Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Programming, Linear”

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 955 records · Page 53Linked to original sources
PubMed1977

Cytodifferentiation in the accessory glands of Tenebrio molitor II. Patterns of leucine incorporation in the tubular glands of post-ecdysial adult males.

The tubular accessory gland of male mealworm beetles undergoes rapid and progressive terminal differentiation in the 8-day period after ecdysis to the adult. Total protein and RNA content are maximal at five and eight days respectively. Rates of leucine incorporation rise gradually through the first four days and then increase abruptly in the 5-to 7-day interval. SDS-polyacrylamide gel electrophoresis demonstrates a variety of proteins; two classes with high mobility (Class A and B) appear prominent in homogenates of 5- to 8-day glands. Double-label procedures show that as the glands mature, an increasing proportion of the total leucine incorporation passes into Class A and B proteins, until at eight days, Class A and B proteins account for 50% of the total for the gland. The relative incorporation into A vs. B also changes linearly over this interval. The developmental program of the tubular gland includes both a linearly biosynthetic increase in the proportion of differentiation-specific proteins and an abrupt change in the overall rates of leucine incorporation.

Age Factors↗
PubMed2004

Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference.

MOTIVATION: Bayesian estimation of phylogeny is based on the posterior probability distribution of trees. Currently, the only numerical method that can effectively approximate posterior probabilities of trees is Markov chain Monte Carlo (MCMC). Standard implementations of MCMC can be prone to entrapment in local optima. Metropolis coupled MCMC [(MC)(3)], a variant of MCMC, allows multiple peaks in the landscape of trees to be more readily explored, but at the cost of increased execution time. RESULTS: This paper presents a parallel algorithm for (MC)(3). The proposed parallel algorithm retains the ability to explore multiple peaks in the posterior distribution of trees while maintaining a fast execution time. The algorithm has been implemented using two popular parallel programming models: message passing and shared memory. Performance results indicate nearly linear speed improvement in both programming models for small and large data sets.

Algorithms↗
PubMed1977

Linear increase in aerobic power induced by a strenuous program of endurance exercise.

Eight subjects exercised for 40 min/day, 6 days/wk for 10 wk. For 3 days/wk they performed six 5-min intervals of bicycling on an ergometer against a resistance that elicited VO2 max, separated by 2-min intervals of exercise requiring 50-60% of Vo2 max. On the alternate 3 days, they ran as far as they could in 40 min. Our purpose was to obtain information regarding the time course and magnitude of the increase in Vo2 max and endurance that occur in response to strenuous exercise when the training stimulus is kept approximately constant relative to maximum aerobic capacity. Average Vo2 max increased 5% (P less than 0.05) during the 1st wk. Endurance, Vo2 max, and time to attainment of peak heart rate all increased linearly during the 10 wk. The average weekly increase in Vo2 max was 0.12 l/min. The total increase in Vo2 max averaged 16.8 ml/kg per min (44%). Four of the eight subjects attained Vo2 max levels approaching or exceeding 60 ml/kg per min. It appears from these results that aerobic work capacity can increase more rapidly and to a greater extent in response to training than has generally been thought.

Adult↗
PubMed2004

Rapid quantification of hepatitis B virus DNA by automated sample preparation and real-time PCR.

Monitoring of hepatitis B virus (HBV) DNA in serum by molecular methods has become the standard for assessment of the replicative activity of HBV. Several molecular assays for the detection and quantification of HBV DNA have been described. However, they usually lack automated sample preparation. Moreover, those assays, which are based on PCR, are limited by a short dynamic range (2 to 3 log units). In the present study, the use of RealArt HBV LC PCR Reagents in conjunction with automated extraction on the COBAS AMPLIPREP analyzer was evaluated. Members of an HBV proficiency program panel were tested; linearity, interassay, and intra-assay variations were determined. The performance of the assay in a routine clinical laboratory was evaluated with a total of 117 clinical specimens. When members of the HBV proficiency program panel were tested by the new molecular assay, the results were found to be within +/-0.5 log unit of the results obtained by reference laboratories. Determination of linearity resulted in a quasilinear curve over more than 6 log units. The interassay variation of the RealArt HBV LC PCR Reagents by use of the automated sample preparation protocol ranged from 16 to 73%, and the intra-assay variation ranged from 9 to 40%. When clinical samples were tested by the new assay with the automated sample preparation protocol and the results were compared with those obtained by the COBAS AMPLICOR HBV MONITOR Test with manual sample preparation, the results for 76% of all samples with positive results by both tests were found to be within +/-0.5 log unit and the results for another 18% were found to be within between 0.5 and 1.0 log unit. In conclusion, the real-time PCR assay with automated sample preparation proved to be suitable for the routine molecular laboratory and required less hands-on time.

