Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Computational methods”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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

At least 1,027 records · Page 57Linked to original sources
PubMed1992

On fluctuation analysis: a new, simple and efficient method for computing the expected number of mutants.

Fluctuation analysis, which is often used to demonstrate random mutagenesis in cell lines (and to estimate mutation rates), is based on the properties of a probability distribution known as the Luria-Delbrück distribution (and its generalizations). The two main new results reported in this paper are (i) a simple, completely general, and computationally efficient procedure for calculating probability distributions arising from fluctuation analysis and (ii) the formula for this procedure when cells in a colony have only grown for a finite number of generations after initial seeding. It is also shown that the procedure reduces to one that was developed earlier when an infinite number of generations is assumed. The derivation of the generating function of the distribution is also clarified. The results obtained should also be useful to experimentalists when only a relatively short time elapses between seeding and harvesting cultures for fluctuation analysis.

Cell Line↗
PubMed1976

A method of computing drug distribution in plasma using stepwise association constants: clofibrate acid as an illustrative example.

A program is described to compute the distribution of ligand among various complexes of ligand and protein using stepwise association constants. The key input data consists of stepwise association constants and the concentration of macromolecule and various concentrations of ligand. The key output data consists of the concentration of free drug and protein and the concentration of the various complexes.

Clofibrate↗
PubMed1976

A method of computing the distribution of a ligand among multiple binding sites on different proteins in plasma: thyroxine as an illustrative example.

This paper describes a computer program for estimating the amount of free or unbound ligand in the plasma as well as the distribution of the ligand among different sets of binding sites on different proteins. The input data consist of: the number and concentrations of proteins involved, the number of binding sites on each protein, the association constant and binding capacity of each set of sites for the ligand, and the total concentrations of ligand. The output provides tables of estimates of the concentration of free drug, the amount of ligand bound by each set of sites on each protein, the concentration of free protein, and the input values for reference. The distribution of thyroxine between thyroid binding globulin, prealbumin, human serum albumin and free drug is used as an illustrative example.

Binding Sites↗
PubMed1995

A Bayesian framework for understanding texture segmentation in the primary visual cortex.

This paper presents a mathematical theory for understanding the computations involved in texture segmentation in the primary visual cortex. We propose that texture segmentation is a part of the early visual system's overall strategy to infer surfaces of objects in a visual scene. Based on this insight, we use the Bayesian inference paradigm to formulate the texture segmentation problem into a maximum a posteriori surface inference problem. The dynamical system for finding the optimal solution of this problem can be characterized by two concurrent and interactive processes: a gradual sharpening of the boundary signals and a simultaneous smoothing of the surface signals. The behavior of these dynamical processes was studied using both analytical and computational methods. We present some computational results and mathematical predictions. This theory suggests a novel framework for understanding the functional roles of the complex cells in the primary visual cortex.

Bayes Theorem↗
PubMed1993

Colloidal carbon particles as a new label for rapid immunochemical test methods: quantitative computer image analysis of results.

Colloidal carbon particles can serve as label in sol particle immunoassays. The universal applicability of these particles in qualitative and (semi)quantitative immunoassays has been demonstrated. Sol particle and/or dipstick immunoassays, not yet optimized in terms of sensitivity, are discussed. The colloidal label has been used successfully in a mouse immunoglobulin isotyping kit. Human serum albumin spotted onto nitrocellulose in a concentration range of 7.8 to 1000 ng could be detected using anti-albumin antibody absorbed onto colloidal carbon particles. It was also possible to perform a competitive assay with this conjugate for a concentration range of free human serum albumin varying from 0.25 to 6.75 micrograms. The Kunitz-type trypsin inhibitor from soybean was determined by a colloidal carbon based immunoassay in a range of 2.5 to 160 ng. In this assay, free and colloidal carbon-bound inhibitor competed for binding specific antibodies spotted onto a nitrocellulose membrane. An image- and data-processing procedure has been developed that enables a rapid and simple quantification of colloidal carbon sol particle immunoassays. The average grey level of a spot is taken as a measure for quantitative purposes. This so-called Sol-particle Image Processed ImmunoAssay (SIPIA) procedure is equally well applicable to assays using other colloidal particles.

Animals↗
PubMed2004

Simulation of chromatography of phenolic compounds with a computational chemical method.

An ab initio simulation of reversed-phase liquid chromatography for phenolic compounds was achieved based on molecular interaction energy values calculated using molecular mechanics calculations (MM2) of the CAChe program. The precision of the predicted retention factors from the molecular interaction energy values was equivalent to the predicted retention factors based on octanol-water partition coefficients (log P) calculated using the molecular orbital package (MOPAC). The prediction of retention factors of phenolic compounds in reversed-phase liquid chromatography in a given pH eluent was possible using the predicted dissociation constant (pKa) from the atomic partial charge without a chemical experiment if the organic modifier effect was known.

Hydrogen-Ion Concentration↗
PubMed2004

Tongue carcinoma: tumor volume measurement.

