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Results for “parameter optimization”

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PubMed2004

Army ants algorithm for rare event sampling of delocalized nonadiabatic transitions by trajectory surface hopping and the estimation of sampling errors by the bootstrap method.

The most widely used algorithm for Monte Carlo sampling of electronic transitions in trajectory surface hopping (TSH) calculations is the so-called anteater algorithm, which is inefficient for sampling low-probability nonadiabatic events. We present a new sampling scheme (called the army ants algorithm) for carrying out TSH calculations that is applicable to systems with any strength of coupling. The army ants algorithm is a form of rare event sampling whose efficiency is controlled by an input parameter. By choosing a suitable value of the input parameter the army ants algorithm can be reduced to the anteater algorithm (which is efficient for strongly coupled cases), and by optimizing the parameter the army ants algorithm may be efficiently applied to systems with low-probability events. To demonstrate the efficiency of the army ants algorithm, we performed atom-diatom scattering calculations on a model system involving weakly coupled electronic states. Fully converged quantum mechanical calculations were performed, and the probabilities for nonadiabatic reaction and nonreactive deexcitation (quenching) were found to be on the order of 10(-8). For such low-probability events the anteater sampling scheme requires a large number of trajectories ( approximately 10(10)) to obtain good statistics and converged semiclassical results. In contrast by using the new army ants algorithm converged results were obtained by running 10(5) trajectories. Furthermore, the results were found to be in excellent agreement with the quantum mechanical results. Sampling errors were estimated using the bootstrap method, which is validated for use with the army ants algorithm.

Journal Article↗

PubMedDate not supplied

[Optimization of the local thermocoagulation process as applied to stereotaxic neurosurgery].

A mathematic model was set up to find the thermal response of tissues to thermocoagulation. This model was studied by means of an analogue computer so as to establish optimal operating parameters for high-resistance heating probes. The smallest size of the layer of incomplete necrosis was used as criteria for optimization. The results suggest that the best performance characteristics in thermal coagulation can be achieved by using controlled temperatures from 77 to 87 degrees C (applied intermittently or continually).

Computers, Analog↗

PubMed1999

Oxygen consumption characteristics of porcine hepatocytes.

Oxygen uptake rate (OUR) of hepatocytes is an important parameter for the design of bioartificial liver assist (BAL) devices. Porcine hepatocytes were cultured in a specially constructed measurement chamber with an incorporated mixing system and a Clark polarographic oxygen electrode. Signal noise associated with conventional Clark electrode implementations was circumvented by the combination of real time digital numerical averaging and subsequent finite impulse response (FIR) spectral filtering. Additional software allowed for the automated generation of cellular oxygen consumption coefficients, namely, Vmax and K0.5, adding a high degree of objectivity to parameter determination. Optimization of the above numerical techniques identified a 0.1 Hz/200 data point sample size and a 0.004 Hz cutoff frequency as ideal parameters. Vmax values obtained for porcine hepatocytes during the first two weeks of culture showed a maximal consumption of 0.9 nmole/sec/10(6) cells occurring on Day 4 post seeding, and a gradual decrease to 0.31 nmole/sec/10(6) cells by Day 15. K0.5 values increased from 2 mm Hg on Day 2 to 8 mm Hg by Day 8, with gradual subsequent decrease to 4 mm Hg by Day 15. The Vmax and K0.5 values measured for porcine cells were higher than maximal values for rat hepatocytes (Vmax: 0.43 nmole/sec/10(6) cells, K0.5: 5.6 mmHg) and thus may necessitate significantly altered BAL device design conditions to ensure no oxygen limitations. Finally, these results highlight the need for species specific characterization of cellular function for optimal BAL device implementations.

Animals↗

PubMedDate not supplied

Heavy metal removal by biosorption using Phanerochaete chrysosporium.

Biosorption using microbial cells as adsorbents is being seen as a cost-effective method for the removal of heavy metals from wastewaters. Biosorption studies with Phanerochaete chrysosporium were performed for copper (II), lead (II), and cadmium (II) to evaluate the effectiveness and to optimize the operational parameters using response surface methodology. The operational parameters chosen were initial metal ion concentration, pH, and biosorbent dosage. Using this method, the metal removal could be correlated to the operational parameters, and their values were optimized. The results showed fairly high adsorptive capacities for all the metals within the settings of the operational parameters. The removal efficiencies followed the order Pb > Cu > Cd. As a general trend, metal removal efficiency decreased as the initial metal ion concentration increased, and the results fitted the Langmuir and Freundlich isotherms well.

