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Results for “parameter optimization”

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PubMed1991

Two-parameter mobile phase optimization for the simultaneous high-performance liquid chromatographic determination of dopamine, serotonin and related compounds in microdissected rat brain nuclei.

A new high-pressure liquid chromatography method with electrochemical detection is described that allows the simultaneous determination of dopamine, serotonin, 3,4-dihydroxyphenylacetic acid, 3-methoxy-4-hydroxyphenylacetic acid, 5-hydroxytryptophan and 5-hydroxyindoleacetic acid in microdissected nuclei from individual rat brains. No sample pre-treatment steps are required. Resolution and analysis time were optimized by a simple limited optimization procedure, involving two-parameter factorial design.

3,4-Dihydroxyphenylacetic Acid↗

PubMed2000

Simulated molecular evolution in a full combinatorial library.

BACKGROUND: The Darwinian concept of 'survival of the fittest' has inspired the development of evolutionary optimization methods to find molecules with desired properties in iterative feedback cycles of synthesis and testing. These methods have recently been applied to the computer-guided heuristic selection of molecules that bind with high affinity to a given biological target. We describe the optimization behavior and performance of genetic algorithms (GAs) that select molecules from a combinatorial library of potential thrombin inhibitors in 'artificial molecular evolution' experiments, on the basis of biological screening results. RESULTS: A full combinatorial library of 15,360 members structurally biased towards the serine protease thrombin was synthesized, and all were tested for their ability to inhibit the protease activity of thrombin. Using the resulting large structure-activity landscape, we simulated the evolutionary selection of potent thrombin inhibitors from this library using GAs. Optimal parameter sets were found (encoding strategy, population size, mutation and cross-over rate) for this artificial molecular evolution. CONCLUSIONS: A GA-based evolutionary selection is a valuable combinatorial optimization strategy to discover compounds with desired properties without needing to synthesize and test all possible combinations (i.e. all molecules). GAs are especially powerful when dealing with very large combinatorial libraries for which synthesis and screening of all members is not possible and/or when only a small number of compounds compared with the library size can be synthesized or tested. The optimization gradient or 'learning' per individual increases when using smaller population sizes and decreases for higher mutation rates.

Algorithms↗

PubMed1992

Exact likelihood evaluation in a Markov mixture model for time series of seizure counts.

This paper provides an alternative to Albert's (1991), Biometrics 47, 1371-1381) approximation to the E-step when using the EM algorithm for parameter estimation in Markov mixture models. Use of a recursive algorithm of Baum et al. (1970, Annals of Mathematical Statistics 41, 164-171) results in exact evaluation of the likelihood, optimal parameter estimates, and very efficient computation. Applications to time series of seizure counts and fetal movements clearly show the advantages of this exact approach.

Algorithms↗

PubMed2002

Automated analysis of data is inferior to visual analysis of ambulatory sleep apnea monitoring.

BACKGROUND: Many ambulatory sleep apnea monitoring devices are equipped with software which allows an automated analysis of data as well as a visual analysis. OBJECTIVE: The Merlin system which records heart rate, snoring sound, efforts, oronasal flow, body position and oxygen saturation was investigated to identify proper parameter settings for the automated analysis and to compare the automated with the visual analysis in patients with mild obstructive sleep apnea syndrome (OSAS). Sensitivity and specificity of the visual and automated analysis of ambulatory monitoring in comparison with visual polysomnographic (PSG) analysis were determined. METHODS AND RESULTS: First, we tried to find the optimal parameters for the automated analysis, using 7 different settings in 17 OSAS patients. Furthermore, we applied the optimized setting to 66 OSAS patients who were admitted (age 50.9 +/- 9.9 years, BMI 32.9 +/- 5 kg/m(2)), and compared the results with the visual analysis of raw data. The patients slept for one night in the sleep laboratory with Merlin and PSG simultaneously to compare the visual and automated analysis of Merlin data with results from the visual analysis of PSG. Automated analysis leads to an underestimation of the respiratory disturbance index (RDI; p < 0.001) compared with both the visual analysis and results of PSG. Using a cutoff level of 5 apneas and hypopneas/h for the diagnosis of OSAS, the sensitivity of Merlin with the automated analysis is 40.6% and the specificity is 100%. With a cutoff level of 15/h, sensitivity and specificity rose to 91.3 and 100%, respectively, which is comparable to the visual analysis. CONCLUSION: Merlin is a reliable device for detection of sleep-related breathing disorders, but recordings should be analyzed visually, especially in patients with a low RDI.