PURPOSE: To validate the semiautomated methods of tongue carcinoma tumor volume measurement by comparing the conventional manual trace method with 2 semiautomated computer methods: seed growing and region deformation. MATERIALS AND METHODS: The study population consisted of 16 patients with histology-proven tongue carcinoma. Two head-and-neck radiologists independently measured the tumor volume demonstrated on pretreatment T2-weighted magnetic resonance data sets. The tumor volumes were measured using manual tracing and semiautomated seed growing and region deformation algorithm. Data were recorded for analysis of interoperator variance and interobserver reliability at volume and pixel levels. RESULTS: There was no significant difference between the manually traced volume and semiautomated segmentation volumes for both operators. No significant difference was found in interobserver variance among the 3 methods at volume level. However, there was significant difference between manual tracing and semiautomated segmentation methods in interobserver reliability at pixel level. CONCLUSION: The semiautomated methods could achieve satisfactory segmentation results. They could also reduce interoperator variance and obtain a higher interobserver reliability. This study validates the use of semiautomated volume measurement methods for tongue carcinoma.

Adult↗
PubMed1987

Description and evaluation of a method for computer analysis of the exercise electrocardiogram.

The new approach to computer processing of exercise electrocardiography has been made easier by the development of microcomputers. Studies are necessary to validate analyzed electrocardiographic data for the diagnosis of ischemia. We describe and assess in this paper a new program for the analysis "on line" of 12 leads during effort. The program detects "normal QRS" and ectopic beats. Amplitude of R wave, length of QRS, ST level after a programmable delay from J point, ST maximal slope and amplitude of T wave are calculated and recorded every 15 sec in the 12 leads. In 200 exercise stress tests quantitative data provided by the processor were compared with visual analysis and with clinical data. ST level less than or equal to -0.8 mm and ST slope less than or equal to 1.2 mV/sec or ST level greater than or equal to +2.0 mm and ST slope less than or equal to 0.6 mV/sec were the best analyzed criteria for ischemia. Using these criteria, sensitivity increased from 86.6% by visual reading to 92% by computer analysis, without change in specificity (94%).

Adult↗
PubMedDate not supplied

Use of computer-assisted methods for the modeling of the retention time of a variety of volatile organic compounds: a PCA-MLR-ANN approach.

A hybrid method consisting of principal component analysis (PCA), multiple linear regressions (MLR), and artificial neural network (ANN) was developed to predict the retention time of 149 C(3)-C(12) volatile organic compounds for a DB-1 stationary phase. PCA and MLR methods were used as feature-selection tools, and a neural network was employed for predicting the retention times. The regression method was also used as a calibration model for calculating the retention time of VOCs and investigating their linear characteristics. The descriptors of the total information index of atomic composition, IAC, Wiener number, W, solvation connectivity index, X1sol, and number of substituted aromatic C(sp(2)), nCaR, appeared in the MLR model and were used as inputs for the ANN generation. Appearance of these parameters shows the importance of the dispersion interactions in the mechanism of retention. Comparison of the MLR and 5-2-1 ANN models indicates the superiority of the ANN over that of the MLR model. The values of 0.913 and 0.738 were obtained for the standard error of prediction set of MLR and ANN models, respectively.

Journal Article↗
PubMed2003

Theoretical insights in enzyme catalysis.

In this tutorial review we show how the methods and techniques of computational chemistry have been applied to the understanding of the physical basis of the rate enhancement of chemical reactions by enzymes. This is to answer the question: Why is the activation free energy in enzyme catalysed reactions smaller than the activation free energy observed in solution? Two important points of view are presented: Transition State (TS) theories and Michaelis Complex (MC) theories. After reviewing some of the most popular computational methods employed, we analyse two particular enzymatic reactions: the conversion of chorismate to prephenate catalysed by Bacillus subtilis chorismate mutase, and a methyl transfer from S-adenosylmethionine to catecholate catalysed by catechol O-methyltransferase. The results and conclusions obtained by different authors on these two systems, supporting either TS stabilisation or substrate preorganization, are presented and compared. Finally we try to give a unified view, where a preorganized enzyme active site, prepared to stabilise the TS, also favours those reactive conformations geometrically closer to the TS.

Bacillus subtilis↗
PubMed2006

Comparative study of perturbative methods for computing electron transfer tunneling matrix elements with a nonorthogonal basis set.

The authors consider the problem of computing tunneling matrix elements for bridge-mediated electron transfer reactions using the Lowdin [J. Math. Phys. 3, 969 (1962); J. Mol. Spectrosc. 13, 326 (1964)] projection-iteration technique with a nonorthogonal basis set. They compare the convergence properties of two different Lowdin projections, one containing the overlap matrix S and the other containing the inverse S-1 in the projected Hamiltonian. It was suggested in the literature that the projected Hamiltonian with S-1 has better convergence properties compared to the projected Hamiltonian with S. The authors test this proposal using a simple analytical model, and ab initio Hartree-Fock calculations on different molecules with several types of basis sets. Their calculations show that, for Gaussian-type basis sets, the projected Hamiltonian containing S has the best convergence properties, especially for diffuse basis sets and in the strong coupling limit. The limit of diffuse basis sets is relevant to tunneling matrix element calculations involving excited states and anionic electron transfer.

Journal Article↗