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PubMed2006

Significant parameters in the optimization of MALDI-TOF-MS for synthetic polymers.

One of the most significant issues in any analytical practice is optimization. Optimization and calibration are key factors in quantitation. In matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), instrument optimization is a limitation restricting quantitation. An understanding of the parameters that are most influential and the effects of these parameters on the mass spectrum is required for optimization. This understanding is especially important when characterizing synthetic polymers by MALDI-TOF-MS, due to the breadth of the polymer molecular mass distribution (MMD). Two considerations are important in quantitation, additivity of signal and signal-to-noise (S/N). In this study, the effects of several instrument parameters were studied using an orthogonal experimental design to understand effects on the signal-to-noise (S/N) of a polystyrene distribution. The instrument parameters examined included detector voltage, laser energy, delay time, extraction voltage, and lens voltage. Other parameters considered were polymer concentration and matrix. The results showed detector voltage and delay time were the most influential of the instrument parameters for polystyrene using all trans-retinoic acid (RA) as the matrix. These parameters, as well as laser energy, were most influential for the polystyrene with dithranol as the matrix.

Journal Article↗

PubMed2006

Spectral embedding finds meaningful (relevant) structure in image and microarray data.

BACKGROUND: Accurate methods for extraction of meaningful patterns in high dimensional data have become increasingly important with the recent generation of data types containing measurements across thousands of variables. Principal components analysis (PCA) is a linear dimensionality reduction (DR) method that is unsupervised in that it relies only on the data; projections are calculated in Euclidean or a similar linear space and do not use tuning parameters for optimizing the fit to the data. However, relationships within sets of nonlinear data types, such as biological networks or images, are frequently mis-rendered into a low dimensional space by linear methods. Nonlinear methods, in contrast, attempt to model important aspects of the underlying data structure, often requiring parameter(s) fitting to the data type of interest. In many cases, the optimal parameter values vary when different classification algorithms are applied on the same rendered subspace, making the results of such methods highly dependent upon the type of classifier implemented. RESULTS: We present the results of applying the spectral method of Lafon, a nonlinear DR method based on the weighted graph Laplacian, that minimizes the requirements for such parameter optimization for two biological data types. We demonstrate that it is successful in determining implicit ordering of brain slice image data and in classifying separate species in microarray data, as compared to two conventional linear methods and three nonlinear methods (one of which is an alternative spectral method). This spectral implementation is shown to provide more meaningful information, by preserving important relationships, than the methods of DR presented for comparison. Tuning parameter fitting is simple and is a general, rather than data type or experiment specific approach, for the two datasets analyzed here. Tuning parameter optimization is minimized in the DR step to each subsequent classification method, enabling the possibility of valid cross-experiment comparisons. CONCLUSION: Results from the spectral method presented here exhibit the desirable properties of preserving meaningful nonlinear relationships in lower dimensional space and requiring minimal parameter fitting, providing a useful algorithm for purposes of visualization and classification across diverse datasets, a common challenge in systems biology.

Algorithms↗

PubMed1979

[A program for optimizing radiation beam parameters in radiotherapy (author's transl)].

A very large-use optimization technique for radiation treatment planning is presented. Very few input data are sufficient to enable the program to work out an optimized dose distribution; optimization is obtained by modifying the intersection point of beams and the size, the wedge and the time of each beam. The technique may be extended to moving beam teletherapy. A memorized collection of typical geometric arrangements allows a good saving in operator's time especially during data preparation.

Computers↗

PubMed2006

Optimization of physical parameters for exo-biopolymer production in submerged mycelial cultures of two entomopathogenic fungi Paecilomyces japonica and Paecilomyces tenuipes.

AIMS: In the present study, two different optimization techniques were used to determine the suitable operating parameters for exo-biopolymer production in submerged mycelial cultures of two entomopathogenic fungi Paecilomyces japonica and Paecilomyces tenuipes. METHODS AND RESULTS: First, the rotating simplex method, a nonstatistical optimization technique, was employed to obtain the best combination of physical parameters (viz. pH, agitation intensity, aeration rate) for maximum exo-biopolymer production by P. japonica in a batch bioreactor. The optimal combination was determined to be a pH of 8.06, an aeration of 3 vvm, without any impeller agitation, producing a 17-time increase in exopolymer production (34.5 g l(-1)) when compared with that achieved in unoptimized flask cultures. Second, the uniform design method, a statistical optimization technique, was employed to determine the best operating parameters for submerged culture of P. tenuipes. The optimal combination for mycelial growth was determined to be a pH of 4.88, an aeration of 2 vvm and an agitation of 350 rpm, while a pH of 4, an aeration of 2 vvm and an agitation of 150 rpm was best for exo-biopolymer production. CONCLUSIONS: The exo-biopolymer production in P. japonica optimized by the rotating simplex method was strikingly improved (max. 34.5 g l(-1)), and the exo-biopolymer production in P. tenuipes optimized by the uniform design method was also significantly increased (max. 3.4 g l(-1)). SIGNIFICANCE AND IMPACT OF THE STUDY: The successful application of these two different optimization techniques in this study implies that these methods are worthy of applying to other fermentation systems for the production of bioactive mycelial biomass and exo-biopolymers in liquid culture of higher fungi.

