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Results for “parameter optimization”

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At least 1,261 records · Page 70Linked to original sources

PubMed2004

Solvent-amino acid interaction energies in three-dimensional-lattice Monte Carlo simulations of a model 27-mer protein: Folding thermodynamics and kinetics.

Amino acid residue-solvent interactions are required for lattice Monte Carlo simulations of model proteins in water. In this study, we propose an interaction-energy scale that is based on the interaction scale by Miyazawa and Jernigan. It permits systematic variation of the amino acid-solvent interactions by introducing a contrast parameter for the hydrophobicity, C(s), and a mean attraction parameter for the amino acids, omega. Changes in the interaction energies strongly affect many protein properties. We present an optimized energy parameter set for best representing realistic behavior typical for many proteins (fast folding and high cooperativity for single chains). Our optimal parameters feature a much weaker hydrophobicity contrast and mean attraction than does the original interaction scale. The proposed interaction scale is designed for calculating the behavior of proteins in bulk and at interfaces as a function of solvent characteristics, as well as protein size and sequence.

Algorithms↗

PubMed2002

Using evolutionary methods to study G-protein coupled receptors.

A novel method to analyze evolutionary change is presented and its application to the analysis of sequence data is discussed. The investigated method uses phylogenetic trees of related proteins with an evolutionary model in order to gain insight about protein structure and function. The evolutionary model, based on amino acid substitutions, contains adjustable parameters related to amino acid and sequence properties. A maximum likelihood approach is used with a phylogenetic tree to optimize these parameters. The model is applied to a set of Muscarinic receptors, members of the G-protein coupled receptor family. Here we show that the optimized parameters of the model are able to highlight the general structural features of these receptors.

Animals↗

PubMed2005

A virtual-modeling and multivariate-optimization examination of HPLC parameter interactions and opportunities for saving analysis time.

The interrelations of parameters in HPLC are very complicated, even in a simple problem. Optimization requires considering all the adjustable parameters in concert, but the amount of work required to do this experimentally is prohibitive. However, if we first choose the selectivity parameters, we can then successfully and rapidly perform a multivariate optimization of the efficiency parameters within a numerical model. By examining this process with a level of detail not normally necessary in routine work, we reveal the complexity of parameter interactions in a simple separation, and the potential for large savings of analysis time by properly balancing parameter values. We show how to reduce a 13 min experimental separation to less than 2 min without utilizing ultra-small particles or pressure beyond the capabilities of an ordinary HPLC instrument. Ultra-small particles will often improve analysis times when the separation is plate-number-limited, but if the particles are smaller than optimal for the required separation, then larger particles will require less analysis time.

Chromatography, High Pressure Liquid↗

PubMedDate not supplied

Optimization of the wedge filter parameters for a radiotherapy treatment planning system.

When a treatment planning system uses an empirical or semianalytical approach to describe the influence of a wedge filter on a photon beam, a number of experimentally determined parameters are required. These may be found from direct measurement. However, if the beam model is sensitive to the parameters, it will be necessary to optimize the parameter values to obtain better correspondence between dose profiles calculated by the model and actual measured profiles. The procedure is time consuming if optimization is done manually. We have developed an optimization scheme, using a personal computer, to find the set of wedge parameters which will result in the best fit of calculated wedge profiles (using the beam model of the treatment planning system) to measured wedge profiles. The procedure is efficient and calculated profiles were found to match measured profiles to within 2% of the central axis value.

Filtration↗

PubMed2002

The precision of anatomical normalization in the medial temporal lobe using spatial basis functions.

We investigated the accuracy of spatial basis function normalization using anatomical landmarks to determine how precisely homologous regions are colocalized. We examined precision in terms of: (1) the number of nonlinear basis functions used by the normalization procedure; (2) the degree of (Bayesian) regularization; and (3) the effect of substituting different templates and how this interacted with the number of basis functions. The face validity of spatial normalization was assessed as a function of these parameters, using the colocalization of homologous landmarks in a test sample of 20 normally developing children and 5 children with bilateral hippocampal pathology. Our results suggest that when optimal normalization parameters are used, anatomical landmarks in the medial temporal lobes are colocalized to within a standard deviation of about 1 mm. When suboptimal parameters are used this standard deviation can increase up to 3 mm. Interestingly the optimal parameters are those that provide a rather constrained normalization as opposed to those that optimize intensity matching at the expense of rendering the warps "unlikely." The implications of our results, for users of voxel-based morphometry, are discussed.

