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Results for “parameter optimization”

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At least 1,315 records · Page 73Linked to original sources

PubMed2005

Automatic control of finite element models for temperature-controlled radiofrequency ablation.

BACKGROUND: The finite element method (FEM) has been used to simulate cardiac and hepatic radiofrequency (RF) ablation. The FEM allows modeling of complex geometries that cannot be solved by analytical methods or finite difference models. In both hepatic and cardiac RF ablation a common control mode is temperature-controlled mode. Commercial FEM packages don't support automating temperature control. Most researchers manually control the applied power by trial and error to keep the tip temperature of the electrodes constant. METHODS: We implemented a PI controller in a control program written in C++. The program checks the tip temperature after each step and controls the applied voltage to keep temperature constant. We created a closed loop system consisting of a FEM model and the software controlling the applied voltage. The control parameters for the controller were optimized using a closed loop system simulation. RESULTS: We present results of a temperature controlled 3-D FEM model of a RITA model 30 electrode. The control software effectively controlled applied voltage in the FEM model to obtain, and keep electrodes at target temperature of 100 degrees C. The closed loop system simulation output closely correlated with the FEM model, and allowed us to optimize control parameters. DISCUSSION: The closed loop control of the FEM model allowed us to implement temperature controlled RF ablation with minimal user input.

Algorithms↗

PubMedDate not supplied

[The effect of antioxidants on the fast burst of Fe2(+)-induced chemiluminescence].

A new micromethod for measuring the intensity of free radical oxidation reactions, based on an analysis of "fast flash" of iron-induced chemiluminescence parameters has been designed. The optimal concentration parameters of the reaction system have been determined. The effects of the antioxidants mexidol, probucol sodium dibunat and fenoxan have been examined in vitro.

Animals↗

PubMed2005

[Freeze-drying of silymarin-loaded solid lipid nanoparticles (SM-SLN)].

OBJECTIVE: To investigate lyophilization of SM-SLN. METHOD: The parameters of lyophilization process was optimized. In addition, the protective effect of various types and concentrations of cryoprotectants were tested by shape, colour and disparity. RESULT: The mixture of 2% lactose and 2% glucose could better prevent nanoparticles from aggregating, the optimal lyophilization process was followed: precooled at -45 degrees C for 10 hr; primary drying at -25 degrees C for 5 hr; secondary drying at 10 degrees C for 3 hr; finally drying at 30 degrees C for 6 hr. CONCLUSION: Changes in particle size distribution during lyophilization could be minimized by optimizing the parameters of the lyophilization process and adding supporting agent.

Drug Carriers↗

PubMed2001

Sensitivity of predicted muscle forces to parameters of the optimization-based human leg model revealed by analytical and numerical analyses.

There are different opinions in the literature on whether the cost functions: the sum of muscle stresses squared and the sum of muscle stresses cubed, can reasonably predict muscle forces in humans. One potential reason for the discrepancy in the results could be that different authors use different sets of model parameters which could substantially affect forces predicted by optimization-based models. In this study, the sensitivity of the optimal solution obtained by minimizing the above cost functions for a planar three degrees-of-freedom (DOF) model of the leg with nine muscles was investigated analytically for the quadratic function and numerically for the cubic function. Analytical results revealed that, generally, the non-zero optimal force of each muscle depends in a very complex non-linear way on moments at all three joints and moment arms and physiological cross-sectional areas (PCSAs) of all muscles. Deviations of the model parameters (moment arms and PCSAs) from their nominal values within a physiologically feasible range affected not only the magnitude of the forces predicted by both criteria, but also the number of non-zero forces in the optimal solution and the combination of muscles with non-zero predicted forces. Muscle force magnitudes calculated by both criteria were similar. They could change several times as model parameters changed, whereas patterns of muscle forces were typically not as sensitive. It is concluded that different opinions in the literature about the behavior of optimization-based models can be potentially explained by differences in employed model parameters.

Humans↗

PubMed2004

Photobiomodulation improves cutaneous wound healing in an animal model of type II diabetes.