DNA, Viral↗
PubMed1991

Immobilized pH gradients (IPG) simulator--an additional step in pH gradient engineering: I. Linear pH gradients.

A new computer program, called immobilized pH gradients (IPG) simulator, is proposed for calculating and optimizing any recipe for use in isoelectric focusing in immobilized pH gradients. Unlike our previous monoprotic electrolyte gradient simulation (MGS) and polyelectrolyte gradient simulation (PGS) programs, based on minimizing CV(beta), the present program has a target function the minimization of the quadratic moment around zero of the residuals (mu 2). With this algorithm it is possible to formulate IPG recipes which have deviations from linearity well below 1% of the given pH interval (a limit set with the previous MGS and PGS programs), in fact, as small as 0.1-0.2% (in pH units). The new simulator performs 2-3 times better than the previous ones in the pH 4-10 range, and is absolutely necessary when working outside this range, at extreme pH values, where CV(beta) cannot work against the buffering power of bulk water, thus generating pH recipes with huge deviations from linearity. In the latter cases, mu 2 performs 10 times better than CV(beta). When utilizing strong titrants for extended pH intervals, the "all or none" rule has been discovered: such titrants should always be used in tandem, since omission of one of the two at either the acidic or basic extremes produces strongly distorted pH profiles. Our new, most powerful simulator also contains equations for creating nonlinear gradients, notably: concave and convex exponentials and sigmoidal (see the companion paper: Righetti, P. G. and Tonani, C., Electrophoresis 1991, 12, 1021-1027).

Algorithms↗
PubMed1983

Pocket computer program for fitting the Michaelis-Menten equation.

This paper presents a program written for the Radio Shack TRS-80 or the Sharp PC 1211 pocket computers for fitting the Michaelis-Menten equation to experimental data by a non-linear regression analysis. The program determines the kinetic parameters Km and Vm, their standard errors and the residual standard error. In addition it performs a simulation of a kinetic experiment using the parameter values previously determined.

Computers↗
PubMed2000

Does interview date affect match list position in the emergency medicine national residency matching program match?

OBJECTIVE: Some residency applicants believe that the date on which they interview with a residency program influences how the program ranks them in the National Residency Matching Program (NRMP). Therefore, the authors studied whether interview date affects match list position in the emergency medicine (EM) residency match. METHODS: Forty-four Accreditation Council for Graduate Medical Education (ACGME)-accredited EM residency programs participated in this multicenter study. The interview date and match list position were collected for each interviewee for the 1997-98 season. Programs were also asked about factors that might potentially bias interview date assignment. Statistical analyses were performed both with and without these programs included. Interview dates and match list positions were standardized into percentile date and percentile rank for each program and were compared using linear regression analysis. Scatterplots graphed interview date vs match list position. Two-sample t-tests compared interview dates for ranked and nonranked interviewees. RESULTS: Data were collected for 3,800 individual interviews; 14% of these resulted in unranked applicants. Twenty-three programs, representing 1,997 interviews, reported potential bias in their interview date assignment. Regression analysis revealed an R(2) of 0.018268 (correlation coefficient = 0. 1352, 95% CI = 0.0992 to 0.1617) for all programs, R(2) of 0.010626 (correlation coefficient = 0.1031, 95% CI = 0.0571 to 0.1485) for programs without reported potential bias, and R(2) of 0.02444 (correlation coefficient = 0.1563, 95% CI = 0.10887 to 0.20309) for programs with reported bias. Scatterplots revealed no linear correlation. Two-sample t-tests for all programs, and programs with and without reported bias showed no significant difference in average interview date for ranked and unranked interviewees (both with p > 0.2). CONCLUSION: In this study, interview date for EM residency positions in the 1997-98 season did not affect match list position among ranked applicants. Moreover, interview date had nno effect on the decision to leave candidates unranked.

Emergency Medicine↗
PubMed1990

Computer simulation (based on a linear-elution-strength approximation) as an aid for optimizing separations by programmed-temperature gas chromatography.