Biomass↗

PubMed2005

Application of the Taguchi analytical method for optimization of effective parameters of the chemical vapor deposition process controlling the production of nanotubes/nanobeads.

Seven variable parameters of the chemical vapor deposition system have been optimized with the help of the Taguchi analytical method for getting a desired product, e.g., carbon nanotubes or carbon nanobeads. It is observed that almost all selected parameters influence the growth of carbon nanotubes. However, among them, the nature of precursor (racemic, R or Technical grade camphor) and the carrier gas (hydrogen, argon and mixture of argon/hydrogen) seem to be more important parameters affecting the growth of carbon nanotubes. Whereas, for the growth of nanobeads, out of seven parameters, only two, i.e., catalyst (powder of iron, cobalt, and nickel) and temperature (1023 K, 1123 K, and 1273 K), are the most influential parameters. Systematic defects or islands on the substrate surface enhance nucleation of novel carbon materials. Quantitative contributions of process parameters as well as optimum factor levels are obtained by performing analysis of variance (ANOVA) and analysis of mean (ANOM), respectively.

Argon↗

PubMed2006

Optimizing cardiac material parameters with a genetic algorithm.

Determining the unknown material parameters of intact ventricular myocardium can be challenging due to highly nonlinear material behavior. Previous studies combining a gradient-search optimization procedure with finite element analysis (FEA) were limited to two-dimensional (2D) models or simplified three-dimensional (3D) geometries. Here we present a novel scheme to estimate unknown material parameters for ventricular myocardium by combining a genetic algorithm (GA) with nonlinear finite element analysis. This approach systematically explores the domain of the material parameters. The objective function to minimize was the error between simulated strain data and finite element model strains. The proposed scheme was validated for a 2D problem using a realistic material law for ventricular myocardium. Optimized material parameters were generally within 0.5% of the true values. To demonstrate the robustness of the new scheme, unknown material parameters were also determined for a realistic 3D heart model with an exponential hyperelastic material law. When using strains from two material points, the algorithm converged to parameters within 5% of the true values. We conclude that the proposed scheme is robust when estimating myocardial material parameters in 2D and 3D models.

Algorithms↗

PubMed2006

Optimization of nutrient parameters for lovastatin production by Monascus purpureus MTCC 369 under submerged fermentation using response surface methodology.

Lovastatin, an inhibitor of HMG-CoA reductase, was produced by submerged fermentation using Monascus purpureus MTCC 369. Five nutritional parameters screened using Plackett-Burman experimental design were optimized by Box-Behnken factorial design of response surface methodology for lovastatin production in shake flask cultures. Maximum lovastatin production of 351 mg/l were predicted in medium containing 29.59 g/l dextrose, 3.86 g/l NH4Cl, 1.73 g/l KH2PO4, 0.86 g/l MgSO4 x 7H2O, and 0.19 g/l MnSO4 x H2O using response surface plots and point prediction tool of DESIGN EXPERT 7.0 (Statease, USA) software.

Culture Media↗

PubMed1990

Calibration in three dimensions: optimizing a two-parameter calibration technique to extend the range of an immunoturbidimetric urinary albumin assay into antigen excess.

I describe a general technique, called "two-parameter calibration," which allows precise determination of analyte from non-monotonic calibration plots and the calibration of immunoturbidimetric assays in antigen excess. Using three-dimensional calibration plots and relative-sensitivity curves, two optimal parameters may be selected from a number of possible options by using criteria presented here. Choosing two different values of delta At1-t2, the change in absorbance from time t1 to t2--as the reaction parameters in an immunoturbidimetric assay for albumin, I have optimized the choice of time interval for two-parameter calibration and extended the working range of the assay by three- to fourfold. The albumin assay shows excellent agreement of observed and expected values (r = 0.996) and also with results of a routine kinetic dye-binding method used on diluted plasma samples (r = 0.970).