OBJECTIVE: We investigated the effects of photobiomodulation (PBM) on cutaneous wound healing in an animal model of type II diabetes, Psammomys obesus (Sand Rats). BACKGROUND DATA: 632-nm light has been established as the most effective wavelength for treatment of cutaneous wounds; however, the inconsistent efficacy of PBM may be due to inadequate treatment parameter selection. METHODS: Using 632-nm light, an initial series of experiments were done to establish optimal treatment parameters for this model. Following creation of bilateral full-thickness skin wounds, non-diabetic Sand Rats were treated with PBM of differing dosages. Wound healing was assessed according to wound closure and histological characteristics of healing. Optimal treatment parameters were then used to treat type II diabetic Sand Rats while a diabetic control group received no irradiation. In order to elucidate the mechanism behind an improvement in wound healing, expression of basic fibroblast growth factor (bFGF) was assessed. RESULTS: Significant improvement in wound healing histology and wound closure were found following treatment with 4 J/cm(2) (16 mW, 250-sec treatments for 4 consecutive days; p < 0.05). The 4 J/cm(2) dosage significantly improved histology and closure of wounds in the diabetic group in comparison to the non-irradiated diabetic group. Quantitative analysis of bFGF expression at 36 h post-injury revealed a threefold increase in the diabetic and non-diabetic Sand Rats after PBM. CONCLUSIONS: The results demonstrate that PBM at an energy density of 4 J/cm(2) is effective in improving the healing of cutaneous wounds in an animal model of type II diabetes, suggesting that PBM (632 nm, 4 J/cm(2)) would be effective in treating chronic cutaneous wounds in diabetic patients.

Animals↗

PubMed2002

Application of an optimization algorithm for estimating intrinsic kinetic parameters of immobilized enzymes.

A simple optimization methodology is applied to estimate the intrinsic kinetic parameters for both reversible and irreversible unireactant immobilized enzyme systems that follow the Michaelis-Menten mechanism. The method utilizes a direct-search optimization algorithm along with the numerical solution of the governing differential equations. The usefulness and validity of the method is demonstrated by comparing the predicted values of the intrinsic kinetic constants using the proposed method with a series of experimental values reported in the literature for different immobilized enzyme systems with irreversible and reversible reactions.

Journal Article↗

PubMed1989

Effect of wavelength on cutaneous pigment using pulsed irradiation.

Several reports have been published over the last two decades describing the successful removal of benign cutaneous pigmented lesions such as lentigines, café au lait macules' nevi, nevus of Ota, and lentigo maligna by a variety of lasers such as the excimer (351 nm), argon (488,514 nm), ruby (694 nm), Nd:YAG (1060 nm), and CO2 (10,600 nm). Laser treatment has been applied to lesions with a range of pigment depths from superficial lentigines in the epidermis to the nevus of Ota in the reticular dermis. Widely divergent laser parameters of wavelength, pulse duration, energy density, and spotsizes have been used, but the laser parameters used to treat this range of lesions have been arbitrary, with little effort focused on defining optimal laser parameters for removal of each type. In this study, miniature black pig skin was exposed to five wavelengths (504, 590, 694, 720, and 750 nm) covering the absorption spectrum of melanin. At each wavelength, a range of energy densities was examined. Skin biopsies taken from laser-exposed sites were examined histologically in an attempt to establish whether optimal laser parameters exist for destroying pigment cells in skin. Of the five wavelengths examined, 504 nm produced the most pigment specific injury; this specificity being maintained even at the highest energy density of 7.0 J/cm2. Thus, for the destruction of melanin-containing cells in the epidermal compartment, 504 nm wavelength appears optimal.

Animals↗

PubMed2002

Optimization of glycerol fed-batch fermentation in different reactor states: a variable kinetic parameter approach.

To optimize the fed-batch processes of glycerol fermentation in different reactor states, typical bioreactors including 500-mL shaking flask, 600-mL and 15-L airlift loop reactor, and 5-L stirred vessel were investigated. It was found that by reestimating the values of only two variable kinetic parameters associated with physical transport phenomena in a reactor, the macrokinetic model of glycerol fermentation proposed in previous work could describe well the batch processes in different reactor states. This variable kinetic parameter (VKP) approach was further applied to model-based optimization of discrete-pulse feed (DPF) strategies of both glucose and corn steep slurry for glycerol fed-batch fermentation. The experimental results showed that, compared with the feed strategies determined just by limited experimental optimization in previous work, the DPF strategies with VKPs adjusted could improve glycerol productivity at least by 27% in the scale-down and scale-up reactor states. The approach proposed appeared promising for further modeling and optimization of glycerol fermentation or the similar bioprocesses in larger scales.