Adolescent↗

PubMedDate not supplied

Optimization of temperature distributions in scanned, focused ultrasound hyperthermia.

Scanned, focused ultrasound systems (SFUS) have considerable flexibility in shaping the power deposition field during hyperthermia treatments. When utilizing this adaptability many complicated, interacting decisions must be made to obtain an optimal steady-state temperature distribution. This optimization problem is studied using a 3-D, radially symmetric simulation program which searches for a set of optimal scan parameters. The conjugate-gradient optimization technique with a golden section search was used to obtain the optimal temperature distributions attainable with a single circular scan of a tumour. The variable scan parameters of the single transducer heating system optimized (and under the control of the therapist) are: transducer tilt and rotation angles, focal depth, output acoustical power, and scan radius. This single scan study includes the effects of tumour and normal tissue blood perfusions, tumour depth, skin temperature boundary condition, as well as tumour size and shape. A similar, but less comprehensive, study was done for larger tumours using two concentric circular scans. The results show that (1) the optimization process can produce a set of scan parameters that give a considerably better temperature distribution than could be obtained ad hoc, and (2) the optimal scan parameter configuration obtained produces a close-to-ideal tumour temperature distribution for a wide variety of clinically relevant conditions. Thus, when extended to include data from individual patients such optimization should be a very useful tool in patient treatment planning, and should enhance the present capabilities of clinical scanned, focused ultrasound systems.

Body Temperature↗

PubMed1988

Cervical spinal cord stimulation for spasticity in cerebral palsy.

A prospective double-blind study of high cervical spinal cord stimulation conducted in eight moderately disabled, spastic, cerebral palsied children failed to demonstrate any significant improvement over base line function during chronic spinal cord stimulation at either optimal stimulation parameters or random placebo parameters. Chronic stimulation included 4 consecutive months of stimulation for 24 hours each day. Stimulators were randomly programmed at optimal parameters for 2 of the 4 months and at placebo parameters for the remaining 2 months. At the end of each month of chronic stimulation, subjects were assessed with a multidisciplinary test battery that included a self-assessment, specific clinical examinations, tests of gross and fine motor control, neuropsychological and neurophysiological tests, a detailed gait analysis, and video recordings. By 6 months after the completion of the study, only 1 of the 8 subjects continued to use his stimulator on a regular basis, with minimal benefit.

Adolescent↗

PubMed2001

[Electric pulse mediated high efficient gene transfer].

OBJECTIVE: To study gene transfer mediated by electric pulse and optimize the parameters of electric pulse in vivo. METHODS: 10 micrograms plasmid pcD2/LacZ was injected into the quadriceps of 220 Kunming mice. One to two minutes after the DNA injection electric pulse with different parameters was given to the injection site. Three days after, activity of beta-galactosidase was measured, and the expression of Laz2 gene in muscle was determined by histochemical staining. RESULTS: The activity of beta-galactosidase in electric pulse group (131.6 U/mg +/- 86.6 U/mg protein) was 30 fold higher than that in direct injection group (4.9 U/mg +/- 1.0 U/mg protein) (P < 0.05). Histochemical analysis of muscles injected with a LacZ expression plasmid also showed that in vivo electric pulse increased both the number of positively stained muscle fibers and the density of staining. When the electric pulse was with the parameters of 200 V/cm, 40 ms, 6 pulses and 1HZ, maximal gene expression was achieved. CONCLUSION: Electric pulse, with optimal parameters, increases gene expression. Electric pulse makes much more gene expression than mere intramuscular DNA injection.

Animals↗

PubMed2000

On the design of optimal dynamic experiments for parameter estimation of a Ratkowsky-type growth kinetics at suboptimal temperatures.