Albumins↗

PubMed2007

Alpha-crystallin assisted refolding of enzyme substrates: optimization of external parameters.

alpha-Crystallin is known to act as a molecular chaperone by preventing the aggregation of partially unfolded substrate proteins. It is also known to assist the refolding of a number of denatured enzymes, but the activity yield is often less than 20%. In this paper, we have tried to tune the refolding ability of alpha-crystallin in vitro by optimizing various external parameters. We wanted to find out the best possible condition under which it can exhibit maximum refolding capacity. We found that under suitable condition in vitro alpha-crystallin can refold denatured malate dehydrogenase, carbonic anhydrase and lactate dehydrogenase to recover more than 40% activity. We also measured the effect of several external factors such as nucleotides, osmolytes, electrolytes, temperature etc. on the in vitro alpha-crystallin mediated reactivation of above stated enzymes. We found that nucleotides and electrolytes had little effect on the refolding ability of alpha-crystallin. However, in presence of different osmolytes, we found that its ability to reactivate denatured substrate proteins enhanced significantly. Refolding in presence of pre-incubated alpha-crystallin reveals that hydrophobicity had stronger influence on the refolding capacity of alpha-crystallin than its oligomeric size.

Animals↗

PubMed1991

[Cardiac magnetic resonance. Optimization of the parameters in the evaluation of right and left ventricular function].

MR imaging is the only non-invasive tomographic imaging modality capable of imaging the heart along planes that are parallel to each other and in any desired direction. Such reconstruction algorithms can thus be applied to MR images as the Simpson's rule which allows volume estimation of all cardiac cavities, although very irregular in shape, like the right ventricle. The authors optimized the technical parameters to obtain a set of multiphase double-angulated images on both the short and the long axes of the heart, in about 1-hour time. This technique was used to examine 31 patients suffering from several cardiopathies. The images allowed both end-diastolic and end-systolic volumes to be estimated, as well as the ejection fractions of both ventricles. In the left ventricle the area-length method and the Simpson's rule were applied, whereas only the latter was employed in the right ventricle. The correlation coefficients of US and MR data were, for the 3 parameters, r = 0.813, r = 0.920, and r = 0.879, respectively, in the first case, and r = 0.905, r = 0.923, and r = 0.890 in the second one. The time required to analyze the obtained data, which is done manually, is still considerably long.

Cardiac Volume↗

PubMed2003

Optimization of scanning parameters for multi-slice CT colonography: experiments with synthetic and animal phantoms.

AIM: To determine the optimal collimation, pitch, tube current and reconstruction interval for multi-slice computed tomography (CT) colonography with regard to attaining satisfactory image quality while minimizing patient radiation dose. MATERIALS AND METHODS: Multi-slice CT was performed on plastic, excised pig colon and whole pig phantoms to determine optimal settings. Performance was judged by detection of simulated polyps and statistical measures of the image parameters. Fat and muscle conspicuity was measured from images of dual tube-current prone/supine patient data to derive a measure of tube current effects on tissue contrast. RESULTS: A collimation of 4 x 2.5 mm was sufficient for detection of polyps 4 mm and larger, provided that a reconstruction interval of 1.25 mm was used. A pitch of 1.5 allowed faster scanning and reduced radiation dose without resulting in a loss of important information, i.e. detection of small polyps, when compared with a pitch of 0.75. Tube current and proportional radiation dose could be lowered substantially without deleterious effects on the detection of the air-mucosal interface, however, increased image noise substantially reduced conspicuity of different tissues. CONCLUSION: An optimal image acquisition set-up of 4 x 2.5 mm collimation, reconstruction interval of 1.25 mm, pitch of 1.5 and dual prone/supine scan of 40/100 mA tube current is proposed for our institution for scanning symptomatic patients. Indications are that where CT colonography is used for colonic polyp screening in non-symptomatic patients, a 40 mA tube current could prove satisfactory for both scans.

Animals↗

PubMed2006

Optimization of analytical parameters for inferring relationships among Escherichia coli isolates from repetitive-element PCR by maximizing correspondence with multilocus sequence typing data.