Adult↗

PubMed1997

Temperature-controlled CO2 laser tissue welding of ocular tissues.

Lasers can be used for binding tissues by welding, but the clinical application of this method has been limited by the difficulties in defining and maintaining the optimal conditions. Fiberoptic radiometry allows accurate remote temperature measurements for control of laser tissue welding. We evaluated the use of a temperature-controlled tissue welding system to close corneal and corneoscleral wounds. Eighty ex vivo bovine eyes were used for the determination of welding parameters optimal for corneal wound closure. A 4 mm central corneal cut was closed with use of a CO2 laser (600 mw, 0.9 mm spot size), with tissue temperatures ranging from 45-70 degrees C and welding time ranging from 1-30 seconds. Wound strength was measured as burst pressure of the sealed wound. The welding parameters found to cause the strongest wound binding were used to weld a limbal incision of 4 mm in 10 adult albino rabbits. The fellow eye of each animal was used as a control, and the same wound was closed with one 10/0 mersilen suture. Two animals were killed immediately after the procedure, and the eyes were sent for histologic examination. Eight rabbits were followed for 1 month. Clinical examination and refraction were done 1 day, 1 week, 2 weeks, and 1 month after the procedure. Corneal topographic evaluations were done 1 week after the procedure. After 1 month the animals were killed and the eyes were examined histologically. The optimal results of wound binding by laser welding in the enucleated bovine eyes were achieved with 55-60 degrees C and at a welding time of 12-20 seconds. At these parameters the burst pressure of corneal wounds was 70 mm Hg. All laser-welded limbal wounds in the rabbits were tightly closed at the end of procedure and during the follow-up period. The refractive results after laser welding were equal to those of the controlled suture-closed wound. Laser tissue welding combined with tissue temperature monitoring can be used to close corneal wounds.

Animals↗

PubMedDate not supplied

Evolutionary-algorithm-based strategy for computer-assisted structure elucidation.

An evolutionary algorithm (EA) using a graph-based data structure to explore the molecular constitution space is presented. The EA implementation proves to be a promising alternative to deterministic approaches to the problem of computer-assisted structure elucidation (CASE). While not relying on any external database, the EA-guided CASE program SENECA is able to find correct solutions within calculation times comparable to that of other CASE expert systems. The implementation presented here significantly expands the size limit of constitutional optimization problems treatable with evolutionary algorithms by introducing novel efficient graph-based genetic operators. The new EA-based search strategy is discussed including the underlying data structures, component design, parameter optimization, and evolution process control. Typical structure elucidation examples are given to demonstrate the algorithm's performance.

Journal Article↗

PubMed1984

Fitting physiological models to data.

Methods of fitting models to experimental data obtained from biological systems are reviewed. The Michaelis-Menten model is used as the working example of a familiar and well-studied biological model. Criteria for selecting models include goodness of fit, freedom from systematic errors, and simplicity. A given model is usually fitted and the optimal parameters determined by minimization of an objective function, usually the sum of the squared errors. Freedom from systematic errors is best judged graphically. The important mathematical methods of fitting models are derived from the calculus and include linear and quadratic programming. The latter leads to minimization of the sum of squares of errors. Optimal search procedures, which also perform this minimization, are surveyed. Other properties of models, such as the proper number of parameters and whether linearization is appropriate, are discussed. The specialized problems of biological models and data are considered.

Models, Biological↗

PubMed2002

Adsorption of a diverse set of organic vapors on quartz, CaCO3, and alpha-Al2O3 at different relative humidities.

Adsorption constants of a diverse set of 50 organic vapors have been measured on quartz (SiO(2)), CaCO(3), and alpha-Al(2)O(3) at different relative humidities at 15 degrees C. For nonpolar compounds we found an exponential decrease of the adsorption constants on a given mineral between 40 and 97% relative humidity. Extrapolated to 100% relative humidity, the adsorption constants of nonpolar compounds on the different minerals coincide and agree with those measured on a bulk water surface. The adsorption constants of polar compounds also decrease with increasing humidity up to 90%, but between 90% and 100% they increase again. We speculate that this effect is due to a change in the orientation of the water molecules that form the surface at which the organic vapors adsorb at this high humidity. The compound variability in the adsorption constants of all compounds on a given surface at a given relative humidity could be described rather well with a linear free energy relationship using Abraham's solvation parameters for the van der Waals and electron-donor/acceptor properties of the compounds. The remaining deviation between fitted and experimental data was found to be systematic, which indicated that an optimized parameter set for the used compounds could still considerably improve the fit.

