SEARCH · PubMed Health

Results for “parameter optimization”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 703 records · Page 39Linked to original sources

PubMed1998

Photodynamic therapy of subfoveal choroidal neovascularization: clinical and angiographic examples.

BACKGROUND: Conventional photocoagulation of subfoveal choroidal neovascularization (CNV) is often accompanied by visual loss due to thermal damage to adjacent retinal structures. Photodynamic therapy (PDT) allows vascular occlusion by selective photochemical destruction of vascular endothelial cells only. In a pilot study we evaluated the use of PDT in CNV. METHODS: In a clinical phase I/II trial, patients with subfoveal CNV were treated with PDT. Benzoporphyrin derivative monoacid ring A (BPD) was used as sensitizer at a drug dose of 6 mg/m2 or 12 mg/m2. Irradiation was performed via a diode laser emitting at 690 nm coupled into a slit lamp. Safe and maximum tolerated light doses were defined by dose escalation from 25 to 150 J/cm2. Photodynamic effects were documented ophthalmoscopically and angiographically. RESULTS: Sixty-one patients received a single course of BPD-PDT. Preliminary results suggest no damage to retinal structures within the treated area clinically. Retinal perfusion was not altered, while CNV demonstrated immediate absence of fluorescein leakage in the majority of lesions subsequent to PDT. At optimized parameters (6 mg/m2 and 50 J/cm2) complete cessation of leakage from classic CNV occurred in 100% of cases at 1 week and in 50% at week 4. In 70-80% of classic CNV, leakage reappeared at week 12, but markedly less than before treatment. CONCLUSION: PDT allows temporary absence of leakage from CNV with preservation of visual acuity. The long-term prognosis of CNV secondary to age-related macular degeneration treated with repeated courses of PDT is being evaluated in a phase III trial.

Adult↗

PubMed2000

Photodynamic therapy of choroidal hemangioma: two case reports.

BACKGROUND: Photocoagulation, cryotherapy and radiotherapy have been used to treat angiomatous lesions. Depending on the location of the angioma, these treatments can cause additional, significant functional damage. Photodynamic therapy (PDT) however, allows a selective occlusion of vascular lesions without damaging adjacent retinal structures. METHODS: Two patients with isolated choroidal hemangiomas involving the posterior pole were treated with PDT. Treatments were performed using a diode laser at 692 nm, a light dose of 100 J/cm2 and 6 mg/m2 body surface area verteporfin (BPD-MA). PDT was applied in two courses in one eye and in four in the other eye at 1-4 months intervals. Patients were followed up for 9-12 months with visual acuity measurements and dilated ophthalmoscopy. Ultrasound, indocyanine green angiographic and fluorescein angiographic images were evaluated at each visit. RESULTS: Tumor heights were 3.3 and 4.6 mm on pretreatment ultrasound. After therapy, patients with isolated choroidal hemangioma showed total regression of the lesion and improved visual acuity due to resorption of retinal edema. Serous retinal detachment and cystoid macular edema resolved. Ultrasound demonstrated a progressive decrease in tumor height after each PDT application, with complete disappearance of the lesion. Retinal vessels were not affected by the treatment, and retinal function recovered in areas with previous tumor involvement. CONCLUSION: PDT allows selective treatment of large intraocular angiomatous lesions. Without optimized parameters, complete regression of choroidal hemangiomas, resolution of secondary complications and improvement of visual acuity were documented.

Adult↗

PubMed2006

Assessment of formal and low structured kinetic modeling of polyhydroxyalkanoate synthesis from complex substrates.