It is generally known that accurate model building, i.e., proper model structure selection and reliable parameter estimation, constitutes an essential matter in the field of predictive microbiology, in particular, when integrating these predictive models in food safety systems. In this context, Versyck et al. (1999) have introduced the methodology of optimal experimental design techniques for parameter estimation within the field. Optimal experimental design focuses on the development of optimal input profiles such that the resulting rich (i.e., highly informative) experimental data enable unique model parameter estimation. As a case study, Versyck et al. (1999) [Versyck, K., Bernaerts, K., Geeraerd, A.H., Van Impe, J.F., 1999. Introducing optimal experimental design in predictive modeling: a motivating example. Int. J. Food Microbiol., 51(1), 39-51] have elaborated the estimation of Bigelow inactivation kinetics parameters (in a numerical way). Opposed to the classic (static) experimental approach in predictive modelling, an optimal dynamic experimental setup is presented. In this paper, the methodology of optimal experimental design or parameter estimation is applied to obtain uncorrelated estimates of the square root model parameters [Ratkowsky, D.A., Olley, J., McMeekin, T.A., Ball, A., 1982. Relationship between temperature and growth rate of bacterial cultures. J. Bacteriol. 149, 1-5] describing the effect of suboptimal growth temperatures on the maximum specific growth rate of microorganisms. These estimates are the direct result of fitting a primary growth model to cell density measurements as a function of time. Apart from the design of an optimal time-varying temperature profile based on a sensitivity study of the model output, an important contribution of this publication is a first experimental validation of this innovative dynamic experimental approach for uncorrelated parameter identification. An optimal step temperature profile, within the range of model validity and practical feasibility, is developed for Escherichia coli K12 and successfully applied in practice. The presented experimental validation result illustrates the large potential of the dynamic experimental approach in the context of uncorrelated parameter estimation. Based on the experimental validation result, additional remarks are formulated related to future research in the field of optimal experimental design.

Escherichia coli↗

PubMed2005

Optimization and application of lithium parameters for the reactive force field, ReaxFF.

To make a practical molecular dynamics (MD) simulation of the large-scale reactive chemical systems of Li-H and Li-C, we have optimized parameters of the reactive force field (ReaxFF) for these systems. The parameters for this force field were obtained from fitting to the results of density functional theory (DFT) calculations on the structures and energy barriers for a number of Li-H and Li-C molecules, including Li(2), LiH, Li(2)H(2), H(3)C-Li, H(3)C-H(2)C-Li, H(2)C=C-LiH, HCCLi, H(6)C(5)-Li, and Li(2)C(2), and to the equations of state and lattice parameters for condensed phases of Li. The accuracy of the developed ReaxFF was also tested by comparison to the dissociation energies of lithium-benzene sandwich compounds and the collision behavior of lithium atoms with a C(60) buckyball.

Journal Article↗

PubMed2004

Parallel and nonparallel simultaneous multislice black-blood double inversion recovery techniques for vessel wall imaging.

PURPOSE: To reduce long examination times of black-blood vessel wall imaging by acquiring multiple slices simultaneously and by using parallel acquisition techniques. MATERIALS AND METHODS: DIR-rapid acquisition with relaxation enhancement (RARE) techniques imaging up to 10 simultaneous slices per acquisition with single and multiple 180 degrees -reinversion pulses were developed. A slab-selective reinversion multislice DIR-RARE sequence incorporating generalized autocalibrating partially parallel acquisitions (GRAPPA) imaging was implemented. Four-channel and eight-channel carotid coils were built to test these sequences. A total of 11 subjects were studied. Contrast-to-noise ratio (CNR) and signal-to-noise ratio (SNR) efficiency factor (SEF, SNR/unit time/slice) were measured from aortic images of three healthy subjects to determine optimal MR parameters. The DIR-RARE-GRAPPA sequence was run on aortas and carotid arteries of the five remaining healthy subjects and three atherosclerotic patients with optimal parameters (acquisition times 12-21 seconds). RESULTS: SEFs of slab-selective protocols were significantly higher than those of slice-selective protocols, and SEFs of DIR-RARE-GRAPPA protocols were significantly higher than corresponding non-GRAPPA protocols (P < 0.05). CNR was not significantly different for all imaging protocols. The DIR-RARE-GRAPPA multislice sequence showed 8.35-fold time improvement vs. single-slice DIR-2RARE sequence. CONCLUSION: Future MRI atherosclerotic plaque studies can be performed in substantially shorter times using these methods.

