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Results for “parameter optimization”

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PubMed1996

Large scale cultivation of an anti-D (IgM) antibody producing human/mouse heterohybridoma.

A human/mouse heterohybridoma cell line secreting anti-Rh(D) antibody was established by the fusion of Epstein-Barr Virus (EBV) transformed human B lymphocytes and human/mouse heteromyelomas. During scaling-up the cell line was adapted to suspension culture, then medium composition was gradually altered into a more economical one. The adapted cell line has kept its multiplication and antibody secreting characteristics in the new medium. Parameters of large scale batch cultivation in bioreactors were optimized in working volume of 3.6 litre and production was carried out under these parameters in working volume of 24 litre. Optimized parameters were the follows: (i) the cell line is highly sensitive to dissolved oxygen (DO) level, its optimal DO is 10%; (ii) optimal inoculum cell count is 3 x 10(5) cell/ml; (iii) Marine-blade impeller was chosen for supporting the requested oxygen transfer. Using the optimized parameters HUMAN Co. Ltd. produces the Monoclonal Anti-D (IgM) reagent, which has been registered in 1995 in Hungary and now it is on the market.

Adaptation, Physiological↗

PubMed2005

Optimal design for model discrimination and parameter estimation for itraconazole population pharmacokinetics in cystic fibrosis patients.

Optimal sampling times are found for a study in which one of the primary purposes is to develop a model of the pharmacokinetics of itraconazole in patients with cystic fibrosis for both capsule and solution doses. The optimal design is expected to produce reliable estimates of population parameters for two different structural PK models. Data collected at these sampling times are also expected to provide the researchers with sufficient information to reasonably discriminate between the two competing structural models.

Administration, Oral↗

PubMed2026

Informing agent-based models with spatial data using convolutional autoencoders.

MOTIVATION: Spatial computational models such as agent-based models (ABMs) offer powerful in silico tools to study tumor dynamics, yet imaging data are still rarely used to inform these models directly. RESULTS: We present an ABM optimization framework that leverages convolutional encoders to compare spatial patterns between experimental imaging data and ABM-generated outputs within a shared latent space. This quantitative comparison was used to estimate ABM parameters across three datasets, ranging from synthetic data to 3D tumoroid-T cell co-culture microscopy and histopathology images from The Cancer Genome Atlas skin cutaneous melanoma samples. Estimated parameters were evaluated using data-derived features and experimental knowledge, including experimental conditions and gene expressions. Simulations using optimized parameters reproduced key spatial features of the training images, such as tumor boundary complexity and tumor-tumor neighborhood structure. Together, these results demonstrate a flexible framework for ABM parameter optimization using spatial data across modalities, enabling systematic investigation of how spatial architecture influences tumor progression and immune interactions. AVAILABILITY AND IMPLEMENTATION: Source code is available at https://github.com/SysBioOncology/ AutoencoderABM under the GPL-3.0 license, with corresponding data sets at https://zenodo.org/records/19022344.

Autoencoder↗

PubMed2002

Optimization of a semianalytical ocean color model for global-scale applications.

Semianalytical (SA) ocean color models have advantages over conventional band ratio algorithms in that multiple ocean properties can be retrieved simultaneously from a single water-leaving radiance spectrum. However, the complexity of SA models has stalled their development, and operational implementation as optimal SA parameter values are hard to determine because of limitations in development data sets and the lack of robust tuning procedures. We present a procedure for optimizing SA ocean color models for global applications. The SA model to be optimized retrieves simultaneous estimates for chlorophyll (Chl) concentration, the absorption coefficient for dissolved and detrital materials [a(cdm)(443)], and the particulate backscatter coefficient [b(bp)(443)] from measurements of the normalized water-leaving radiance spectrum. Parameters for the model are tuned by simulated annealing as the global optimization protocol. We first evaluate the robustness of the tuning method using synthetic data sets, and we then apply the tuning procedure to an in situ data set. With the tuned SA parameters, the accuracy of retrievals found with the globally optimized model (the Garver-Siegel-Maritorena model version 1; hereafter GSM01) is excellent and results are comparable with the current Sea-viewing Wide Field-of-view sensor (SeaWiFS) algorithm for Chl. The advantage of the GSM01 model is that simultaneous retrievals of a(cdm)(443) and b(bp)(443) are made that greatly extend the nature of global applications that can be explored. Current limitations and further developments of the model are discussed.

Journal Article↗

PubMed2001

Optimization of solvation models for predicting the structure of surface loops in proteins.