Repetitive-element PCR (rep-PCR) is a method for genotyping bacteria based on the selective amplification of repetitive genetic elements dispersed throughout bacterial chromosomes. The method has great potential for large-scale epidemiological studies because of its speed and simplicity; however, objective guidelines for inferring relationships among bacterial isolates from rep-PCR data are lacking. We used multilocus sequence typing (MLST) as a "gold standard" to optimize the analytical parameters for inferring relationships among Escherichia coli isolates from rep-PCR data. We chose 12 isolates from a large database to represent a wide range of pairwise genetic distances, based on the initial evaluation of their rep-PCR fingerprints. We conducted MLST with these same isolates and systematically varied the analytical parameters to maximize the correspondence between the relationships inferred from rep-PCR and those inferred from MLST. Methods that compared the shapes of densitometric profiles ("curve-based" methods) yielded consistently higher correspondence values between data types than did methods that calculated indices of similarity based on shared and different bands (maximum correspondences of 84.5% and 80.3%, respectively). Curve-based methods were also markedly more robust in accommodating variations in user-specified analytical parameter values than were "band-sharing coefficient" methods, and they enhanced the reproducibility of rep-PCR. Phylogenetic analyses of rep-PCR data yielded trees with high topological correspondence to trees based on MLST and high statistical support for major clades. These results indicate that rep-PCR yields accurate information for inferring relationships among E. coli isolates and that accuracy can be enhanced with the use of analytical methods that consider the shapes of densitometric profiles.

Alleles↗

PubMed2006

Optimization of physicochemical parameters for the enhancement of carbonyl reductase production by Candida viswanathii.

Culture conditions have been optimized for a newly isolated yeast strain Candida viswanathii PBR2 which is capable of reducing a wide variety of aryl ketones with high stereospecificity. Studies on the culture conditions and catalytic performance of this microorganism showed that the carbonyl reductase occurs constitutively in the cells and its production is enhanced by feeding with acetophenone (2 mM) during the early period of cultivation. Mannitol (1%, wv(-1)) was found to be beneficial both for growth and enzyme production. Supplementation of the media with yeast extract (1.0%, wv(-1)) and Ca(2+ ) (4 mM) enhanced the enzyme production. The optimal temperature and pH for the growth and enzyme production were 25 degrees C and 9.0, respectively. Excellent conversions along with almost absolute enantioselectivity were observed when the resting cells of this yeast strain were exploited to carry out the stereoselective reduction of a number of aryl ketones.

Alcohol Oxidoreductases↗

PubMedDate not supplied

Computer modeling of three-dimensional reconstruction algorithm of cathodoluminescence material properties, analysis of errors, and optimization of variable parameters.

Three-dimensional (3-D) reconstruction of cathodoluminescence (CL) properties of materials (Saparin et al. 1997) is a new nondestructive technique that measures quantum yield information of subsurface layers as a set of two-dimensional image sections. This technique is able to synthesize a 3-D image without destroying the sample. The basis for this technique is the fact that the electrons in scanning electron microscopy penetrate the sample at different depths with a variation of accelerating voltage. The detected CL emission integrates the information from the full volume occupied by the charge carriers. Estimating the errors that occur during the reconstruction process is complex since these errors are caused by necessary approximations, noise, and the imperfection of the 3-D reconstruction algorithm that is employed. An analysis of the factors that affect the accuracy of the technique has been made. The estimation of systematic errors and the optimization of variable parameters were calculated by computer modeling.

Journal Article↗

PubMed2004

Singular-value analysis and optimization of experimental parameters in fluorescence molecular tomography.

The advent of specific molecular markers and probes employing optical reporters has encouraged the application of in vivo diffuse tomographic imaging at greater spatial resolutions and hence data-set volumes. This study applied singular-value analysis (SVA) of the fluorescence tomographic problem to determine optimal source and detector distributions that result in data sets that are balanced between information content and size. Weight matrices describing the tomographic forward problem were constructed for a range of source and detector distributions and fields of view and were decomposed into their associated singular values. These singular-value spectra were then compared so that we could observe the effects of each parameter on imaging performance. The findings of the SVA were then confirmed by examining reconstructions of simulated and experimental data acquired with the same optode distributions as examined by SVA. It was seen that for a 20-mm target width, which is relevant to the small-animal imaging situation, the source and detector fields of view should be set at approximately 30 mm. Equal numbers of sources and detectors result in the best imaging performance in the parallel-plate geometry and should be employed when logistically feasible. These data provide guidelines for the design of small-animal diffuse optical tomographic imaging systems and demonstrate the utility of SVA as a simple and efficient means of optimizing experimental parameters in problems for which a forward model of the data collection process is available.