If the dependence of retention on temperature is specified for the various components of a sample in isothermal gas chromatography (GC), it is possible to predict retention, bandwidth, and resolution for programmed-temperature GC separations as a function of experimental conditions. The use of a linear-elution-strength (LES) approximation for isothermal retention allows these predictions to be carried out more easily and conveniently, in turn facilitating rapid simulations with a personal computer. This approach to GC method development appears promising, especially if segmented-temperature programs are used. The LES approximation also provides added insight into how different factors affect separation in programmed-temperature GC.

Chromatography, Gas↗
PubMed1992

A microcomputer program for determining turnover rates during non-steady state conditions: application to monoamine turnover.

A program to calculate the turnover rate of monoaminergic neurotransmitters was written for use on microcomputers. The program is based on non-steady state models, i.e., measuring the rate of change of levels of neurotransmitters or their metabolites after pharmacological inhibition of synthetic or degradative enzymes. Methods have been developed to estimate monoamine turnover by measuring the rate of decrease of catecholamine levels after treatment with alpha-methyl-p-tyrosine (AMPT), a tyrosine hydroxylase inhibitor, or the increase in serotonin levels after pargyline, an inhibitor of monoamine oxidase. This program is suitable for examining either linear increases or exponential decreases in monoamine levels. The program has been tested in our laboratory for the determination of serotonin, dopamine or norepinephrine turnover after hormonal or pharmacological manipulations. The program is readily adaptable for calculation of the turnover rate of other biological molecules under non-steady state conditions.

Biogenic Monoamines↗
PubMed1996

SCATPLOT: a computer program for determination of binding parameters of non-linear non-cooperative ligand-substrate interactions.

The importance of computer-assisted analysis of a non-linear binding phenomenon through Scatchard equation has been widely acknowledged. While several user-friendly softwares [LIGAND, SCTFIT, ALLFIT] are available for determining the binding parameters of nonlinear Scatchard phenomenon, there is no easily available software covering the class of phenomena described by the McGhee and von Hippel formalism [J. Mol. Biol. 86, 469-489 (1974)]. We report here user-friendly software, SCATPLOT, developed in Turbo BASIC, for the numerical estimation of binding parameters of a non-cooperative ligand-substrate interaction doing best fit to the experimental data on the basis of McGhee and von Hippel equation for a nonlinear Scatchard plot. A new parameter has also been incorporated to guide the process of least square analysis and subsequent determination of binding parameters.

Algorithms↗
PubMedDate not supplied

[Kinetics of the reactions joining DNA fragments, catalyzed by DNA-ligase. II. Heterogeneous mixture of fragments. Optimization of the reaction conditions].

The system of kinetic equations was proposed describing the joining of heterogeneous DNA fragments by DNA-ligase. The DNA fragments were considered as flexible rods and characterized only by molecular weights and concentrations. The program for calculating the concentrations of all circular and linear DNA forms is described. The program has been written in FORTRAN IV and calculations were made with EC 10--10. For the maximal yield of the multimeric circular DNA molecules it is recommended to begin the ligation at a high DNA concentration and then after a certain fixed time to dilute the reaction mixture. The optimum time intervals and ratios of fragment concentrations were calculated. The yield of different ligation products has been determined. The calculations of optimum reaction conditions were carried out for the construction of hybrid molecules containing DNA fragments with or without selective genetic markers.

DNA↗
PubMed2001

Solving a linear model of nonfatal risk behavior and injuries in school children.

A calculating method and computer program have been developed for solving an overdetermined system of linear equations. It was applied for calculation of group risk exposure of school children (10-15 years) to nonfatal injuries in sport recreation and playing (SRP). Interviewed non-injured school children were separated into non-overlapping groups of risky behavior. Data on interviewed non-injured and non-interviewed injured children were put into a linear system of equations consisting of a 4 x 3 matrix scheme. Each equation represents children of the same age and sex and consists of the percentage of interviewed children grouped into high medium or low risk behavior and of the percentage of injured children. Four methods of calculating the matrix system were evaluated and the best implemented as a new developed computer program. The resulting linear group risk factors enable the prediction of behavior outcome. Data on interviewed injured children were compared with the results obtained. The validation procedure is proposed by testing the sensitivity and robustness of the method.

Adolescent↗
PubMed1991

A computer program for many-beam image simulation of amplitude-contrast images.