A formal kinetic mathematical model for poly-(3-hydroxybutyrate-co-3-hydroxyvalerate-co-4-hydroxybutyrate) [P(3HB-co-3HV-co-4HB)] terpolyester synthesis from glucose and galactose derived from whey permeate supplemented with gamma-butyrolactone by the archaeon Haloferax mediterranei was created. Further, a low structured mathematical model for poly-3-hydroxybutyrate synthesis from whey permeate by Pseudomonas hydrogenovora was developed. In both cases, biosyntheses for obtaining the experimental data used for compiling the models were performed via fed-batch cultivations. The model developed for H. mediterranei consists of 10 differential and 11 algebraic equations, including 27 kinetic constants. The model compiled for P. hydrogenovora encompasses 10 differential and 3 algebraic equations, including 36 kinetic constants. Both models were solved by Runge-Kuta variable step numerical integration with Monte Carlo parameter optimization procedure. Difficulties arising from the modeling of redirection of metabolic fluxes from biomass growth toward polyhydroxyalkanoate synthesis and byproducts are discussed.

Computer Simulation↗

PubMed1999

Monitoring of intracranial compliance: correction for a change in body position.

The objectives of our study were 1. to investigate whether the intracranial compliance changes with body position; 2. to test if the pressure-volume index (PVI) calculation is affected by different body positions; 3. to define the optimal parameter to correct PVI for changes in body position and 4. to investigate the physiological meaning of the constant term (P0) in the model of the intracranial volume-pressure relationship. Thirteen patients were included in this study. All patients were subjected to 2 to 3 different body positions. In each position, either classic bolus injection was performed for measurement of intracranial compliance and calculation of PVI or the new Spiegelberg compliance monitor was used to calculate PVI continuously. Four different models were used for calculating the constant pressure term P0 and the P0 corrected PVI values. Pressure volume index not corrected for the constant term P0 significantly decreased with elevating the patients head (r = 0.70, p < 0.0001). In contrast, volume-pressure response and ICP pulse amplitude did not change with position. Using the constant term P0 to correct the PVI we found no changes between the different body positions. Our results suggest that during the variation in body position there is no change in intracranial compliance but a change in hydrostatic offset pressure which causes a shifting of the volume-pressure curve along the pressure axis without its shape being affected. PVI measurements should either be performed only with the patient in the 0 degree recumbent position or that the PVI calculation should be corrected for the hydrostatic difference between the level of the ICP transducer and the hydrostatic indifference point of the craniospinal system close to the third thoracic vertebra.

Adult↗

PubMed2006

Optimum two-stage designs in case-control association studies using false discovery rate.

Genetic association studies using case-control designs are often done to identify loci associated with disease susceptibility. These studies are often expensive to perform, due to a large number of genetic markers. Several types of two-stage designs are proposed and used from the point of cost effectiveness. We proposed to control the false discovery rate for multiple-testing correction in two-stage designs, using optimal sample sizes and criteria for selecting markers associated with a disease in each stage to minimize the cost of genotyping. The expected power and cost of two-stage designs were compared with those of one-stage designs, under the assumptions that the genetic markers are independent and total sample size is fixed. The results showed that the proposed two-stage procedure usually reduced the cost of genotyping by 40-60%, with a power similar to that of the one-stage designs. In addition, the sample size and selection criteria, which are optimized parameters, are defined as a function of a prior probability that marker-disease association is true. So, the effects of mis-specification of a prior probability on efficiency were also considered.

Case-Control Studies↗

PubMed2005

Estimation of time-varying coherence function using time-varying transfer functions.

We introduce a new method to estimate reliable time-varying coherence functions (TVCF) for causal systems. The technique is based on our previously developed method to estimate time-varying transfer functions (TVTF), known as the time-varying optimal parameter search algorithm [Zou, R., H. Wang, and K. H. Chon. A robust time-varying identification algorithm using basis functions. Ann. Biomed. Eng. 31: 840-853, 2003]. The TVCF is estimated by the multiplication of two TVTFs. The two TVTFs are obtained using signal x as the input and signal y as the output to produce the first TVTF, and signal y as the input and signal x as the output to produce the second TVTF. Demonstration of the feasibility and efficacy of the proposed approach is provided with both simulation examples and application to renal blood flow and pressure data. The proposed approach provides higher time-frequency resolution TVCF than afforded by the short time Fourier transform based TVCF.