A novel procedure for optimizing the atomic solvation parameters (ASPs) sigma(i) developed recently for cyclic peptides is extended to surface loops in proteins. The loop is free to move, whereas the protein template is held fixed in its X-ray structure. The energy is E(tot) = E(FF)(epsilon = nr) + summation operator sigma(i)A(i), where E(FF)(epsilon = nr) is the force-field energy of the loop-loop and loop-template interactions, epsilon = nr is a distance-dependent dielectric constant, and n is an additional parameter to be optimized. A(i) is the solvent-accessible surface area of atom i. The optimal sigma(i) and n are those for which the loop structure with the global minimum of E(tot)(n, sigma(i)) becomes the experimental X-ray structure. Thus, the ASPs depend on the force field and are optimized in the protein environment, unlike commonly used ASPs such as those of Wesson and Eisenberg (Protein Sci 1992;1:227-235). The latter are based on the free energy of transfer of small molecules from the gas phase to water and have been traditionally combined with various force fields without further calibration. We found that for loops the all-atom AMBER force field performed better than OPLS and CHARMM22. Two sets of ASPs [based on AMBER (n = 2)], optimized independently for loops 64-71 and 89-97 of ribonuclease A, were similar and thus enabled the definition of a best-fit set. All these ASPs were negative (hydrophilic), including those for carbon. Very good (i.e., small) root-mean-square-deviation values from the X-ray loop structure were obtained with the three sets of ASPs, suggesting that the best-fit set would be transferable to loops in other proteins as well. The structure of loop 13-24 is relatively stretched and was insensitive to the effect of the ASPs.

Hydrogen↗

PubMed1980

Determination of the optimal feeding regime during biosynthesis of erythromycin.

A systems approach to the analysis of the process of fermentaton of erythromycin in demonstrated. On the basis of biochemical and bioengineering data obtained in hydrodynamic tests and pilot plant fermentations of erythromycin a mathematical model for optimal technological parameters of growth of Streptomyces erythreus and product formation was postulated. The optimal regime was simulated and subsequently verified. The production of erythromycin increased to 112%.

Culture Media↗

PubMed2005

Low-dose intra-arterial contrast-enhanced MR aortography in patients based on a theoretically derived injection protocol.

Multiple intra-arterial contrast agent injections are necessary during MR-guided endovascular interventions. In respect to the approved limits of maximum daily gadolinium dose, a low-dose injection protocol is mandatory. The objective of this study was to derive and apply a low-dose injection protocol for intra-arterial 3D contrast-enhanced MR aortography in patients. Injection rate (Qinj), concentration of injected gadolinium [Gd]inj and aortal blood flow rate (Qblood) were included for the theoretical evaluation of signal intensity (SI) of the arterial lumen. SI simulations were carried out at Qinj=2 versus 4 ml/s in the [Gd]inj range between 0-500 mM. Qinj and [Gd]inj with SI above the 75% threshold of the maximal SI were regarded as optimal injection parameters. [Gd]inj=50 mM and Qinj=4 ml/s were considered as optimal and were administered in five patients for 3D MR aortography. All images revealed clear delineation of the abdominal aorta and its major branches. Mean+/-SD of contrast-to-noise ratios of the abdominal aorta, common iliac and renal artery were 70.2+/-15.2, 58.6+/-12.3 and 67.4+/-12.3. Approximately seven intra-aortal injections would be permissible in patients during MR-guided interventions without exceeding the maximal dose of gadolinium.

Aged↗

PubMed1986

Non-linear fitting program for biological data.

A simple microcomputer program written in Microsoft Basic estimates pharmacokinetic parameters using the coordinate search technique to minimize the sum of squared errors. The program developed for portable computers combines a plot of data and curve fitting so as to find rapidly the initial parameters with the subsequent optimization of the parameter estimate.

Computers↗

PubMed2006

Biological decolorization of dye solution containing Malachite Green by microalgae Cosmarium sp.

The potential of Cosmarium species, belonging to green algae, was investigated as a viable biomaterial for biological treatment of triphenylmethane dye, Malachite Green (MG). The results obtained from the batch experiments revealed the ability of algal species in removing dye. The effects of operational parameters (temperature, pH, dye concentration and algal concentration) on decolorization were examined. Optimal initial pH was determined 9. The stability and efficiency of the algae in long-term repetitive operations were also examined. Michaelis-Menten kinetics was used to describe the apparent correlation between the decolorization rate and the dye concentration. The optimal kinetic parameters, nu(max) and K(m) are 7.63 mg dye g cell(-1)h(-1) and 164.57 ppm, respectively. All assays were conducted in triplicates.

