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PubMed1998

Numerical evaluation of the production of radionuclides in a nuclear reactor (Part I).

Numerical evaluation of nuclear transmutations is essential for optimization of radionuclide production. Accordingly, we have developed a generalized computer program called LAURA for predicting the production rates of radionuclides in a nuclear reactor. The program is generalized in the sense that it can be used for calculation of the production rate of any member of a network undergoing spontaneous decay and/or induced neutron transformation in a nuclear reactor. In this paper (Part I), we describe the mathematical basis for the development of LAURA. Expressions based on the Rubinson (1949) approach have been used for the evaluation of the depletion functions. This method is also valid when some of the depletion constants have identical values; thus, the approximate solution of Raykin and Shlyakhter (1989) can be used to account for the effects of feedback due to alpha decay.

Algorithms↗
PubMed1998

Interactions among P450 enzymes when combined in reconstituted systems: formation of a 2B4-1A2 complex with a high affinity for NADPH-cytochrome P450 reductase.

The purpose of this study is to characterize the interactions among P450 1A2, P450 2B4, and P450 reductase in mixed reconstituted systems. Previously, our laboratory demonstrated that in the presence of certain substrates, 1A2 can influence the catalytic characteristics of 2B4 [Cawley et al. (1995) Biochemistry 34, 1244-1247]. The goal of the current study is to distinguish between two models to explain these interactions: one model where substrate increases the affinity of one P450 enzyme for the reductase, and another model where substrate increases the affinity of one P450 for the reductase through the formation of a 1A2-2B4 complex. According to this model, the 1A2 moiety of 1A2-2B4 forms a high-affinity complex with reductase. Reductase, 1A2, and 2B4 were reconstituted with dilauroylphosphatidylcholine, and the effect of reductase concentration on 7-pentoxyresorufin-O-dealkylation was examined with 2B4-reductase and 1A2-reductase binary systems, and in ternary systems containing different 2B4:1A2 ratios. At subsaturating [reductase], there was a dramatic inhibition of the 2B4-dependent activity in the ternary system as compared with the binary systems. These results are consistent with the formation of a ternary (reductase-1A2-2B4) complex where the reductase is bound specifically to 1A2. At higher reductase concentrations where the reductase-binding sites on 1A2 become saturated, the results are consistent with the formation of a quaternary complex in which reductase binds to both P450 enzymes (reductase-1A2-2B4-reductase). Analogous experiments using the 1A2-preferred substrate 7-ethoxyresorufin showed a stimulation of 7-ethoxyresorufin-O-deethylation in the mixed reconstituted system, demonstrating that the high-affinity 2B4-1A2-reductase complex was functionally active and not merely an inhibitory complex.

Animals↗
PubMed1989

Computer-based implementation of the ST-segment/heart rate slope.

The ST-segment/heart rate (ST/HR) slope has markedly improved the accuracy of the exercise electrocardiogram for the identification and quantification of coronary artery disease. However, clinical use of this technique has been limited by time-consuming manual ST-segment measurements and calculator-based linear regression analyses after testing. To assess the accuracy of on-line computerized measurement of ST-segment depression and recently implemented ST/HR slope algorithms, 50 patients exercised with a Marquette Electronics CASE 12 system and 50 patients exercised with a Quinton Q5000 system were evaluated. Computerized ST-segment measurements, to the nearest 10 microV, were compared with averaged manual measurements from the raw signal, to the nearest 25 microV, at peak exercise in leads II and CM5. The CASE 12 and Q5000 algorithms for selection of data and calculation of the maximal ST/HR slope were compared with the ST/HR slope calculated from end-stage data points according to a standard off-line procedure. Manual ST-segment measurements correlated highly with CASE 12 and Q5000 determinations (r = 0.996 to 0.998). The slopes of their regression lines approached unity (range 0.98 to 1.02), and the standard errors of the estimate ranged from 12 to 15 microV. Each on-line program selected data points and determined ST/HR slopes in complete accordance with standard calculations. It is concluded that computer-based measurement of the ST/HR slope can be performed with a high degree of accuracy.

Adult↗
PubMed1992

Measures of clinical agreement for nominal and categorical data: the kappa coefficient.