Adult↗

PubMed2000

Optimizing DREAR and SnB parameters for determining Se-atom substructures.

The determination of the anomalous scattering substructure is the first essential step in any successful macromolecular structure determination using the multiwavelength anomalous diffraction (MAD) technique. The diffE method of calculating difference Es in conjunction with SnB has had considerable success in determining large Se-atom substructures. An investigation of the parameters used in both the data-reduction and error-analysis routines (DREAR) as well as the SnB phasing process itself was undertaken to optimize these parameters for more efficient use of the procedure. Two sets of selenomethionyl S-adenosylhomocysteine hydrolase MAD data were used as test data. The elimination of all erroneously large differences prior to phasing was found to be critical and the best results were obtained from accurate highly redundant intensity measurements. The high-resolution data collected in the typical MAD experiment are sufficient, but the inclusion of low-resolution data below 20 A improved the success rate considerably. Although the best results have been obtained from single-wavelength peak anomalous diffraction data alone, independent SnB analysis of data measured at other wavelengths can provide confirmation for questionable sites.

Computer Simulation↗

PubMed2001

Optimization of quartz tube pyrolysis atmospheric pressure ionization mass spectrometry for the generation of bacterial biomarkers.

Experimental procedures were investigated to improve the efflux of biomolecule pyrolyzates from quartz tube pyrolysis under atmospheric pressure ionization mass spectrometry conditions. Heating regimes, airflows, and ion focusing parameters were optimized to increase the informative mass spectral signals generated from the pyrolysis of Gram-positive bacterial spores and vegetative cells. Dipicolinic acid (DPA) is found in 5-15% by weight in Gram-positive Bacillus spores, and the parameter optimization procedures provided an intense mass spectral signature of the m/z 168 protonated DPA molecule with a minimization of pyrolytic and ionization fragments. Moreover, mass spectral information from the optimization protocols yielded peaks and mass patterns characteristic of DNA and RNA nitrogen bases, protein diketopiperazines, and amino sugars.

Bacillus↗

PubMed1984

Problems and pitfalls in estimating average pharmacokinetic parameters.

The problems of obtaining optimal average parameter estimates (APE) from experimental pharmacokinetic data are considered. Four different approaches, three parametric and one non-parametric tests, are compared, using selected individual alcohol concentration data. Pooling the raw data for estimating APE can obscure individual pharmacokinetic characteristics, whereas averaging individual parameter estimates (IPE) exposes unique statistical problems. Furthermore, careful consideration should be given to weighting procedures. The advantages and shortcomings of all four methods are discussed. It is concluded that none can be considered as a universally applicable statistical method in view of the purpose for which the information, derived from a set of data, e.g. an alcohol-kinetic study, is required.

Computers↗

PubMed2002

Basal glycogenolysis in mouse skeletal muscle: in vitro model predicts in vivo fluxes.

A previously published mammalian kinetic model of skeletal muscle glycogenolysis, consisting of literature in vitro parameters, was modified by substituting mouse specific Vmax values. The model demonstrates that glycogen breakdown to lactate is under ATPase control. Our criteria to test whether in vitro parameters could reproduce in vivo dynamics was the ability of the model to fit phosphocreatine (PCr) and inorganic phosphate (Pi) dynamic NMR data from ischemic basal mouse hindlimbs and predict biochemically-assayed lactate concentrations. Fitting was accomplished by optimizing four parameters--the ATPase rate coefficient, fraction of activated glycogen phosphorylase, and the equilibrium constants of creatine kinase and adenylate kinase (due to the absence of pH in the model). The optimized parameter values were physiologically reasonable, the resultant model fit the [PCr] and [Pi] timecourses well, and the model predicted the final measured lactate concentration. This result demonstrates that additional features of in vivo enzyme binding are not necessary for quantitative description of glycogenolytic dynamics.