Biomass↗

PubMed2005

Parameters involved in the conversion of real-time PCR assays from the ABI prism 7700 to the Cepheid SmartCycler II.

OBJECTIVE: We examined several critical parameters that must be optimized when converting between the ABI Prism 7700 real-time PCR platform and the Cepheid SmartCycler II while using the same primer and probe sequences. DESIGN AND METHODS: A lyophilized master mix, MgCl(2) concentration, PCR cycling conditions, and ramp times were evaluated. RESULTS: Optimization of each parameter, including use of the OmniMix HS-lyophilized beads, 6 mM MgCl(2) concentration, changes in PCR cycling parameters, and increased ramp time were necessary to convert this real time PCR assay to a new platform. CONCLUSION: We conclude that careful consideration of several analytical parameters can result in a smooth transition of assays between real time PCR platforms.

Indicators and Reagents↗

PubMed1999

Simultaneous Optimization of Feeding Rate and Operation Parameters for Fed-Batch Fermentation Processes.

An efficient method is introduced for simultaneously determining optimal polices of feeding rate and operation parameters for a fermentation process. Such an optimization problem is converted into the finite dimensional optimization problem using the control parametrization technique. The hybrid differential evolution is introduced to solve the converted problem. The optimal production rate obtained by the simultaneous optimization approach could be significantly improved with comparison to a simplified optimization problem, which is considered the optimal feed control only, as observed from the simulation results.

Journal Article↗

PubMed1998

Crossover designs with correlated observations.

Crossover designs are widely used in different medical investigations where a number of treatments have to be compared. Sequences of treatments are given to subjects, and in practice the observations within each subject are likely to be correlated. This paper is concerned with the construction of crossover designs for such cases. The design problem is nonlinear in the parameters, and design optimality depends on the parameters defining the correlation structure. When the correlation structure is known, local optimum designs are obtained. When the distribution of its parameters is known, optimum Bayesian crossover designs are constructed. The optimum sizes of the groups of subjects receiving the same sequence of treatments are also determined.

Algorithms↗

PubMed2000

Health issues for women with epilepsy: a descriptive survey to assess knowledge and awareness among healthcare providers.

The American Academy of Neurology and the American College of Obstetricians and Gynecologists recently issued practice parameters for women with epilepsy. These parameters suggest optimal care practices. To assess knowledge of the issues covered in the parameters and to facilitate educational efforts to promote best care, the Epilepsy Foundation conducted a survey of healthcare professionals likely to provide care to women with epilepsy. The survey sampled 3535 healthcare professionals across a wide range of specialties. Most respondents did not know the specific effects of estrogen and progesterone on the seizure threshold, were not aware of menstrual-associated seizure patterns, and could not identify which antiepileptic drugs interfere with oral contraceptives. The majority of respondents did not know that women with epilepsy have higher rates of infertility, reproductive endocrine disorders, and sexual dysfunction. Most respondents did not know the frequency of birth defects in children born to women with epilepsy. Providers seeing the largest number of persons with epilepsy were more likely to have correct answers. By specialty, neurologists provided the highest number of correct responses, followed (in descending order) by endocrinologists, obstetricians/gynecologists, internal medicine physicians, family practice physicians, and pediatricians. These results suggest that women with epilepsy are not receiving adequate counseling and that care practices may not conform to those recommended.

Attitude of Health Personnel↗

PubMed2005

Parameter-space screening: a powerful tool for high-throughput crystal structure determination.

The determination of protein structures on a genomic scale requires both computing capacity and efficiency increases at many stages along the complex process. By combining bioinformatics workflow-management techniques, cluster-based computing and popular crystallographic structure-determination software packages, an efficient and powerful new tool for structural biology/genomics has been developed. Using the workflow manager and a simple web interface, the researcher can, in a few easy steps, set up hundreds of structure-determination jobs, each using a slightly different set of program input parameters, thus efficiently screening parameter space for the optimal input-parameter combination, i.e. a set of parameters that leads to a successful structure determination. Upon completion, results from the programs are harvested, analyzed, sorted based on success and presented to the user via the web interface. This approach has been applied with success in more than 30 cases. Examples of successful structure determinations based on single-wavelength scattering (SAS) are described and include cases where the 'rational' crystallographer-based selection of input parameters values had failed.

Computational Biology↗

PubMed1997

The two-stage model of carcinogenesis: overcoming the nonidentifiability dilemma.