A computer program for the simulation of amplitude-contrast electron micrographs is described. The program is based on the n-beam dynamical theory of diffraction contrast as described by Howie and Whelan (see Howie, A., and Whelan, M.J. (1961) Proc. R. Soc. Lond. [Biol]). The displacement fields associated with crystal lattice defects are calculated using linear anisotropic elasticity. The program can be used to simulate images of crystals containing line or planar defects or combinations of these defects. The line defects can be oriented freely within the foil, and are not restricted to being mutually parallel, but must be straight. Different techniques available for solving the diffraction problem, with or without the column approximation, are discussed.

Crystallization↗
PubMed1993

TopFit: a PC-based pharmacokinetic/pharmacodynamic data analysis program.

The program TopFit was developed and validated within the European pharmaceutical industry. It provides both pharmacokinetic data analysis support for international regulatory submissions of new drugs, and sophisticated techniques for model-based kinetic/dynamic evaluation during drug development. TopFit features are: (1) non-compartmental methods; (2) standard compartment models assembled from input and disposition modules; (3) a potentially unlimited number of linear user-defined models that accommodate metabolites, effects, and absorption profiles; (4) a library of 24 non-linear models. No user programming is required. A well-defined file structure allows ready exchange of data with other programs such as SAS. TopFit version 2.0 is now commercially available, with comprehensive documentation, in the form of an MS-DOS application for the PC.

Data Interpretation, Statistical↗
PubMed1996

Isoelectric focusing and titration curves in biomedicine and in agrofood industries: a multimedia teaching program.

The aim of this 45 min, 60 megabyte, modular program is to initiate students, scientists and engineers of biotechnology, biomedicine and agrofood industries into isoelectric focusing (IEF) and titration curves for analytical (e.g. IEF, zone electrophoresis, isotachophoresis, electrotransfer) and preparative (e.g. ion-exchange chromatography, chromatofocusing) application of charge-dependent methods. For advanced teaching, the following theoretical and practical aspects may be of interest: pH gradient engineering, IEF resolving power, generation of pH gradient, sample-ampholyte interactions, pH gradient drift, immobilized pH gradients (IPG), IPG-two-dimensional (2-D) electrophoresis, preparative methods with multi-compartments and IPG membranes, capillary IEF, isozyme analysis, etc.). The program associates fixed and animated drawings, and computer-assisted simulations, with spoken and written commentaries (in English). It is illustrated with numerous IEF gel patterns and titration curves and some video sequences to be run on a multimedia PC with MS Windows 3.1 (or later releases) as the only software. The linear presentation of the program may be used directly on the PC, or may be projected on a screen from the PC, for small classes or for a larger audience (200 persons). Its development as an interactive multimedia program is in progress and will soon be available on the Internet.

Computer-Assisted Instruction↗
PubMed1995

Growth changes in the cranial base and the face: a longitudinal cephalometric study of linear and angular changes in adult Norwegians.

The purpose of this study was to examine the natural growth changes which occur between 22 and 33 years of age. The material consisted of two series of cephalograms of 74 females and 90 males with approximately 11 years between the two series. None of the subjects had orthodontic retainers when the first exposure was undertaken, or orthodontic treatment, or surgery during the observation period. The measurements were carried out by using a modified Dentofacial Planner program SHORT, and both linear and angular measurements were made. The overall changes were an increase in anterior facial height which mostly occurred in the lower face, and an increase in the length of the mandible. These changes were statistically significant in both genders. The females also had a significant posterior rotation of the mandible. There was a significant decrease in the thickness of the upper lip both in females and males, and the males had a significant increase in thickness of the soft tissue on the mandibular profile. Although there were some statistical changes in the observation period, none of the linear changes exceeded 1.35 mm. The largest angular change was a 1.44 degrees retroclination of the upper incisors in females. The differences between the genders were statistically significant only in three angular and two soft tissue measurements.

Adult↗
PubMed1994

Effects of slow flow on slice profile and NMR signal in fast imaging sequences.

A computer program has been developed to evaluate the selective-slice profiles obtained in the steady state for fast gradient-echo imaging. Both spoiled and refocused gradient-echo pulse sequences have been considered. By numerically solving the Bloch equations modified for the effects of flow, for a three-dimensional volume of spins, for realistic RF excitations and linear gradient combinations, the program permits the combined effects of flow and imaging variables on the magnetization slice profile to be assessed quantitatively. We have found that the gradient pattern in gradient-echo pulse sequences is a significant factor for determining the steady-state slice profiles and the strength of the NMR signal from the flowing spins.

Algorithms↗