Animals↗

PubMed2005

Gene expression and immune response kinetics using electroporation-mediated DNA delivery to muscle.

BACKGROUND: Injection of DNA encoding exogenic proteins into muscle tissue combined with electroporation often results in a transient increase of the encoded protein concentration in the muscle and the blood. The reduction is normally due to an immune response against the exogenic protein but other factors may also be involved. How various electroporation parameters affect the concentration kinetics of syngenic and exogenic proteins is studied in relation to immune response and muscle damage after electroporation-mediated DNA transfer to muscle. METHODS: Electroporation was applied to mouse quadriceps and rat tibialis anterior muscles after injection of DNA encoding either secreted alkaline phosphatase (SEAP), beta-galactosidase (beta-gal), luciferase or a mouse IgG molecule. Protein concentrations in blood or muscle and antibody responses were measured for a period up to 3 months. Tissue inflammation and muscle cell damage were studied on muscle cross-sections and assessed by measuring the concentrations of creatine phosphokinase (CPK) in blood. RESULTS: Mice with the highest SEAP concentration in blood at day 7 also had the highest rate of decrease afterwards, the strongest antibody responses against SEAP and the highest acute levels of CPK in blood. DNA-transfected muscle fibers were significantly reduced in number from days 7 to 14. Mononuclear cells surrounded the reporter gene expressing muscle fibers, thus indicating a cellular immune response. When using DNA encoding a syngenic protein the protein concentration in blood was relatively stabile over a 3-month period, but showed different kinetics for various electroporation parameters. CONCLUSIONS: Our findings suggest that the optimal electroporation parameters for DNA vaccination may be different from the optimal parameters for long-term expression of genes encoding syngenic proteins.

Alkaline Phosphatase↗

PubMed2003

Optimization of beam parameters and treatment planning for intensity modulated proton therapy.

One of the objectives of the ongoing research and development work at the Northeast Proton Therapy Center (NPTC) in Boston is to perform optimized intensity modulated proton therapy (IMPT) treatments. Such treatments may be delivered by magnetically scanning a narrow proton pencil beam across the target volume, while both the scanning speed and the intensity of the beam are modulated. Localization of the proton dose in space allows one to yield dose distributions that are highly conformal to the target volume, thus minimizing the dose delivered to the surrounding healthy tissue. The aim of the current research is to determine technically optimal and clinically relevant specifications for the scanned beam delivery system, which is being developed in collaboration with Ion Beam Applications (IBA); and to create a link between the treatment planning and the beam delivery. IMPT treatment planning is performed for patient cases treated at the NPTC, with KonRad Pro software developed at the German Cancer Research Center (DKFZ). For the IMPT delivery, the proton intensity maps, optimized for discrete pencil beam spots, need to be translated into continuous scanning patterns. At the same time it is necessary to minimize the discrepancy between the planned and delivered doses which may result from such conversion, as well as from the technical limitations of the delivery system. Possibilities have been investigated for improving the proton dose conformity by optimizing the beam and scanning nozzle parameters, and by taking the specifics and limitations of the system into account in the treatment planning stage.

Chordoma↗

PubMed1994

Optimization of beam parameters for dual-energy digital subtraction angiography.

Dual-energy digital subtraction angiography (DSA) is immune to the misregistration artifacts which plague conventional temporal subtraction DSA. However, since the signal-to-noise ratio (SNR) of dual-energy DSA is lower than temporal subtraction it is important to optimize the dual-energy technique with respect to the SNR. This study investigates the optimization of x-ray exposure parameters for the low- and high-energy x-ray beams, drawing upon our experience with dual-energy DSA studies in 20 cardiac patients. It is shown that the SNR is optimized, with respect to patient exposure, when the image intensifier (II) exposure for the high-energy beam is approximately 5 times higher than the low-energy beam. The unequal distribution of exposure between the low- and high-energy beams is achieved by selecting different video apertures for the two beams, and is therefore referred to as the "dual-aperture" technique. The dual-aperture technique achieves the same SNR as the single-aperture technique (which uses equal II exposures for the two beams) with 45% less patient exposure. In addition, the dual-aperture technique enhances the ability to maintain an optimum low-energy kVp, which increases the dual-energy signal amplitude. The optimum high-beam filter thickness for use with the dual-aperture approach is determined. The optimum filter thickness, which is dependent upon the desired tube loading, is found to range from 1.3 to 2.0 mm Cu for tube loads ranging from 188 to 688 J/beam pair.

Adult↗