Animals↗

PubMed2006

A high resolution approach to estimating time-frequency spectra and their amplitudes.

A high resolution approach to estimating time-frequency spectra (TFS) and associated amplitudes via the use of variable frequency complex demodulation (VFCDM) is presented. This is a two-step procedure in which the previously developed time-varying optimal parameter search (TVOPS) technique is used to obtain TFS, followed by using the VFCDM to obtain even greater TFS resolution and instantaneous amplitudes associated with only the specific frequencies of interest. This combinational use of the TVOPS and the VFCDM is termed the TVOPS-VFCDM. Simulation examples are provided to demonstrate the performance of the TVOPS-VFCDM for high resolution TFS as well as instantaneous amplitude estimation. The simulation results show that the TVOPS-VFCDM approach provides the highest resolution and most accurate amplitude estimates when compared to the smoothed pseudo Wigner-Ville, continuous wavelet transform and Hilbert-Huang transform methods. Application of the TVOPS-VFCDM to renal blood flow data indicates some promise of a quantitative approach to understanding the dynamics of renal autoregulatory mechanisms as well as a possible approach to quantitatively discriminating between different strains of rats.

Algorithms↗

PubMed2006

Simultaneous blood-tissue exchange of oxygen, carbon dioxide, bicarbonate, and hydrogen ion.

A detailed nonlinear four-region (red blood cell, plasma, interstitial fluid, and parenchymal cell) axially distributed convection-diffusion-permeation-reaction-binding computational model is developed to study the simultaneous transport and exchange of oxygen (O2) and carbon dioxide (CO2) in the blood-tissue exchange system of the heart. Since the pH variation in blood and tissue influences the transport and exchange of O2 and CO2 (Bohr and Haldane effects), and since most CO2 is transported as HCO3(-) (bicarbonate) via the CO2 hydration (buffering) reaction, the transport and exchange of HCO3(-) and H+ are also simulated along with that of O2 and CO2. Furthermore, the model accounts for the competitive nonlinear binding of O2 and CO2 with the hemoglobin inside the red blood cells (nonlinear O2-CO2 interactions, Bohr and Haldane effects), and myoglobin-facilitated transport of O2 inside the parenchymal cells. The consumption of O2 through cytochrome-c oxidase reaction inside the parenchymal cells is based on Michaelis-Menten kinetics. The corresponding production of CO2 is determined by respiratory quotient (RQ), depending on the relative consumption of carbohydrate, protein, and fat. The model gives a physiologically realistic description of O2 transport and metabolism in the microcirculation of the heart. Furthermore, because model solutions for tracer transients and steady states can be computed highly efficiently, this model may be the preferred vehicle for routine data analysis where repetitive solutions and parameter optimization are required, as is the case in PET imaging for estimating myocardial O2 consumption.

Animals↗

PubMed2006

Human melanoma cells transplanted into zebrafish proliferate, migrate, produce melanin, form masses and stimulate angiogenesis in zebrafish.

In this research, we optimized parameters for xenotransplanting WM-266-4, a metastatic melanoma cell line, including zebrafish site and stage for transplantation, number of cells, injection method, and zebrafish incubation temperature. Melanoma cells proliferated, migrated and formed masses in vivo. We transplanted two additional cancer cell lines, SW620, a colorectal cancer cell line, and FG CAS/Crk, a pancreatic cancer cell line and these human cancers also formed masses in zebrafish. We also transplanted CCD-1092Sk, a human fibroblast cell line established from normal foreskin and this cell line migrated, but did not proliferate or form masses. We quantified the number of proliferating melanoma and normal skin fibroblasts by dissociating xenotransplant zebrafish, dispensing an aliquot of CM-DiI labeled human cells from each zebrafish onto a hemocytometer slide and then visually counting the number of fluorescently labeled cancer cells. Since zebrafish are transparent until approximately 30 dpf, the interaction of labeled melanoma cells and zebrafish endothelial cells (EC) can be visualized by whole-mount immunochemical staining. After staining with Phy-V, a mouse anti-zebrafish monoclonal antibody (mAb) that specifically labels activated EC and angioblasts, using immunohistology and 2-photon microscopy, we observed activated zebrafish EC embedded in human melanoma cell masses. The zebrafish model offers a rapid efficient approach for assessing human cancer cells at various stages of tumorigenesis.