Adsorption↗

PubMed2004

High-throughput screening for stability and inhibitory activity of compounds toward cytochrome P450-mediated metabolism.

With the advent of combinatorial chemistry and high-throughput screening technology, thousands of molecules can now be rapidly synthesized and screened for biological activity against large numbers of protein targets, greatly increasing the speed with which lead compounds are identified during the early stages of drug discovery. However, rapid optimization of parameters that determine whether a high-affinity ligand or a potent inhibitor will become a successful drug remains a challenge in improving the efficiency of the drug discovery process. Parameters that define absorption, distribution, metabolism, and excretion properties of drug candidates are important determinants of therapeutic efficacy, and thus should be optimized during early stages of drug discovery. Although the speed with which drugs are screened for properties such as absorption, cytochrome P450 (CYP) inhibition, and metabolic stability has increased over the past several years, the screening rate/capacity is still several orders of magnitude lower than those for high-throughput methods used in lead identification, resulting in a bottleneck in the drug discovery process. This review discusses current methods used in the in vitro screening of drugs for their stability toward CYP-mediated oxidative metabolism. This is a critical screen in the drug discovery process because metabolism by CYP represents an important clearance mechanism for the vast majority of compounds, thus affecting their oral bioavailability and/or duration of action.

Animals↗

PubMed1988

Particle counting by fluorescence correlation spectroscopy. Simultaneous measurement of aggregation and diffusion of molecules in solutions and in membranes.

A method for simultaneous determination of molar weights (M) and lateral diffusion constants (D) of particles in three- and two-dimensional systems is described. Spontaneous concentration fluctuations in space and time are analyzed, by monitoring fluctuations in the fluorescence from fluorescein-labeled molecules (1 dye/molecule is sufficient), excited by a rotating laser spot. For particles in solution, M values are determined over the range of 3 x 10(2) to 3 x 10(11) daltons, and D values can be determined from approximately 10(-7) to 10(-10) cm2/s. The time for a determination is approximately 1 min. Aggregation can be followed by changes of either M or D. This method is used to study the calcium dependence of vesicle aggregation or fusion, and the time course of aggregate formation of porin (an Escherichia Coli outer membrane protein) in lipid monolayers. Essential parameters for the development of the method are described. Equations to estimate the signal-to-noise ratios and to find the optimal free parameters for a specific application are derived. The theoretical predictions for the correlation function of the signal and for the signal-to-noise ratio are compared with observed values.

Chemical Phenomena↗

PubMed2003

Distributed versus compartment models for PET receptor studies.

Although distributed models are generally accepted as being more realistic than compartment models, use of simpler compartment models is pervasive in nuclear medicine applications, particularly in positron emission tomography (PET). Here, we report on comparisons made between distributed and compartment model outputs to address the question of whether differences between them are sufficient to justify distributed models for analysis of PET receptor experiments. For both two- and three-injection experiments, "data" sets were obtained by simulation using a distributed model and a wide range of parameter values. Optimal fits of the compartment model output to these "data" were achieved with three strategies in which values of different groups of parameter were estimated. Compartment model outputs yielded good fits to all the distributed model outputs and the values of the corresponding parameters were in close agreement. Given the temporal resolution typically available with PET, the use of a distributed model has no advantage over a compartment model for PET receptor quantification.

Computer Simulation↗

PubMed1999

Identification of phytoplankton from flow cytometry data by using radial basis function neural networks.

We describe here the application of a type of artificial neural network, the Gaussian radial basis function (RBF) network, in the identification of a large number of phytoplankton strains from their 11-dimensional flow cytometric characteristics measured by the European Optical Plankton Analyser instrument. The effect of network parameters on optimization is examined. Optimized RBF networks recognized 34 species of marine and freshwater phytoplankton with 91. 5% success overall. The relative importance of each measured parameter in discriminating these data and the behavior of RBF networks in response to data from "novel" species (species not present in the training data) were analyzed.