Bioreactors↗

PubMed2005

What are the relevant parameters for the geometrical optimization of an implantable bioartificial pancreas?

A sphere within a cylinder representing the islet encapsulated in a hollow fiber can model an implantable bioartificial pancreas. Based on a finite element model for insulin response to a glucose load in the presence of various oxygen supplies, the present study aimed at pointing out the major parameters influencing this secretion. The computational results treated with the Taguchi method clearly demonstrated that geometrical parameters (fiber length and islet density) should be precisely optimized for an enhanced insulin response. This requires the collection of more relevant experimental data concerning the islet oxygen consumption. Moreover, the relative errors on glucose consumption or insulin secretion by the islets do not seem to affect the whole optimization process, which should focus on the oxygen supply to islets.

Bioartificial Organs↗

PubMed2026

MarkerMatch: a proximity-based probe-matching algorithm for joint analysis of copy-number variants from different genotyping arrays.

MOTIVATION: Copy-number variants (CNVs) are a form of genetic structural variation with increasing importance in complex human disorders. Both DNA sequencing and microarray data can be used to detect CNVs, which can be used in genetic association tests. Unlike genotypes, CNV detection in microarrays requires the use of observed intensity signals at each probe, which limits the imputability for analyses that span multiple array types. Thus far, a consensus set of probes (those present on all arrays) has been used to circumvent the problem of differing array-specific sensitivities. This has led to excessive reduction in overall sensitivity since arrays can have an undesirably low probe overlap. To overcome this limitation, we developed MarkerMatch, a proximity-based algorithm that matches probes across different genotyping microarrays to maximize the number of probes considered in the CNV calling algorithm, thereby increasing the resolution and sensitivity while preserving precision. RESULTS: By analyzing CNV calls from 4906 individuals genotyped across three different arrays, we show that the MarkerMatch approach improves sensitivity by increasing the density of probes available for CNV calling while maintaining precision or improving it relative to the current practice (e.g. use of consensus probes only). We further demonstrate that MarkerMatch matches the CNV detection from current practice in terms of F1 score and PPV for larger CNVs. We also optimize MarkerMatch parameters, DMAX and Method, and find an optimal DMAX setting at 10 kb, with no clear optimal candidate based on Method, indicating that parameters for this metric should be determined on a use case basis. AVAILABILITY: The R package for MarkerMatch is available at: https://github.com/FranjoIM/MarkerMatch. The code used for analysis and implementation is available at: https://doi.org/10.5281/zenodo.18460979. The live notebook is available at https://fivankovic.notion.site/2026-markermatch.

DNA Copy Number Variations↗

PubMed2000

Laterally attached liquid crystalline polymers as stationary phases in reversed-phase high-performance liquid chromatography. II. Optimization of the molecular parameter of the polymer.

Stationary phases obtained by coating side-chain liquid crystalline polymers (LCPs) with the mesogenic rod like units laterally attached to a polysiloxane backbone via a flexible spacer have been already reported. These phases show excellent planarity and shape recognition for polynuclear aromatic hydrocarbon (PAH) solutes in reversed-phase liquid chromatography. Optimization of these stationary phases in terms of molecular parameters of the polymer is here described. Fifteen stationary phases have been prepared varying different parameters such as the spacer length, the aliphatic tail length, and the proportion of laterally attached mesogenic units along the polymer chain. The results show that the combination of a long spacer and long terminal chains, which generates a smectic phase in the polymer bulk, leads to the best chromatographic performances towards planarity and shape recognition for PAH solutes.

Chromatography, High Pressure Liquid↗

PubMed1991

Optimal design of experiments to estimate LDL transport parameters in arterial wall.