Animals↗

PubMed2005

Optimization of theaflavin biosynthesis from tea polyphenols using an immobilized enzyme system and response surface methodology.

Theaflavins were synthesized from tea polyphenols extracted from green tea using an immobilized polyphenol oxidase system. To optimize the production of theaflavins, response surface methodology was applied to determine the effects of five critical variables and their mutual interactions on theaflavin biosynthesis at five levels. A total of 52 individual experiments were performed and a statistical model predicted that the highest theaflavin concentration was 0.766 mg ml(-1) at optimized conditions. Using these optimal parameters under experimental conditions in three independent replicates, the average value of the biosynthesized theaflavin concentration reached 0.75 +/- 0.017 mg ml(-1) and matched the value predicted by the model.

Biflavonoids↗

PubMed2007

Evaluation of biosorption potency of Acinetobacter sp. for removal of hexavalent chromium from tannery effluent.

Two bacterial consortia were developed by continuous enrichment of microbial population of tannery and pulp and paper mill effluent contained Serratia mercascens, Pseudomonas fluorescence, Escherichia coli, Pseudomonas aeruginosa and Acinetobacter sp. identified by 16S rDNA method. The consortia evaluated for removal of chromate [(Cr(VI)] in shake flask culture indicated pulp and paper mill consortium had more potential for removal of chromate. Acinetobacter sp. isolated from pulp and paper mill consortium removed higher amount of chromate [Cr(VI)] under aerobic conditions. Parameters optimized in different carbon, nitrogen sources, and pH, indicated maximum removal of chromate in sodium acetate (0.2%), sodium nitrate (0.1%) and pH 7 by Acinetobacter sp. Bacteria was applied in 2-l bioreactor significantly removed chromate after 3 days. The results of the study indicated removal of more than 75% chromium by Acinetobacter sp. determined by diphenylcarbazide colorimetric assay and atomic absorption spectrophotometer after 7 days. Study of microbial [Cr(VI)] removal and identification of reduction intermediates has been hindered by the lack of analytical techniques. Therefore, removal of chromium was further substantiated by transmission electron microscopy (TEM), scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDX) which indicated bioaccumulation of chromium in the bacterial cells.

Acinetobacter↗

PubMed2006

Development and validation of a modular, extensible docking program: DOCK 5.

We report on the development and validation of a new version of DOCK. The algorithm has been rewritten in a modular format, which allows for easy implementation of new scoring functions, sampling methods and analysis tools. We validated the sampling algorithm with a test set of 114 protein-ligand complexes. Using an optimized parameter set, we are able to reproduce the crystal ligand pose to within 2 A of the crystal structure for 79% of the test cases using our rigid ligand docking algorithm with an average run time of 1 min per complex and for 72% of the test cases using our flexible ligand docking algorithm with an average run time of 5 min per complex. Finally, we perform an analysis of the docking failures in the test set and determine that the sampling algorithm is generally sufficient for the binding pose prediction problem for up to 7 rotatable bonds; i.e. 99% of the rigid ligand docking cases and 95% of the flexible ligand docking cases are sampled successfully. We point out that success rates could be improved through more advanced modeling of the receptor prior to docking and through improvement of the force field parameters, particularly for structures containing metal-based cofactors.

Algorithms↗

PubMed2006

Development of an optimized electrochemical process for subsequent coating of 316 stainless steel for stent applications.