Flow Cytometry↗

PubMed2002

Standardization of Neisseria meningitidis serogroup B colorimetric serum bactericidal assay.

The correlate of protection for serogroup B meningococci is not currently known, but for serogroup C it is believed to be the serum bactericidal assay (SBA). The current SBAs are labor intensive and the variations in protocols among different laboratories make interpretation of results difficult. A colorimetric SBA (cSBA), based on the ability of Neisseria meningitidis serogroup B to consume glucose, leading to acid production, was standardized by using group B strain Cu385-83 as the target. The cSBA results were compared to those obtained for a traditional colony-counting microassay (mSBA). Glucose and bromocresol purple pH indicator were added to the medium in order to estimate growth of cSBA target cell survivors through color change. Different variants of the assay parameters were optimized: growth of target cells (Mueller Hinton agar plates), target cell number (100 CFU/per well), and human complement source used at a final concentration of 25%. After the optimization, three other group B strains (H44/76, 490/91, and 511/91) were used as targets for the cSBA. The selection of the assay parameters and the standardization of cSBA were done with 13 sera from vaccinated volunteers. The titers were determined as the higher serum dilution that totally inhibited the bacterial growth marked by the color invariability of the pH indicator. This was detected visually as well as spectrophotometrically and was closely related to a significant difference in the growth of target cell survivors determined using Student's t test. Intralaboratory reproducibility was +/-1 dilution. The correlation between bactericidal median titers and specific immunoglobulin G serum concentration by enzyme immunoassay was high (r = 0.910, P < 0.01). The bactericidal titers generated by the cSBA and the mSBA were nearly identical, and there was a high correlation between the two assays (r = 0.974, P < 0.01). The standardized cSBA allows easy, fast, and efficient evaluation of samples.

Adolescent↗

PubMed1999

Models of the apparent mass of the seated human body exposed to horizontal whole-body vibration.

BACKGROUND: Many environments contain vibration with simultaneous vertical and horizontal components. Mathematical lumped parameter models of the mechanical impedance of the seated human body have previously been defined for exposure to vertical vibration. This paper proposes models for the response of the seated body when exposed to horizontal vibration. METHODS: Four target functions were derived from previously reported measurements of the apparent masses of seated subjects exposed to fore-and-aft and lateral vibration at both 0.5 and 1.0 ms(-2) r.m.s. Parameters were optimized for six different three degree-of-freedom models to fit the modulus of the model responses to the four target functions. RESULTS: The modulus and phase of the apparent masses optimized for all combinations of vibration magnitude and direction were close to the responses previously measured and reported in the literature. Fitted parameters for all models with elements in series showed at least one element with a parameter that tended to zero. CONCLUSIONS: Models with three parallel single degree-of-freedom systems with a rigid support generally gave the closest representation of the apparent mass of the seated body exposed to horizontal vibration. More experimental data on the effect of gender, posture and magnitude of vibration on the apparent masses of seated subjects would be useful to enable these models to be improved.

Adult↗

PubMed1996

White noise approach for estimating the passive electrical properties of neurons.