To quantify transport processes in atherosclerosis, the arterial wall is often exposed to labeled lipoproteins. In vivo experiments are desirable for estimation of transport parameters, but they are technically difficult. A dynamic mass transfer model has been developed to describe experimental transmural profiles of lipoprotein accumulation as a function of luminal permeability, diffusion, convection, and degradation. To avoid extraneous experiments and to assure successful parameter estimation, an optimal design of experiments is needed. For our purposes a design was considered optimal when it maximized the sensitivity of the model output to changes in parameter values as indicated by the determinant of the Hessian matrix of the objective function. A comparison was made between two designs: dual-time designs prescribing unequal circulation times for two distinguishable injections of labeled low-density lipoprotein (LDL) and dual-species designs requiring simultaneous circulation of LDL and tyramine-cellobiose-modified LDL. Circulation time was optimized for both designs. Although both were heavily dependent on the circulation times, dual-time designs required better preliminary knowledge of parameter values. Because labeled degradation products of the modified tracer become anchored in the arterial tissue, information about the degradation process is retained in the dual-species study. For this reason, dual-species designs were generally superior to dual-time designs.

Animals↗

PubMed2006

Determination of uranine tracer dye from underground water of Mecsek Hill, Hungary.

The underground water system of Mecsek Hill, Hungary was studied using spectrofluorometry. A quantitative dye-tracing technique was used to map the connections between ground water recharge points and the springs and wells. Excitation-emission matrices were used to establish optimal spectroscopic parameters for spectral measurements. Only an EEM gives full spectrofluorimetric information about the sample and makes possible the determination of the optimal wavelength parameters. The uranine concentration was determined by measuring the synchronous excitation spectra of water samples. It was found that under the 4 microg/L uranine concentration, no special chemical treatment was necessary if the pH values remained between 7 and 8. However, above this concentration, the solution should be diluted to avoid spectral distortion from the increasing absorbance of the sample. Long-term concentration measurements were conducted based on spectrofluorometry.

Fluorescein↗

PubMed2006

Latency detection in motor responses: a model-based approach with genetic algorithm optimization.

The latency of a response is one of the most frequently reported parameters when describing the characteristics of a motor system. Such measurement provides important information both to the basic researcher investigating the neural circuitry of the underlying physiological system and to the clinician gathering information for diagnosing a patient. Our concern here is that when the latency of a response is determined on experimentally recorded data by using the most commonly referenced techniques to find the onset of a motor response, the resulting figure encompasses both the neural processing time and the dynamics of the system producing the response (e.g., the musculoskeletal apparatus). Therefore, the resulting latency measurement cumulates information relative to two substantially different sources and thus having different implications. The goal of our study is that of suggesting a technique allowing the separation of the relative contributions of neural transmission and processing time from that of the dynamics of the motor system. This is accomplished by using a technique based on fitting a model to the experimentally recorded response, thus allowing to exploit as much as is known with regards to the dynamics of the studied motor system (e.g., model order and constraints on the values of the model parameters). The optimization of the model parameters for fitting the experimental data is carried out using a real-valued genetic algorithm, allowing to avoid trapping in local, suboptimal minima. The use of this approach allows to estimate the pure delay in the response introduced by neural processing more accurately than the traditional latency detection techniques based on adaptive thresholds.

Algorithms↗

PubMed2003

Direct tissue analysis using matrix-assisted laser desorption/ionization mass spectrometry: practical aspects of sample preparation.

Practical guidelines for the preparation of tissue sections for direct analysis by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry are presented. Techniques for proper sample handling including tissue storage, sectioning and mounting are described. Emphasis is placed on optimizing matrix parameters such as the type of matrix molecule used, matrix concentration, and solvent composition. Several different techniques for matrix application are illustrated. Optimal instrument parameters and the necessity for advanced data analysis approaches with regards to direct tissue analysis are also discussed.

Animals↗

PubMed1998

Heuristic lipophilicity potential for computer-aided rational drug design: optimizations of screening functions and parameters.