The desire to determine the extent inter-rater measurements obtained in a clinical setting are free from measurement error and reflect true scores has spurned a renewed interest in assessment of reliability. The kappa coefficient is considered the statistic of choice to analyze the reliability of nominal and categorical types of data recorded on the same patient by more than one clinician. This paper presents a simple computer program written in PASCAL that can be used in a clinical environment to quickly determine the reliability of nominal or categorical data. This computer program calculates both weighted and non-weighted kappa coefficients with their corresponding standard errors as well as bias-correcting jackknife estimates of kappa for use with small sample sizes.

Data Interpretation, Statistical↗
PubMed1999

Calculations of NMR dipolar coupling strengths in model peptides.

Ab initio MP2 and density functional quantum chemistry calculations are used to explore geometries and vibrational properties of N-methylacetamide and of the alanine dipeptide with backbone angles characteristic of helix and sheet regions in proteins. The results are used to explore one-bond direct dipolar couplings for the N-H, C alpha-H alpha, C'-N, and C alpha-C' bonds, as well as for the two-bond C'-H interaction. Vibrational averaging affects these dipolar couplings, and these effects can be expressed as effective bond lengths that are 0.5-3% larger than the true bond lengths; bending and torsion vibrations have a bigger influence on the effective coupling than do stretching vibrations. Because of zero-point motion, these effects are important even at low temperature. Hydrogen bonding interactions at the amide group also increase the N-H effective bond length. Although vibrational contributions to effective bond lengths are small, they can have a significant influence on the extraction of order parameters from relaxation data, and a knowledge of relative bond lengths is needed when several types of dipolar couplings are to be simultaneously used for refinement. The present computational results are compared to both solid- and liquid-state NMR experiments. The analysis suggests that secondary structural elements in many proteins may be more rigid than is commonly thought.

Acetamides↗
PubMed1994

An algorithm for identifying regions of a DNA sequence that satisfy a content requirement.

We present a dynamic programming algorithm for identifying regions of a DNA sequence that meet a user-specified compositional requirement. Applications of the algorithm include finding C + G-rich regions, locating TA + CG-deficient regions, identifying CpG islands, and finding regions rich in periodical three-base patterns. The algorithm has an advantage over the simple window method in that the algorithm shows the exact location of each identified region. The algorithm has been implemented as a portable C program called LCP (Local Content Program). LCP is extremely efficient in computer time and memory; it instantly locates all regions of a long DNA sequence meeting a given requirement. The LCP program was used to analyze the rabbit alpha-like globin gene cluster sequence.

Algorithms↗
PubMed1986

Computer-aided analysis of infrared, circular dichroism and absorption spectra.

Marquardt and Powell optimization methods without constraints on the optimized spectral parameters were employed for decomposition of complex i.r., c.d. and absorption spectra into component bands. The procedure resolved experimental spectra into eight component bands and it can be easily adjusted for a larger set of component bands. The CPU time required for achievement of satisfactory convergence of parameters for eight component bands is rather large even when using mainframe computers and therefore division of spectra into a few non-overlapped parts is advisable. The program also can be used for calculation of absorption, c.d. and difference spectra from formatted raw spectral data.

Algorithms↗
PubMed1993

Short algorithm to compensate for sampling-volume errors in diffusion-cell studies.

This communication describes a short algorithm enabling arbitrarily large but equal samples to be taken from the two chambers of a diaphragm diffusion cell without introducing any systematic error. It creates a transformed time-scale, dependent on sampling volume, which linearizes the output, fits this to a straight line by simple linear regression, and computes the diffusion coefficient from the slope. The advantages of sampling equal fractions from both chambers are discussed in terms of the greater precision this allows. The procedure may have uses in other fields.

Algorithms↗
PubMed2006

PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics.