1. The passive electrical properties of whole cell patched dentate granule cells were studied with the use of zero-mean Gaussian white noise current stimuli. Transmembrane voltage responses were used to compute the first-order Wiener kernels describing the current-voltage relationship at the soma for six cells. Frequency domain optimization techniques using a gradient method for function minimization were then employed to identify the optimal electrical parameter values. Low-power white noise stimuli are presented as a favorable alternative to the use of short-pulse current inputs for investigating neuronal passive electrical properties. 2. The optimization results demonstrated that the lumped resistive and capacitive properties of the recording electrode must be included in the analytic input impedance expression to optimally fit the measured cellular responses. The addition of the electrode resistance (Re) and capacitance (Ce) to the original parameters (somatic conductance, somatic capacitance, axial resistance, dendritic conductance, and dendritic capacitance) results in a seven-parameter model. The mean Ce value from the six cells was 5.4 +/- 0.3 (SE) pF, whereas Re following formation of the patch was found to be 20 +/- 2 M omega. 3. The six dentate granule cells were found to have an input resistance of 600 +/- 20 M omega and a dendritic to somatic conductance ratio of 6.3 +/- 1.1. The electronic length of the equivalent dendritic cylinder was found to be 0.42 +/- 0.03. The membrane time constant in the soma was found to be 13 +/- 3 ms, whereas the membrane time constant of the dendrites was 58 +/- 5 ms. Incorporation of morphological estimations led to the following distributed electrical parameters: somatic membrane resistance = 25 +/- 4 k omega cm2, somatic membrane capacitance = 0.48 +/- 0.05 microF/cm2, Ri (input resistance) = 72 +/- 5 omega cm, dendritic membrane resistance = 59 +/- 4 k omega cm2, and dendritic membrane capacitance = 0.97 +/- 0.06 microF/cm2. On the basis of capacitive measurements, the ratio of dendritic surface area to somatic surface area was found to be 34 +/- 2. 4. For comparative purposes, hyperpolarizing short pulses were also injected into each cell. The short-pulse input impedance measurements were found to underestimate the input resistance of the cell and to overestimate both the somatic conductance and the membrane time constants relative to the white noise input impedance measurements.

Animals↗

PubMed2003

Combined MR data acquisition of multicontrast images using variable acquisition parameters and K-space data sharing.

A new technique to reduce clinical magnetic resonance imaging (MRI) scan time by varying acquisition parameters and sharing k-space data between images, is proposed. To improve data utilization, acquisition of multiple images of different contrast is combined into a single scan, with variable acquisition parameters including repetition time (TR), echo time (TE), and echo train length (ETL). This approach is thus referred to as a "combo acquisition." As a proof of concept, simulations of MRI experiments using spin echo (SE) and fast SE (FSE) sequences were performed based on Bloch equations. Predicted scan time reductions of 25%-50% were achieved for 2-contrast and 3-contrast combo acquisitions. Artifacts caused by nonuniform k-space data weighting were suppressed through semi-empirical optimization of parameter variation schemes and the phase encoding order. Optimization was assessed by minimizing three quantitative criteria: energy of the "residue point spread function (PSF)," energy of "residue profiles" across sharp tissue boundaries, and energy of "residue images." In addition, results were further evaluated by quantitatively analyzing the preservation of contrast, the PSF, and the signal-to-noise ratio. Finally, conspicuity of lesions was investigated for combo acquisitions in comparison with standard scans. Implications and challenges for the practical use of combo acquisitions are discussed.

Algorithms↗

PubMed2002

[Adaptive restoration of single ion channel signal under filtering and colored background noise].

In order to overcome the effects of the anti-aliasing filter and the colored background noise, an adaptive algorithm is proposed to estimate the parameters of ion channel kinetics and the background noise, and whereafter the ion channel signal could be restored from the strong noisy patch-clamp recordings. The algorithm cross-couples the recursive expectation-maximization algorithm, which estimates optimally the parameters of hidden Markov model, and the recursive extended least square algorithm, which estimates optimally the characteristics of the background noise. Simulation suggests that this cross-coupling algorithm convergences consistently, and is very robust to the inexact conformation number.

Algorithms↗

PubMed1996

On the dangers of adjusting the parameters values of mechanism-based mathematical models.

Mechanism-based mathematical models describe systems in terms of identifiable physical processes, and the parameters are assumed to have fundamental physical significance. Ideally, the parameter values are measured independent of the system being modeled, but these values are often adjusted to give the best fit of model predictions to experimental data. A systematic investigation of the effects of such parameter adjustment was conducted by developing a model system comprising a known reaction mechanism and known rate constants. Simulations of experiments were run, and then attempts were made to model the system under a variety of problematic, but realistic, conditions. (1) When one rate constant was seriously in error, adjustment of a different rate constant gave the greatest improvement in the model fit. (2) When a contaminant was present in the experiment, the effects could be hidden by the adjustment of the rate constants. (3) When an incorrect reaction mechanism was assumed, the error could be hidden by parameter adjustment if the concentrations of only one of the reacting species were considered or if an unweighted fit was used for the optimization. (4) Parameter values adjusted for one set of experimental conditions gave a poorer fit than did the unadjusted parameter values when attempting to model a new set of experimental condition (addition of an inhibitor). These results show the potential dangers of adjusting parameter values and the importance of measuring as many variables as possible in a complex system.