The two-stage mathematical model of carcinogenesis has been shown to be nonidentifiable whenever tumor incidence data alone is used to fit the model (Hanin and Yakovlev, 1996). This lack of identifiability implies that more than one parameter vector satisfies the optimization criteria for parameter estimation, e.g., maximum likelihood estimation. A question of greater concern to persons using the two-stage model of carcinogenesis is under what conditions can identifiable parameters be obtained from the observed experimental data. We outline how to obtain identifiable parameters for the two-stage model.

Animals↗

PubMedDate not supplied

A statistical model to optimize enzyme-linked immunosorbent assay parameters for detection of Mycoplasma gallisepticum and M. synoviae antibodies in egg yolk.

An enzyme-linked immunosorbent assay (ELISA) was developed to quantify Mycoplasma gallisepticum (MG) and M. synoviae (MS) antibodies in egg-yolk extract. Various parameters of ELISA were evaluated and optimized. A statistical model was developed to study the relationship between ELISA absorbance (A) and antigen concentration, antibody concentration, and time of reading of the test. These factors explained 62% of the variability in A for the MG antigen and 74% of the variability in A for the MS antigen. The optimum concentration of MG antigen was 4 micrograms protein/ml, and that for MS antigen was 3 micrograms protein/ml. A similar model was developed to study the relation between A and conjugate concentration, antibody concentration, and time of reading of the test. The optimum concentration of the conjugate was found to be 1:4000. The within-run and between-run coefficients of variation for MG were 8% and 9%, respectively, and those for MS were 9% and 7%, respectively, indicating a high degree of reproducibility of these tests. There was a high correlation between ELISA and hemagglutination-inhibition test results.

Animals↗

PubMedDate not supplied

Transcutaneous electrical nerve stimulation. Relevance of stimulation parameters to neurophysiological and hypoalgesic effects.

Although Transcutaneous Electrical Nerve Stimulation (TENS) has become a popular modality in pain management over the past 20 yr, there is still debate over its mechanisms of action and the precise relevance of stimulation parameters to its hypoalgesic effects. Thus, confusion still surrounds the selection of optimal stimulation parameters. Two separate studies (total n = 88) were carried out to investigate the effect of four combinations of TENS pulse durations (50 microseconds & 200 microseconds) and frequencies (4 Hz and 110 Hz) on nerve conduction in the human superficial radial nerve and on Mechanical Pain Threshold (MPT) within the associated sensory distribution of the nerve over the dorsum of the hand. Results showed that application of one combination of TENS parameters (110 Hz, 200 microseconds) directly over the course of the nerve produced a significant increase in both peripheral nerve conduction latency (P < or = 0.05; analysis of variance (ANOVA)) and MPT (P < or = 0.01). In addition, there was a high correlation (r = 0.9) between shifts in MPT and negative peak latency for the groups treated with this combination of TENS parameters. The results of this study thus illustrate that combinations of TENS parameters are important to the peripheral neurophysiological effects of this modality and, further, its associated hypoalgesic effects, at least on the model of pain used here.

Action Potentials↗

PubMed1990

Optimization and application of particle beam high-performance liquid chromatography/mass spectrometry to compounds of pharmaceutical interest.

Particle beam high-performance liquid chromatography/mass spectrometry (HPLC/MS) parameters were optimized for the sensitive analysis of several drugs in agricultural products such as milk and tissue. Sensitivity of the particle beam interface was greatest for solvents with low heat capacities (methanol greater than acetonitrile greater than isopropanol greater than water). Furthermore, optimal sensitivity was obtained at low solvent flow rates (about 0.4-0.6 ml min-1). Parameters such as desolvation temperature, helium flow rate to the nebulizer and nebulizer position resulted in minimal change in sensitivity. The source temperature was optimized to obtain suitable vaporization with minimal thermal degradation (200-300 degrees C). The determination of a variety of compounds (including beta-lactams, cephapirin, tetracyclines, methylene blue, furosemide, spectinomycin, cytidine, 2-chloro-4-nitrobenzamide and thiamine) was possible using the particle beam interface. Under full-scan conditions, detection limits were in the 100 ng range for most drugs. With selected ion monitoring, particle beam HPLC/MS was demonstrated for the analysis of p.p.m. levels of these drugs in milk and tissue extracts. Precision of the particle beam analysis was usually better than 15% RSD. For the same compounds, HPLC/MS with a thermospray interface often resulted in less structural information (single ion spectra) then obtained by particle beam with thermospray detection limits varying from 10 ng to 1 microgram.

Animals↗