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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↗

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↗

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↗

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↗

PubMed2000

Local current spread in electrically compact neurons of the fly.

Analyses of active and passive membrane properties predict an asymmetry in the spread of electrical current through a neuron. Simulated current injection into a large-diameter compartment of a biophysically realistic model neuron causes a local potential shift that can spread throughout the cell. In contrast, causing the same local potential shift in the dendritic tip of the same neuron results in only minimal changes in electrical potential in the rest of the cell. Using calcium as a reporter of electrical activity in neurons in the fly's lobula plate we find that current injected into the thick axon caused depolarization throughout the cell, whereas activation of a dendritic region remained local. These results have important implications for the ability of integrating neurons to perform local computations of synaptic input without additional hardware.

Animals↗

PubMed1999

Monte Carlo Simulation of Particle Aggregation and Simultaneous Restructuring.

Ultrafine ("nano"-) particles produced from highly supersaturated vapors or liquids often undergo rapid coagulation and slow interspherule coalescence. Resulting "aggregates" typically contain hundreds of small spherules bound together in tenuous structures characterized by mass fractal dimensions much less than 3. Such aggregates have large and relatively accessible initial surface area but are metastable with respect to more compact configurations, especially in high temperature environments (e.g., flames). Subject to deliberately idealized "uncoupled" rate laws for coagulation and coalescence, we illustrate the power of Monte Carlo simulation methods to obtain the self-preserving joint distribution function (with respect to both particle size and surface area) of populations of coagulating fractal aggregates in the continuum regime, simultaneously undergoing finite-rate restructuring (e.g., via surface-energy-driven viscous flow). Unconditional distributions with respect to either particle volume or area are also obtained from the Monte Carlo simulations. These are conveniently quantified by fitting them to log-normal distributions and we report the sensitivity of the associated spreads to characteristic fusion/coagulation time ratio, chi, and particle fractal dimension, Df, here prespecified. We also calculate and report selected "mixed" moments of the joint pdf with respect to particle volume and surface area needed for engineering calculations of deposition or diffusion-controlled vapor scavenging, as well as the important ratio of actual mean area to that area corresponding to the mean particle volume in the aerosol population. This work sets the stage for tractable simulations of particle dynamics in more complex coagulating systems requiring multi-internal (state-) variables for their more realistic and self-consistent description. Copyright 1999 Academic Press.

Journal Article↗

PubMed1994

Kinetics of protein folding. A lattice model study of the requirements for folding to the native state.

A three-dimensional lattice model of a protein is used to investigate the properties required for its folding to the native state. The polypeptide chain is represented as a 27 bead heteropolymer whose lowest energy (native) state can be determined by an exhaustive enumeration of all fully compact conformations. A total of 200 sequences with random interactions are generated and subjected to Monte Carlo simulations to determine which chains find the ground state in a short time; i.e. which sequences overcome the folding problem referred to as the Levinthal paradox. Comparison of the folding and non-folding sequences is used to identify the features that are required for fast folding to the global energy minimum. It is shown that successful folding does not require certain attributes that have been previously proposed as necessary for folding; these include a high number of short versus long-range contacts in the native state, a high content of the secondary structure in the native state, a strong correlation between the native contact map and the interaction parameters, and the existence of a high number of low energy states with near-native conformation. Instead, the essential difference between the folding and the non-folding sequences is the nature of the energy spectrum. The necessary and sufficient condition for a sequence to fold rapidly in the present model is that the native state is a pronounced energy minimum. As a consequence, the thermodynamic stability of the native state of a folding sequence has a sigmoidal dependence on temperature. This permits such a sequence to satisfy both the thermodynamic and the kinetic requirements for folding; i.e. the native state predominates thermodynamically at temperatures that are high enough for folding to be kinetically possible. The applicability of the present results to real proteins is discussed.

Algorithms↗

PubMed2000

Structural and functional implications of tau hyperphosphorylation: information from phosphorylation-mimicking mutated tau proteins.