Animals↗

PubMed2002

Optimization of square wave anodic stripping voltammetry (SWASV) for the simultaneous determination of Cd, Pb, and Cu in seawater and comparison with differential pulse anodic stripping voltammetry (DPASV).

Square wave anodic stripping voltammetry (SWASV) was optimized for the simultaneous determination of Cd, Pb and Cu in coastal seawater samples. Background subtraction was adapted to improve peak detection and quantification. Optimum background voltammograms were obtained by applying a 7.5 s equilibration potential at -975 mV (vs. Ag/AgCl, 3M KCl) before starting the background scan. Voltammetric scan parameters were optimized to obtain maximum sensitivity while retaining good peak resolution and discrimination from background. Optimal parameters were: frequency 100 Hz, pulse amplitude 25 mV, current sampling delay time 2 ms, step height 8 mV. The sensitivity of optimized SWASV proved to be more than double that of differential pulse anodic stripping voltammetry (DPASV), and analysis time was halved. Samples containing around 13 (Cd), 30 (Pb), 200 (Cu) ng/l (typical averages of the coastal area of the Marche region) can be analyzed using a 5 min deposition time and the total analysis time using three standard additions is about 1 h and half, excluding the mercury film preparation and the outgassing of the sample, which can be made in parallel using a second cell cup.

Cadmium↗

PubMed2005

A dual optimization method for the material parameter identification of a biphasic poroviscoelastic hydrogel: Potential application to hypercompliant soft tissues.

A dual-indentation creep and stress relaxation methodology was developed and validated for the material characterization of very soft biological tissue within the framework of the biphasic poroviscoelastic (BPVE) constitutive model. Agarose hydrogel, a generic porous medium with mobile fluid, served as a mechanical tissue analogue for validation of the experimental procedure. Indentation creep and stress relaxation tests with a solid plane-ended cylindrical indenter were performed at identical sites on a gel sample with dimensions large enough with respect to indenter size in order to satisfy an infinite layer assumption. A finite element (FE) formulation coupled to a global optimization algorithm was utilized to simultaneously curve-fit the creep and stress relaxation data and extract the BPVE model parameters for the agarose gel. A numerical analysis with artificial data was conducted to validate the uniqueness of the computational procedure. The BPVE model was able to successfully cross-predict both creep and stress relaxation behavior for each pair of experiments with a single unique set of material parameters. Optimized elastic moduli were consistent with those reported in the literature for agarose gel. With the incorporation of appropriately-sized indenters to satisfy more stringent geometric constraints, this simple yet powerful indentation methodology can provide a straightforward means by which to obtain the BPVE model parameters of biological soft tissues that are difficult to manipulate (such as brain and adipose) while maintaining a realistic in situ loading environment.

Connective Tissue↗

PubMed2003

Determining and optimizing the precision of quantitative measurements of perfusion from dynamic contrast enhanced MRI.

PURPOSE: To examine the sensitivity of quantitative dynamic contrast enhanced MRI (DCE-MRI) perfusion maps to errors in the various source images and to determine optimal imaging parameters for reducing this sensitivity. MATERIALS AND METHODS: A detailed analysis of the precision of a DCE-MRI protocol was performed using the "propagation of errors" technique to investigate the effect of errors in the source images on errors in K(trans). Optimal parameter values and interactions between parameters were examined. The propagation of errors analysis was validated by Monte-Carlo simulations. RESULTS: The precision of K(trans) was found to be most sensitive to artifacts in the tissue portion of the baseline images and least sensitive to noise in the arterial portion of the dynamic images. The tip-angle strongly affected the precision, with the optimum being a function of tissue T1(0). CONCLUSION: Protocol optimization requires matching the tip-angle to the anticipated T1(0) of the tissue of interest; however such optimization yields a relatively small improvement. Future developmental efforts would be most productively focused on minimizing the artifact level.

Artifacts↗