Animals↗

PubMed2006

Peptide conformation in gas phase probed by collision-induced dissociation and its correlation to conformation in condensed phases.

A kinetic peptide fragmentation model for quantitative prediction of peptide CID spectra in an ion trap mass spectrometer has been reported recently. When applying the model to predict the CID spectra of large peptides, it was often found that the predicted spectra differed significantly from their experimental spectra, presumably due to noncovalent interactions in these large polypeptides, which are not considered in the fragmentation model. As a result, site-specific quantitative information correlated to the secondary/tertiary structure of an ionized peptide may be extracted from its CID spectrum. To extract this information, the kinetic peptide fragmentation model was modified by incorporating conformation-related parameters. These parameters are optimized for best fit between the predicted and the experimental spectrum. A conformational stability map is then generated from these conformation-related parameters. Analysis of a few bioactive alpha-helical peptides including melittin, glucagon and neuropeptide Y by this technique demonstrated that their stability maps in the gas phase correlate strongly to their secondary structures in the condensed phases.

Animals↗

PubMed2006

Lignocellulosic fiber charge enhancement by catalytic oxidation during oxygen delignification.

A series of one-stage oxygen delignification treatments with a softwood (SW) kraft pulp were studied employing 0.0-0.5% of a bismuth ruthenium pyrochlore oxide catalyst. The results demonstrated that a 0.09-0.18% charge of catalyst in an oxygen stage provided a 52.2-116.0% increase of carboxylic acid groups in the cellulosic component of kraft pulps without a significant decrease in fiber viscosity. A 3-factor at 3-level (L(9)3(3)) orthogonal experimental design was used to identify the main factors influencing acid group formation in pulp carbohydrates. The relative significance of experimental parameters for polysaccharide acid group formation was the molar equivalent NaOH, oxygen pressure, and finally, reaction temperature under the experimental conditions studied. The optimized reaction parameters for fiber charge development were shown to be 85-100 degrees C, 2.5% NaOH, and 800-960 kPa oxygen pressure. Pulps with higher fiber carboxylic acid content introduced by catalytic oxidation during oxygen delignification yielded a 10.9-33.7% increase in fiber charge after elemental chlorine free (ECF) pulp bleaching. The enhanced fiber charge resulted in 6.7-17.1% increase in paper sheet tensile index at comparable pulp viscosity.

Journal Article↗

PubMed1989

Biochemical and functional correlates of myocardium-like transformed skeletal muscle as a power source for cardiac assist devices.

Skeletal muscles, such as the latissimus dorsi muscle, can be transformed to gain considerable fatigue resistance to be suitable either for cardiomyoplasty, or to power a cardiac assist device. Such transformation of the skeletal muscle can be achieved by low frequency electrical stimulation for several weeks. In this article, we reviewed the stimulation protocol, and subsequent histochemical, biochemical, and functional changes in the skeletal muscle, and compared them to those of the cardiac muscle. The parameters that should be useful for stimulating such a muscle to assist the heart are defined. The issues currently under study, including the optimal transformation parameters, the feasibility of working transformation, and the importance of device design to minimize vascular compromise of the muscle, are also discussed. It is concluded that there is a great potential to use the plasticity of skeletal muscle for clinical purposes, specifically by transforming the skeletal muscle to resemble the myocardium in order to use it either to replace or repair the myocardium, or as the endogenous power source for a cardiac assist device.

Animals↗

PubMed1993

The economics of culling dairy cows with clinical mastitis.

Culling dairy cows with clinical mastitis reduces the incidence of the disease in dairy herds, but the costs of such action, in terms of reduced milk production and increased replacement costs, are generally thought to outweigh the benefits. To test this hypothesis a stochastic dynamic programming model was developed to establish the economically optimum time of replacement for dairy cows subject to variable levels of clinical mastitis infection, using average United Kingdom production and price parameters. The optimal stage at which to replace a dairy cow was found to be sensitive to changes in mastitis incidence and in critical price parameters within the bounds of commercial experience. This result indicates that an objective culling policy based on clinical mastitis records in addition to milk production potential may be economically viable.

Animals↗