Journal Article↗

PubMed2003

Detection and typing of HSV-1, HSV-2, CMV and EBV by quadruplex PCR.

The development of a multiplex polymerase chain reaction (PCR) method for rapid and accurate detection and typing of herpes simplex virus type 1 (HSV-1), and type-2 (HSV-2), cytomegalovirus (CMV) and Epstein-Barr virus (EBV) is very important for clinical diagnosis to allow the deliver of therapy as early as possible. Large scale amplifications by multiplex PCR of viral DNA can lower the cost and time for viral diagnosis. In this study, therefore sensitive quadruplex PCR was achieved by optimizing parameters such as primers, and 1.5 mM magnesium and 200 uM dNTPs concentrations. The concentrations of HSV-1, HSV-2, CMV and EBV primers were 0.5, 0.3, 0.25 and 0.25 pmoles, respectively. Optimal annealing temperature was 54 degrees C. Employing these conditions, we could detect 10 copies of reconstructed template plasmid DNA, which were cloned to vectors containing target sequences of viral DNA. PCR products of 271 bp for HSV-1, 231 bp for HSV-2, 368 bp for CMV, and 326 bp for EBV were separated on 5.0% polyacrylamide gel electrophoresis and confirmed by direct sequencing. The present study showed that the quadruplex PCR assay described herein has potential application in clinical diagnosis, when rapid, accurate detection and typing of viruses HSV-1, HSV-2, CMV or EBV are necessary.

Cytomegalovirus↗

PubMed2004

A dynamic, architectural plant model simulating resource-dependent growth.

BACKGROUND AND AIMS: Physiological and architectural plant models have originally been developed for different purposes and therefore have little in common, thus making combined applications difficult. There is, however, an increasing demand for crop models that simulate the genetic and resource-dependent variability of plant geometry and architecture, because man is increasingly able to transform plant production systems through combined genetic and environmental engineering. MODEL: GREENLAB is presented, a mathematical plant model that simulates interactions between plant structure and function. Dual-scale automaton is used to simulate plant organogenesis from germination to maturity on the basis of organogenetic growth cycles that have constant thermal time. Plant fresh biomass production is computed from transpiration, assuming transpiration efficiency to be constant and atmospheric demand to be the driving force, under non-limiting water supply. The fresh biomass is then distributed among expanding organs according to their relative demand. Demand for organ growth is estimated from allometric relationships (e.g. leaf surface to weight ratios) and kinetics of potential growth rate for each organ type. These are obtained through parameter optimization against empirical, morphological data sets by running the model in inverted mode. Potential growth rates are then used as estimates of relative sink strength in the model. These and other 'hidden' plant parameters are calibrated using the non-linear, least-square method. KEY RESULTS AND CONCLUSIONS: The model reproduced accurately the dynamics of plant growth, architecture and geometry of various annual and woody plants, enabling 3D visualization. It was also able to simulate the variability of leaf size on the plant and compensatory growth following pruning, as a result of internal competition for resources. The potential of the model's underlying concepts to predict the plant's phenotypic plasticity is discussed.

Algorithms↗

PubMedDate not supplied

Black blood dual phase turbo FLASH MR imaging of the heart.

An MR imaging scheme for dark blood cardiac images acquired simultaneously in end diastolic and end systolic phases, in breath-hold times, is presented. The sequence consists of a magnetization preparation period followed by two segmented k-space acquisitions. Image quality was investigated with respect to different sequence parameters (optimal values are indicated in brackets): (a) echo time (TE)/repetition time (TR)/ flip angle (FA) (3/6.2 msec/20 degrees); (b) number of lines/ segments in the acquisition window (11 lines/segment); (c) location of acquisition windows and inversion time; and (d) thickness of slice "reinverted" during preparation (1.53 times the acquisition slice thickness). The image quality of the basal slices at end systole was critically dependent on the last parameter. High quality short axis views of the heart, with good blood signal suppression, were acquired with the optimized sequence on four volunteers from apex to base at two phases in 10 breath-holds.

Blood↗

PubMedDate not supplied

A new 9Be(alpha,n) cross-section evaluation for use in the SOURCES computer code.