Metallic endovascular stents are used as medical devices to scaffold biological lumen, most often diseased arteries, after balloon angioplasty. They are commonly made of 316L stainless steel or Nitinol, two alloys containing nickel, an element classified as potentially toxic and carcinogenic by the International Agency for Research on Cancer. Although they are largely implanted, the long-term safety of such metallic elements is still controversial, since the corrosion processes may lead to the release of several metallic ions, including nickel ions in diverse oxidation states. To avoid metallic ion release in the body, the strategy behind this work was to develop a process aiming the complete isolation of the stainless steel device from the body fluids by a thin, cohesive and strongly adherent coating of RF-plasma-polymerized fluoropolymer. Nevertheless, prior to the polymer film deposition, an essential aspect was the development of a pre-treatment for the metallic substrate, based on the electrochemical polishing process, aiming the removal of any fragile interlayer, including the native oxide layer and the carbon contaminated layer, in order to obtain a smooth, defect-free surface to optimize the adhesion of the plasma-deposited thin film. In this work, the optimized parameters for electropolishing, such as the duration and the temperature of the electrolysis, and the complementary acid dipping were presented and accurately discussed. Their effects on roughness as well as on the evolution of surface topography were investigated by Atomic Force Microscopy, stylus profilometry and Scanning Electron Microscopy. The modifications induced on the surface atomic concentrations were studied by X-ray Photoelectron Spectroscopy. The improvements in terms of the surface morphology after the pre-treatment were also emphasized, as well as the influence of the original stainless steel surface finish.

Coated Materials, Biocompatible↗

PubMed1994

Photodynamic destruction of endometrial tissue with topical 5-aminolevulinic acid in rats and rabbits.

OBJECTIVE: The goal of this study was to determine the optimal parameters for photodynamic endometrial destruction with topically applied 5-aminolevulinic acid, a precursor for the endogenous synthesis of the fluorescent photosensitizer protoporphyrin IX. STUDY DESIGN: 5-Aminolevulinic acid pharmacokinetics were measured in rat and rabbit models by analyzing tissue frozen sections 3 to 12 hours after topical administration. Dose-response studies were conducted for 100 to 400 mg/ml 5-aminolevulinic acid. Photodynamic therapy was performed intraluminally, and tissue morphologic features were evaluated 3 and 7 days after treatment. RESULTS: Peak fluorescence was observed 3 hours after topical administration. Glandular fluorescence significantly exceeded stromal and myometrial in all studies, particularly for 200 mg/ml 5-aminolevulinic acid. Histologic studies revealed persistent epithelial destruction with minimal regeneration. CONCLUSION: Topical 5-aminolevulinic acid photodynamic therapy can be used for highly effective, long-lasting destruction of endometrial epithelium. However, optical dosimetry can vary, particularly in the rabbit model, and this appears to have an impact on long-term reepithelialization.

Administration, Topical↗

PubMed1984

Use of S1 nuclease and formamide in combination for the reassociation studies on GC-rich DNA.

The optimal parameters in the use of nuclease S1 in DNA reassociation kinetics in the presence of formamide have been determined. The conditions are especially suitable for the study of DNA rich in mole percent GC. A 10-fold dilution of the reassociation samples leading to a decrease in both NaCl and formamide concentrations, consequently resulting in a lowering of Tm by only 1.5 degree C, and the S1 digestion at temperatures identical to the reassociation assay in order to retain the stability of the duplex, are two important aspects of this system. Under these conditions, the kinetics of reassociation followed the theoretically predicted pattern, while the earlier reported methods have shown lower values.

Chemical Phenomena↗

PubMed1980

CO binding to mitochondrial mixed valence state cytochrome oxidase at low temperatures.