Abnormal tau-immunoreactive filaments are a hallmark of tauopathies, including Alzheimer's disease (AD). A higher phosphorylation ("hyperphosphorylation") state of tau protein may represent a critical event. To determine the potential role of tau hyperphosphorylation in these disorders, mutated tau proteins were produced where serine/threonine residues known to be highly phosphorylated in tau filaments isolated from AD patients were substituted for glutamate to simulate a paired helical filament (PHF)-like tau hyperphosphorylation. We demonstrate that, like hyperphosphorylation, glutamate substitutions induce compact structure elements and SDS-resistant conformational domains in tau protein. Hyperphosphorylation-mimicking glutamate-mutated tau proteins display a complete functional loss in its ability to promote microtubule nucleation which can partially be overcome by addition of the osmolyte trimethylamine N-oxide (TMAO), which is similar to phosphorylated tau. In addition, glutamate-mutated tau proteins fail to interact with the dominant brain protein phosphatase 2A isoform ABalphaC, and exhibit a reduced ability to assemble into filaments. Interestingly, wild-type tau and phosphorylation-mimicking tau similarly bind to microtubules when added alone, but the mutated tau is almost completely displaced from the microtubule surface by equimolar concentrations of wild-type tau. The data indicate that glutamate-mutated tau proteins provide a useful model for analyzing the functional consequences of tau hyperphosphorylation. They suggest that several mechanisms contribute to the abnormal tau accumulation observed during tauopathies, in particular a selective displacement of hyperphosphorylated tau from microtubules, a functional loss in promoting microtubule nucleation, and a failure to interact with phosphatases.

Actin Cytoskeleton↗

PubMed2001

Solution structure of microcin J25, the single macrocyclic antimicrobial peptide from Escherichia coli.

The three-dimensional solution structure of microcin J25, the single cyclic representative of the microcin antimicrobial peptide class produced by enteric bacteria, was determined using two-dimensional 1H NMR spectroscopy and molecular modeling. This hydrophobic 21-residue peptide exhibits potent activity directed to Gram-negative bacteria. Its primary structure, cyclo(-V1GIGTPISFY10GGGAGHVPEY20F-), has been determined previously [Blond, A., Péduzzi, J., Goulard, C., Chiuchiolo, M. J., Barthélémy, M., Prigent, Y., Salomón, R.A., Farías, R.N., Moreno, F. & Rebuffat, S. (1999) Eur. J. Biochem., 259, 747-755]. Conformational parameters (3JNHCalphaH coupling constants, quantitative nuclear Overhauser enhancement data, chemical shift deviations, temperature coefficients of amide protons, NH-ND exchange rates) were obtained in methanol solution. Structural restraints consisting of 190 interproton distances inferred from NOE data, 11 phi backbone dihedral angle and 9 chi1 angle restraints derived from the coupling constants and three hydrogen bonds in agreement with the amide exchange rates were used as input for simulated annealing calculations and energy minimization in the program XPLOR. Microcin J25 adopts a well-defined compact structure consisting of a distorted antiparallel beta sheet, which is twisted and folded back on itself, thus resulting in three loops. Residues 7-10 and 17-20 form the more regular part of the beta sheet. The region encompassing residues Gly11-His16 consists of a distorted beta hairpin, which divides into two small loops and is stabilized by an inverse gamma turn and a type I' beta turn. The reversal of the chain leading to the Phe21-Pro6 loop results from a mixed beta/gamma turn. A cavity, in which the hydrophilic Ser8 side-chain is confined, is delimited by two crab pincer-like regions that comprise residues 6-8 and 18-1.

Amino Acid Sequence↗

PubMed2001

Activation of cell division protein FtsZ. Control of switch loop T3 conformation by the nucleotide gamma-phosphate.