In this research we test and compare three possible atom-based screening functions used in the heuristic molecular lipophilicity potential (HMLP). Screening function 1 is a power distance-dependent function, bi/[formula: see text] Ri-r [formula: see text] gamma, screening function 2 is an exponential distance-dependent function, bi exp(-[formula: see text] Ri-r [formula: see text]/d0), and screening function 3 is a weighted distance-dependent function, sign(bi) exp[-xi [formula: see text] Ri-r [formula: see text]/magnitude of bi)]. For every screening function, the parameters (gamma, d0, and xi) are optimized using 41 common organic molecules of 4 types of compounds: aliphatic alcohols, aliphatic carboxylic acids, aliphatic amines, and aliphatic alkanes. The results of calculations show that screening function 3 cannot give chemically reasonable results, however, both the power screening function and the exponential screening function give chemically satisfactory results. There are two notable differences between screening functions 1 and 2. First, the exponential screening function has larger values in the short distance than the power screening function, therefore more influence from the nearest neighbors is involved using screening function 2 than screening function 1. Second, the power screening function has larger values in the long distance than the exponential screening function, therefore screening function 1 is effected by atoms at long distance more than screening function 2. For screening function 1, the suitable range of parameter gamma is 1.0 < gamma < 3.0, gamma = 2.3 is recommended, and gamma = 2.0 is the nearest integral value. For screening function 2, the suitable range of parameter d0 is 1.5 < d0 < 3.0, and d0 = 2.0 is recommended. HMLP developed in this research provides a potential tool for computer-aided three-dimensional drug design.

Computer-Aided Design↗

PubMed2006

Ab initio protein fold prediction using evolutionary algorithms: influence of design and control parameters on performance.

True ab initio prediction of protein 3D structure requires only the protein primary structure, a physicochemical free energy model, and a search method for identifying the free energy global minimum. Various characteristics of evolutionary algorithms (EAs) mean they are in principle well suited to the latter. Studies to date have been less than encouraging, however. This is because of the limited consideration given to EA design and control parameter issues. A comprehensive study of these issues was, therefore, undertaken for ab initio protein fold prediction using a full atomistic protein model. The performance and optimal control parameter settings of twelve EA designs where first established using a 15-residue polyalanine molecule-design aspects varied include the encoding alphabet, crossover operator, and replacement strategy. It can be concluded that real encoding and multipoint crossover are superior, while both generational and steady-state replacement strategies have merits. The scaling between the optimal control parameter settings and polyalanine size was also identified for both generational and steady-state designs based on real encoding and multipoint crossover. Application of the steady-state design to met-enkephalin indicated that these scalings are potentially transferable to real proteins. Comparison of the performance of the steady state design for met-enkephalin with other ab initio methods indicates that EAs can be competitive provided the correct design and control parameter values are used.

Algorithms↗

PubMed1995

Place cells recorded in the parasubiculum of freely moving rats.

Previous studies have identified neurons in the hippocampus, subiculum, and entorhinal cortex which discharge as a function of the animal's location in the environment. In contrast, neurons in the postsubiculum and anterior thalamic nucleus discharge as a function of the animal's head direction in the horizontal plane, independent of its behavior and location in the environment. Because the parasubiculum (PaS) has extensive connections, either directly or indirectly, with these structures, it is centrally located to influence the neuronal activity in these areas. This study was therefore designed to determine the types of behavioral and spatial correlates in neurons from the PaS. Single unit recordings were conducted in the PaS of freely moving rats trained to retrieve food pellets thrown randomly into a cylindrical apparatus. A total of 10.3% of the cells were classified as place cells because they discharged in relation to the animal's location in the cylinder. A large percentage of cells (41.4%) were classified as theta cells. The remaining cells had nondiscernable behavioral correlates. Quantitative analysis of the firing rate maps for the place cells showed they had higher levels of background activity and contained larger firing fields than values reported previously for hippocampal place cells. Directional analysis showed that only three out of 16 cells contained a secondary directional correlate; the firing rate for the remaining cells was not affected by the animal's directional heading within the firing field. A time shift analysis, which shifted the spike time series relative to the animal location series, was conducted to determine whether the quality of the location-specific firing could be improved. The time shifts for three different spatial parameters were optimal when cell discharge led the animal's position. Furthermore, the optimal time shifts for two of these parameters (firing area and information content) were less than the optimal shift reported for hippocampal place cells and suggested that PaS cell discharge lagged behind hippocampal place cell activity. Rotation of the cue card with the animal out of view led to near equal rotation of the firing field when the animal was returned to the apparatus. These results indicate that a small population of cells in the PaS encode the animal's location in its environment, although the representation of space encoded by these cells is different from the type of representation encoded by hippocampal place cells.

Animals↗