The kinetics and thermodynamics of the reaction of mixed valence state membrane-bound cytochrome oxidase with CO over the 178-203 K range has been studied by multichannel optical spectroscopy at three wavelength pairs (444-463 nm in the Soret region, and 590-630 and 608-630 nm in the alpha region) and analysed by non-linear optimization techniques. As in the case of the fully reduced membrane-bound cytochrome oxidase-CO reaction (Clore, G.M. and Chance, E.M. (1978) Biochem J. 175, 709-725), the normalized progress curves at the three wavelength pairs are significantly different indicating, on the basis of Beer's law, the presence of a minimum of three optically distinct species. The only model that satisfies the triple statistical requirement of a standard deviation within the standard error of the data, a random distribution of residuals and good determination of the optimized parameters, is a two species sequential mechanism: flash photolysis of the mixed valence state cytochrome oxidase-CO complex (species IIMC) yields unliganded mixed valence state cytochrome oxidase (species EM) and free CO which then recombine to form species IMC; species IMC is then converted into species IIMC. All the thermodynamic parameters describing the model are calculated and compared to those obtained for the fully reduced membrane-bound cytochrome oxidase-CO reaction (Clore and Chance (1978) Biochem. J. 175, 709-725). Although there are some qualitative similarities in the kinetics and thermodynamics of the reactions of mixed valence state (alpha 23+Cu+B.ALPHA 3+Cu2+A) and fully reduced (a3 2+Cu B + . a2+Cu A+) cytochrome oxidase with CO, there are large and significant quantitative differences in zero-point activation energies and frequency factors; over the temperature range studied, the mixed valence state cytochrome oxidase-CO reaction is found to proceed at a significantly slower rate than the fully reduced cytochrome oxidase-CO reaction. These differences indicate that changing the valence states of cytochrome a and CuA has a significant effect on the CO binding properties of cytochrome a 3 and possibly CuB.

Carbon Monoxide↗

PubMed1981

A re-evaluation of the low-temperature kinetics of the reaction of fully reduced mitochondrial cytochrome oxidase with carbon monoxide and the spectral characterization of species Ic in the Soret and visible regions.

The kinetics of the reaction of fully reduced membrane bound cytochrome oxidase with CO following photolysis of the fully reduced cytochrome oxidase-CO complex habe been re-examined by re-analysing the data of Clore and Chance (1978) Biochem. J. 175, 709-725) at six temperatures in the 178-203 K range simultaneously at only a single wavelength pair, 444-463 nm. The choice of the 444-463 nm wavelength pair was based on the fact that the absorbance change produced at 444-463 nm on photolysis of the CO complex is sufficiently large and the separation between monitoring and reference wavelengths sufficiently small to render the effects of any possible time dependent scattering changes insignificant. On the basis of our analysis only a two step mechanism (Model 1 of Clore and Chance (1978) Biochem. J. 175, 709-725) satisfies the triple requirement of a S.D. within the standard error of the data, a random distribution of residuals and good determination of the optimized parameters. The single step mechanism of De Fonseka and Chance (1978) Biochem. J. 175, 1137-1138) fails to satisfy all three requirements. The pure difference spectra of species Ic minus E, E minus IIc and Ic minus IIc are calculated from the computed kinetics of the individual species and repetitive slow wavelength scanning difference spectra (reaction sample minus the CO complex) taken during the course of the reaction of fully reduced cytochrome oxidase with CO at 176 K.

Animals↗

PubMedDate not supplied

NL-FIT: a microcomputer program for non-linear fitting.

A program for a microcomputer (HP 85) has been written using BASIC language. Given the analytical form of a model y: R leads to R the program computes the optimal parameters for non-linear least-squares fitting and gives information for its statistical evaluation. The program uses the Gauss-Newton algorithm with Marquardt's modification and other tricks. During the run a message is displayed if there is a high correlation between one or more couples of parameters to establish an interactive dialogue with the user on critical problems. The authors' aim was to make the program sufficiently quick and easy to use, efficient for a wide class of models and robust enough to deal with bad starting parameters.

Computers↗