The effect of bound nucleotide on the conformation of cell division protein FtsZ from Methanococcus jannaschii has been investigated using molecular dynamics and site-directed mutagenesis. The molecular dynamics indicate that the gamma-phosphate of GTP induces a conformational perturbation in loop T3 (Gly88-Gly99 segment), in a position structurally equivalent to switch II of Ha-ras-p21. In the simulated GTP-bound state, loop T3 is pulled by the gamma-phosphate into a more compact conformation than with GDP, related to that observed in the homologous proteins alpha- and beta-tubulin. The existence of a nucleotide-induced structural change in loop T3 has been confirmed by mutating Thr92 into Trp (T92W-W319Y FtsZ). This tryptophan (12 A away from gamma-phosphate) shows large differences in fluorescence emission, depending on which nucleotide is bound to FtsZ monomers. Loop T3 is located at a side of the contact interface between two FtsZ monomers in the current model of FtsZ filament. Such a structural change may bend the GDP filament upon hydrolysis by pushing against helix H8 of next monomer, thus, generating force on the membrane during cell division. A related curvature mechanism may operate in tubulin activation.

Amino Acid Sequence↗

PubMed2002

High Q-factor Bragg-reflection sapphire-loaded cavity TE01delta mode resonators.

An innovative method of enhancing the quality factor of TE01delta cavity resonators with a dielectric tube made of monolithic sapphire is presented. Very high Q-factor is achieved by employing a Bragg reflection technique. A TE01delta mode in a copper cavity was measured to have a Q-factor of 1 x 10(5) at 8.78 GHz and 290 K. This is only 30% less than the limit due to the loss tangent of the dielectric material. The technique confines electromagnetic energy in the sapphire dielectric and in the vacuum well away from the cavity walls, thus reducing the surface losses in the copper shield. The technique offers some significant advantages over other methods. One advantage is the very low spurious mode density, which can improve filter and resonator design capabilities. Another is the small compact design, with a single sapphire piece, as compared to previously published Bragg reflection techniques. Finite element simulations and experimental data for this method were compared and found to be in very good agreement. The cavity dimensions were optimized to achieve maximum quality factor.

Aluminum Oxide↗

PubMed2000

Use of MM-PB/SA in estimating the free energies of proteins: application to native, intermediates, and unfolded villin headpiece.

We investigated the stability of three different ensembles of the 36-mer villin headpiece subdomain, the native, a compact folding intermediate, and the random coil. Structures were taken from a 1-micros molecular dynamics folding simulation and a 100-ns control simulation on the native structure. Our approach for each conformation is to first determine the solute internal energy from the molecular mechanics potential and then to add the change resulting from solvation (DeltaG(solv)). Explicit water was used to run the simulation, and a continuum model was used to estimate DeltaG(solv) with the finite difference Poisson-Boltzmann model accounting for the polarization part and a linearly surface area-dependent term for the non-polar part. We leave out the solute vibrational entropy from these values but demonstrate that there is no statistical difference among the native, folding intermediate, and random coil ensembles. We find the native ensemble to be approximately 26 kcal/mol more stable than the folding intermediate and approximately 39 kcal/mol more stable than the random coil ensemble. With an experimental estimate for the free energy of denaturation equal to 3 kcal/mol, we approximate the non-native degeneracy to lie between 10(16) and 10.(25) We also present a possible scheme for the mechanism of folding, first-order exponential decay of a putative transition state, with an estimate for the t(1/2) of folding of approximately 1 micros.

Carrier Proteins↗

PubMed1996

On the mechanical characterization of compact bone structure using the homogenization theory.

In a previous paper (Crolet et al., 1993, J. Biomechanics 26, 677-687), a modelling of the mechanical behavior of compact bone was presented, in which the homogenization theory was the basic tool of computation. In this simulation, approximations were used for the modelling of the lamellae and the osteons: the lamella and the osteon were divided into cylindrical sectors, each sector being approximated as a parallelepiped having a periodic structure (fibrous composite for the lamella, superimposition of plates for the osteon). The present study deals with a new model without these approximations. First, it can be proved that the homogenized elasticity tensor for a lamella, which has non-periodic structure, is obtained at each geometrical point as a homogenized tensor of a periodic problem. Similarly, for the osteonal structure, the components of the homogenized tensor are determined at each point as the result of a periodic homogenization. The software OSTEON, which is the computational method associated with this model, allows one to obtain a better understanding of the effects of many bony parameters. The obtained results are in accordance with experimental data.

Algorithms↗