affects machine output as well as the shape of resulting dose distributions. A model has been developed to simulate this scatter component for applicators consisting of trimming plates of arbitrary shape. This model involves sampling established kernels of scatter from edge elements of appropriate materials, obtained through Monte Carlo simulations. The result of the model is a phase space (position, direction, energy, charge, weighting) of applicator scattered particles which can be incorporated into a further Monte Carlo simulation, or as input into another advanced treatment planning algorithm. This model is evaluated by comparison of measured profiles and applicator scatter component depth dose curves with Monte Carlo simulations using simulated phase-space data as input. Results are very consistent and reveal information on the angular and spatial variation characteristics of this beam component. The results obtained verify the developed model as an accurate predictor of the characteristics of applicator scattered particles.

Computer Simulation↗
PubMed1989

Motional phase artifacts in Fourier transform MRI.

Most magnetic resonance imaging (MRI) techniques are subject to a "motional blurring" arising from the acquisition of data in the presence of a frequency-encoding gradient. The Fourier transform of the signal from a spin moving along a magnetic field gradient obeys an equation analogous to the free space Schrödinger equation. Computer simulations of the Bloch equations illustrate the implications of this motional blurring in MRI.

Computer Simulation↗
PubMed2006

Quantitative CBV measurement from static T1 changes in tissue and correction for intravascular water exchange.

The steady-state (SS) approach has been proposed to measure quantitative cerebral blood volume (CBV). However, it is known that the CBV value in SS (CBVSS) is subject to error resulting from the effects of water diffusion from the intra- to extravascular space. CBVSS measurements were simulated in both fast- and no-water-exchange limits, and compared with measured CBVSS values to determine which limiting case is appropriate. Twenty-eight patients were scanned with a segmented Look-Locker echo-planar imaging (LL-EPI) sequence before and after the injection of 0.1 mmol/kg of a T1-shortening contrast agent. Signal changes and T1 values of brain parenchyma and the blood pool were measured pre- and postcontrast. These signal changes and T1 values, in combination with the simulated results, were used to estimate water-exchange rates. We found that the intra- to extravascular water-exchange rates in white matter (WM) and gray matter (GM) were 0.9 and 1.6 s-1, respectively. With these water-exchange rates, the fast-water-exchange limit of the CBV values showed good agreement with the simulation (r=0.86 in WM, and 0.78 in GM). The CBV values with the correction for water-exchange effects were recalculated as 2.73+/-0.44 and 5.81+/-1.12 of quantitative cerebral blood water volume (%) in WM and GM, respectively.

Blood Volume↗
PubMed2003

The vascular network of tumours--what is it not for?

It is becoming almost a dogma that tumours cannot grow beyond 1-2 mm(3) unless they are supported by a rich vascular supply 1. It is true that tumours promote angiogenesis and that highly vascularized carcinomas have, in general, a more aggressive clinical course than carcinomas of low vascularization 23. However, a study of intratumoral angiogenesis reveals that the newly formed vessels are commonly deprived of those structural qualities that would allow them to perform an optimal oxygenation function 3. Thus, most tumours, irrespective of their angiogenic status, behave as if they were 'hypoxic', urging (via angiogenic mediators) for, what would look paradoxical at first sight, more defective angiogenesis. It is hypothesized that tumour cells can grow into solid neoplasms by exploiting the host's pre-existing vessels, without the need for new blood vessel formation. Neovascularization, however, may be important for tumours with an exophytic pattern of growth as these, by their very nature, lose the host's sheltering stroma. Shifting to anaerobic glycolysis and activation of anti-apoptotic pathways are complementary mechanisms for tumour cell survival and growth. Besides, continuous and indiscriminate production of a defective vascular network ensures an increased metastatic potential since the newly formed intratumoral vessels, simulating venular-like spaces, are easily permeable to tumour cells, facilitating metastases.

Angiogenesis Inhibitors↗
PubMed1995

Automatic identification of discrete substates in proteins: singular value decomposition analysis of time-averaged crystallographic refinements.

The singular value decomposition (SVD) provides a method for decomposing a molecular dynamics trajectory into fundamental modes of atomic motion. The right singular vectors are projections of the protein conformations onto these modes showing the protein motion in a generalized low-dimensional basis. Statistical analysis of the right singular vectors can be used to classify discrete configurational substates in the protein. The configuration space portraits formed from the right singular vectors can also be used to visualize complex high-dimensional motion and to examine the extent of configuration space sampling by the simulation.

Computer Simulation↗