We describe a new way to calculate the electrostatic properties of macromolecules which eliminates the assumption of a constant dielectric value in the solvent region, resulting in a Generalized Poisson-Boltzmann-Langevin equation (GPBLE). We have implemented a web server (http://lorentz.immstr.pasteur.fr/pdb_hydro.php) that both numerically solves this equation and uses the resulting water density profiles to place water molecules at preferred sites of hydration. Surface atoms with high or low hydration preference can be easily displayed using a simple PyMol script, allowing for the tentative prediction of the dimerization interface in homodimeric proteins, or lipid binding regions in membrane proteins. The web site includes options that permit mutations in the sequence as well as reconstruction of missing side chain and/or main chain atoms. These tools are accessible independently from the electrostatics calculation, and can be used for other modeling purposes. We expect this web server to be useful to structural biologists, as the knowledge of solvent density should prove useful to get better fits at low resolution for X-ray diffraction data and to computational biologists, for whom these profiles could improve the calculation of interaction energies in water between ligands and receptors in docking simulations.

Binding Sites↗
PubMed1980

An anatomic index of injury severity.

Systems for the quantitation of injury severity are crucial to the study of injury epidemiology, and to comparative evaluations of health care delivery in different regions, patient mixes, and environment. Existing anatomic injury severity scores suffer from subjectivity, and may be computed only at relatively high man-hour expense. In this paper we present an injury severity ranking system termed the Anatomic Index, derived from objective, observed probabilities of mortality, and computable from the same HICDA diagnostic codes widely available in hospitals and through software in hospital computer systems. Mathematic underpinnings of the method, theoretical consequences of underprediction and overprediction of mortality, and advantages of the new Index are presented.

Computers↗
PubMed1976

[Calculation of radioimmunochemical determinations by "spline approximation" (author's transl)].

A simplified method, based on the "spline approximation", is reported for the calculation of the standard curves of radioimmunochemical determinations. It is possible to manipulate the mathematical function with a pocket calculator, thus making it available for a large number of users. It was shown that, in contrast to the usual procedures, it is possible to achieve optimal quality control in the preparation of the standard curves and in the interpolation of unknown plasma samples. The recaluculation of interpolated values from their own standard curve revealed an error of 4.9% which would normally be an error of interpolation. The new method was compared with two established methods for 8 different radioimmunochemical determinations. The measured values of the standard curve showed a weighting, and there was a resulting quality control of these values, which, according to their statistical evalution, were more accurate than those of the others models (Ekins et al., Yalow et al., (1968), in: Radioisotopes in Medicine: in vitro studies (Hayes, R. L., Goswitz, F.A. & Murphy, B. E. P., eds) USA EC, Oak Ridge) and Rodbard et al. (1971), in: Competitive protein Binding Assys(Odell, W. D. & Danghedy, W. H., eds.) Lipincott, Philadelphia and Toronto). In contrast with these other models, the described method makes no mathematical or kinetic preconditions with respect to the dose-response relationship. To achieve optimal reaction conditions, experimentally determined reaction data are preferable to model theories.

Computers↗
PubMed1994

Gas flow and mixing in the airways.

OBJECTIVE: To survey the current state of scientific knowledge of gas flow and mixing in pulmonary airways, especially at high frequencies. DATA SOURCES: Results from the authors' own laboratory studies and Western bioengineering literature on respiratory fluid mechanics. STUDY SELECTION: This survey concentrates on understanding the principal physical mechanisms that underlie the enhancement of airway gas transport in high-frequency oscillation. The results of experimental, computational, and mathematical studies are described. DATA SYNTHESIS: The topic was covered by seven presenters at the Münster Meeting on High Frequency Ventilation, January 31 to February 2, 1993. Six of these presentations are summarized in the six sections of this paper under the following headings: Introductory Survey; Three-Dimensional Numerical Simulation of Inspiratory and Expiratory Flows in Small Airways; Computational and Experimental Models of High-Frequency Oscillation; Unsteady Gas Mixing in Airways; Gas Dispersion From the Lagrangian Viewpoint; and Soluble Gas Mass Transfer in Tubes and Airways. CONCLUSIONS: The dominant mechanism for the enhancement of gas transport along airways at high frequency is likely to lie in the coupling of the secondary motions caused by airway curvature with the oscillatory longitudinal flow. However, laboratory experiments and theoretical analyses have led only to an accurate simulation of the phenomena in idealized geometries, not in real lungs.

Animals↗
PubMed1987

A fast algorithm for the computation of the plasma concentration time curve and confidence limits in linear pharmacokinetics.