Experimental breakup reaction data was the basis for choosing a set of alpha optical potential parameters for calculating the cross section from the 9Be(alpha,alpha'n) reaction with the GNASH code. Although not in complete agreement with experimental values, the promising results suggest additional work and continued research for optimal parameters. Accommodating modifications in the SOURCES code system required improved data and an approximation for the three-body reaction branching fractions is presented as a temporary solution. Experimental spectra from AcBe, CmBe, and simulated AmBe neutron sources are compared to SOURCES calculations using the new branching fractions and serve as benchmarks for this new version of the code.

Alpha Particles↗

PubMed2006

Image interpolation by two-dimensional parametric cubic convolution.

Cubic convolution is a popular method for image interpolation. Traditionally, the piecewise-cubic kernel has been derived in one dimension with one parameter and applied to two-dimensional (2-D) images in a separable fashion. However, images typically are statistically nonseparable, which motivates this investigation of nonseparable cubic convolution. This paper derives two new nonseparable, 2-D cubic-convolution kernels. The first kernel, with three parameters (designated 2D-3PCC), is the most general 2-D, piecewise-cubic interpolator defined on [-2, 2] x [-2, 2] with constraints for biaxial symmetry, diagonal (or 90 degrees rotational) symmetry, continuity, and smoothness. The second kernel, with five parameters (designated 2D-5PCC), relaxes the constraint of diagonal symmetry, based on the observation that many images have rotationally asymmetric statistical properties. This paper also develops a closed-form solution for determining the optimal parameter values for parametric cubic-convolution kernels with respect to ensembles of scenes characterized by autocorrelation (or power spectrum). This solution establishes a practical foundation for adaptive interpolation based on local autocorrelation estimates. Quantitative fidelity analyses and visual experiments indicate that these new methods can outperform several popular interpolation methods. An analysis of the error budgets for reconstruction error associated with blurring and aliasing illustrates that the methods improve interpolation fidelity for images with aliased components. For images with little or no aliasing, the methods yield results similar to other popular methods. Both 2D-3PCC and 2D-5PCC are low-order polynomials with small spatial support and so are easy to implement and efficient to apply.

Algorithms↗

PubMed1991

Automatic classification of cells in cell cycle phases based on Ki-67 antigen quantification by fluorescence microscopy.

Ki-67 antigen is thought to be a marker of cell proliferation, as it can be detected in cycling cells, i.e. cells in G1, S, G2 and M phases, but not in resting cells. The immunocytochemical staining pattern obtained by the Ki-67 monoclonal antibody varies, depending on the cell cycle phases. Analysis of double staining of Ki-67 antigen and DNA in the MCF-7 cell line by videomicrofluorometry allows the description of both the level and the pattern of Ki-67 staining in the form of a set of parameters defining each cell. These parameters were measured in MCF-7 cell populations characterized according to their position in the cell cycle. They were submitted to a statistical analysis (principal component and discriminant analysis) which allowed the determination of the optimal parameters to characterize a given cellular group and permitted the use of these parameters for an automatic classification of cells in the different cell cycle phases. In G1, S, G2, prophase + metaphase and anaphase + telophase cells, these parameters allowed a classification of cells with a good-classification rate of 94.37%. A comparison of this method with methods based on the DNA histogram and bromodeoxyuridine uptake was performed. The classification coefficients stemming from the discriminant analysis were introduced into a program to obtain, automatically, the Ki-67 labelling index and the percentages of cells in each phase. This method, which allows a quick evaluation of the proliferation and the phase indices, may be more widely applicable.

Breast Neoplasms↗

PubMedDate not supplied

The significance of positive controls in testing the oncogenic potential of cell material for virus vaccine production.

For all the parts involved in the production and control of virus vaccine it is important that controls of the cell material should be carried out under optimal conditions for the detection of any abnormal characteristics of the cells. The experiments reported here attempt to establish some of the optimal parameters for testing out the tumor-inducing properties of a human diploid cell culture. All experiments were carried out on 6-week old Syrian hamsters and the main objectives were: (i) to devise an optimal immunosupression scheme and (ii) to find a more suitable positive control for testing the oncogenic potential of the human diploid cells. The anti-hamster lymphocyte serum proved to be a more potent immunosuppresser than hydrocortisone succinate as seen from the development of tumors following injections with KB cells; this scheme was subsequently used in assessing the usefulness of KB and Swiss-12 cells as positive controls. The experiments lend support to the suggestion that a heteroploid fibroblastic culture (such as Swiss-12) should become a standard positive control since not only are the tumors so obtained larger and less prone to early necrosis but, more important, they bear a closer resemblance to the kind of tumors likely to be induced by the diploid cell cultures being tested.