An algorithm is developed for the computation of the plasma concentration time curve for a drug administration regime involving fast injection (bolus) and/or continuous infusion. The effect of the pharmacokinetic model parameter variations on the plasma concentration time curve is analyzed and efficient algorithms for the computation of the parameter-induced first-order variation and confidence bounds of the plasma concentration time curve are also presented. The application of the method is illustrated with pharmacokinetic data for the etomidate.

Algorithms↗
PubMed2005

Rhesus monkeys (Macaca mulatta) spontaneously compute addition operations over large numbers.

Mathematics is a uniquely human capacity. Studies of animals and human infants reveal, however, that this capacity builds on language-independent mechanisms for quantifying small numbers (<4) precisely and large numbers approximately. It is unclear whether animals and human infants can spontaneously tap mechanisms for quantifying large numbers to compute mathematical operations. Moreover, all available work on addition operations in non-human animals has confounded number with continuous perceptual properties (e.g. volume, contour length) that correlate with number. This study shows that rhesus monkeys spontaneously compute addition operations over large numbers, as opposed to continuous extents, and that the limit on this ability is set by the ratio difference between two numbers as opposed to their absolute difference.

Animals↗
PubMed1996

A mathematical model of activity-dependent, anatomical segregation induced by competition for neurotrophic support.

Mathematical or computational models of activity-dependent neural competition typically impose competition in anatomically fixed networks by the use of synaptic normalisation, for which there is very little experimental support. Recent experimental evidence, however, strongly implicates neurotrophic factors in neural plasticity and competition, in addition to their well-known potent effects on neurite outgrowth and synaptogenesis. We therefore present a simple, mathematical model of anatomical segregation induces by activity-dependent competition for a limited supply of a neurotrophic factor provided by target cells to afferents. We extract the behaviour of the model in various regimes, in which the neurotrophic factor is either in critical supply or in abundant supply, by a combination of analytical and numerical methods, and study the effects of correlations in afferent inputs on competition. We apply the model to three different systems: ocular dominance column formation; elimination of polyneuronal innervation at the vertebrate neuromuscular junction; trigeminal brain stem whisker-related structure formation. Several classes of related predictions emerge, including the prediction that kittens reared with strabismus should require a higher concentration of neurotrophic factor infusion into their primary visual cortex than normally reared cats in order to induce the anatomical desegregation of ocular dominance columns. We also speculate on the mechanisms of support of inhibitory rather than excitatory neurons, and suggest the existence of a separate, (Cl-)-mediated activity-dependent pathway for their neurotrophic support.

Animals↗
PubMed1991

Fluxplus, a microcomputer program for interactive calculation of 'in vitro' solute fluxes, uptakes and accumulations in studies of intestinal transport.

A new microcomputer program for interactive comparisons, analysis and calculation of in vitro solute transepithelial fluxes and nutrient uptakes and accumulations by intestinal tissues is described. The program is written in Microsoft GWBASIC for the widely distributed IBM-PC. Flux, uptake and accumulation values are obtained by computation from initial sequential data files and stored in sequential or random-orgaized files, depending on the specific process. Computed unidirectional fluxes are saved together with their associate electrical variables. The program calculates univariate statistics for unidirectional and net fluxes, and allows comparisons between selected groups of experiments by using the Student's t-test. An homocedasticity test is also provided. Active uptake or accumulations of solutes are calculated by substracting the predicted diffusive values at a determined concentration to total uptake or accumulation and from this, kinetic parameters are computed. The program was designed to be user-friendly and includes several functions to permit the user to manage and examine stored data. Examples of outputs illustrate applications of the program.

Animals↗
PubMed1993

MULTPERM: a computer package for the analysis of multivariate data using permutation procedures.

MULTPERM is a user-friendly C program using an exact permutation test for comparing groups when the data involve one or more response variables. The program computes the average within group distance based on a generalized distance function. Statistical significance of group differences is assessed by comparing the average distance for the observed data to the distribution of distances generated by all permutations of subjects to groups. This procedure is nonparametric and is especially appropriate if the assumptions underlying more traditional methods are not satisfied. The program was developed for personal computers and compiled using Borland's Turbo C 2.0. It should be easily ported to other platforms. An approximate test based on the beta distribution is incorporated for large samples.

Child↗