Animals↗

PubMed1992

Pharmacokinetic analysis of the perivascular distribution of bifunctional antibodies and haptens: comparison with experimental data.

A mathematical model is developed to describe the concentration profiles around individual tumor blood vessels for two-step approaches to cancer treatment. The model incorporates plasma pharmacokinetics, interstitial diffusion, reversible binding between antibody and hapten and between antibody and tumor-associated antigens, and physiological parameters to evaluate present experimental approaches and to suggest new guidelines for the effective use of two-step approaches. Results show considerable interaction between the binding kinetics, initial drug doses, and antigen density, with optimal parameter ranges depending on the desired goal: treatment or detection. The hapten concentration in tumors was found to be nonuniform because of specific binding to antibodies. While binding of the hapten to the bifunctional antibody is necessary for improved retention, too large a binding affinity may lead to very poor penetration of the hapten into regions far away from blood vessels. The time delay between antibody and hapten injection was found to be an important parameter. Longer time delays were found to be advantageous, subject to constraints such as internalization of the antibody and tumor growth during treatment. A proper combination of initial doses for the two species was also seen to be crucial for maximum effectiveness. Comparison of the model with the experimental data of Le Doussal et al. (Cancer Res., 51: 6650-6655, 1991) and Stickney et al. (Cancer Res., 50: 3445-3452, 1990) suggests two novel, yet testable, hypotheses: (a) the early pharmacokinetics of low molecular weight agents can have an important effect on later concentrations using two-step approaches; and (b) metabolism may play an important role in reducing concentrations in the tumor and tumor:plasma concentration ratios. These results should help in the effective design of two-step strategies.

Antibodies, Neoplasm↗

PubMed1989

[Basic investigation on hyperthermia by low-frequency ultrasonic].

Ultrasonic heating methods for hyperthermia have been developed because of several advantage i.e., its easiness in steering the applicator for the target, and its non-interference with other electronic equipment. Most of them make hot spots by focusing the ultrasonic beam, using acoustic lens or many transmitters. Therefore, these methods are based on analogous idea to the ray focusing, and higher frequency, i.e., from 500 kHz to 5 MHz, is used. However, there are some problems; hot spots are generated before the focus, and it is difficult to heat the region beyond gas and bones owing to the attenuation and scattering of the ultrasonic beam. Then, we propose a new method for heating the depths and local regions of the body. In this method, to heat the depths of the body low-frequency ultrasound is used since it has larger penetration depth and it is less scattered than higher-frequency ultrasound. To heat only tumours, hot spots are generated by synthesizing acoustic fields resulted from several incident waves. The heat generation and temperature distribution was analyzed using the models with properties similar to tissues for different values of parameters such as frequency, position and the number of sources. The results show that hot spots can be generated at the depths of the body. and that desirable temperature distribution can be obtained by selecting optimal parameters and cooling condition. To determine the temperature distribution more accurately it would be required to introduce the more complicated model of heat removal effect by blood flow and the experimental results. These problems are left for the future investigation.

Humans↗

PubMed2002

Arsenic adsorption onto pillared clays and iron oxides.

Arsenic adsorption was carried out on simple materials such as goethite and amorphous iron hydroxide, and more complex matrices such as clay pillared with titanium(IV), iron(III), and aluminum(III). These matrices were synthesized from a bentonite whose montmorillonitic fraction was pillared according to optimized parameters. These sorbents were characterized by various methods: XRD, FTIR, BET, DTA/TGA, surface acidity, and zetametry. Elimination of arsenite and arsenate as a function of pH was studied. Arsenate elimination was favored at acidic pH, whereas optimal arsenite elimination was obtained at 4<pH<9. For pH values above 10, the pillared clays were damaged and elimination decreased. Equilibrium time and adsorption isotherms were also determined for arsenite and arsenate at each matrix auto-equilibrium pH. Amorphous iron hydroxide had the highest adsorption capacities both towards arsenate and arsenite. Adsorption capacities of goethite and iron- and titanium-pillared clays toward arsenate were similar, but those toward arsenite were different. Desorption experiments from the various matrices were carried out. Iron- and titanium-pillared clays showed a desorption capacity above 95% and around 40% respectively, but no desorption rate could be obtained for iron (hydr)oxides as they were damaged during the process.

Adsorption↗