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PubMed1982

Quantification, smoothing, and confidence limits for single-units' histograms.

In this article the relationships among firing rate, probability of firing and counts per bin are examined. It is suggested that PSTHs, autocorrelations and crosscorrelations of neuronal activity should all be expressed in units of firing rates (spikes/s), since the values obtained by such scaling are independent of bin size and of total time of measurement. A simple method for these histograms is described. Methods to compute confidence limits for PSTHs, autocorrelations and crosscorrelations are suggested. The computations are based on the null hypothesis that the spike train(s) is (are) the realization of (independent) Poisson-point process(es). The validity and the limitations of these computations methods, when applied to spike trains, are discussed. Methods to smooth out random fluctuation with little distortion of the histogram's shape are described. It is suggested that one can minimize the distortion of the histogram in the time-domain and in the frequency-domain by using a bell-shaped bin whose center point slides continuously along the histogram. The article aims at giving the potential user of the methods some insight for the meaning of the formulae. It describes in detail how the methods are applied in practice and illustrates each method by using real data from single-unit recordings.

Animals↗
PubMed2000

Optimization methods in chromatography and capillary electrophoresis.

Many methods have been developed in order to optimize the parameters of interest in either chromatography or capillary electrophoresis. In chemometric approaches experimental measurements are performed in such a way that all factors vary together. An objective function is utilized in which the analyst introduces the desired criteria (selectivity, resolution, time of analysis). Simplex methods and overlapping resolution maps are declining. Factorial designs and central composite designs are more and more popular in electrodriven capillary separations since the number of parameters to master is much larger than in either GC or LC. The use of artificial neural networks is increasing. The advantage of chemometrics tools is that no explicit models are required, conversely the number of experiments to perform may be high and boundaries of the domain are not straightforward to draw and the approach does more than is required. When models are available optimization is easier to perform by regression methods. Computer assisted methods in RPLC are readily available and work well but are still in infancy in CE. Linear solvation energy relationships seem a very valuable tool but estimates of coefficients still require many experiments.

Chromatography, Liquid↗
PubMed2002

Future directions in protein function prediction.

New directions in computational methods for the prediction of protein function are discussed. THEMATICS, a method for the location and characterization of the active sites of enzymes, is featured. THEMATICS, for Theoretical Microscopic Titration Curves, is based on well-established finite-difference Poisson-Boltzmann methods for computing the electric field function of a protein. THEMATICS requires only the structure of the subject protein and thus may be applied to proteins that bear no similarity in structure or sequence to any previously characterized protein. The unique features of catalytic sites in proteins are discussed. Discussion of the chemical basis for the predictive powers of THEMATICS is featured in this paper. Some results are given for three illustrative examples: HIV-1 protease, human apurinic/apyrimidinic endonuclease, and human adenosine kinase.

Adenosine Kinase↗
PubMed2002

Estimation of the net acid load of the diet of ancestral preagricultural Homo sapiens and their hominid ancestors.

BACKGROUND: Natural selection has had < 1% of hominid evolutionary time to eliminate the inevitable maladaptations consequent to the profound transformation of the human diet resulting from the inventions of agriculture and animal husbandry. OBJECTIVE: The objective was to estimate the net systemic load of acid (net endogenous acid production; NEAP) from retrojected ancestral preagricultural diets and to compare it with that of contemporary diets, which are characterized by an imbalance of nutrient precursors of hydrogen and bicarbonate ions that induces a lifelong, low-grade, pathogenically significant systemic metabolic acidosis. DESIGN: Using established computational methods, we computed NEAP for a large number of retrojected ancestral preagricultural diets and compared them with computed and measured values for typical American diets. RESULTS: The mean (+/- SD) NEAP for 159 retrojected preagricultural diets was -88 +/- 82 mEq/d; 87% were net base-producing. The computational model predicted NEAP for the average American diet (as recorded in the third National Health and Nutrition Examination Survey) as 48 mEq/d, within a few percentage points of published measured values for free-living Americans; the model, therefore, was not biased toward generating negative NEAP values. The historical shift from negative to positive NEAP was accounted for by the displacement of high-bicarbonate-yielding plant foods in the ancestral diet by cereal grains and energy-dense, nutrient-poor foods in the contemporary diet-neither of which are net base-producing. CONCLUSIONS: The findings suggest that diet-induced metabolic acidosis and its sequelae in humans eating contemporary diets reflect a mismatch between the nutrient composition of the diet and genetically determined nutritional requirements for optimal systemic acid-base status.

Acid-Base Equilibrium↗
PubMed2005

Computed tomography demonstrates short axial globe length in cases with idiopathic intracranial hypertension.

BACKGROUND: Cases with idiopathic intracranial hypertension (IIH) have been anecdotally found to demonstrate relatively short axial lengths on ultrasound A-scans. This finding has not been rigorously documented. We therefore systematically investigated globe shape in these cases using computed tomography. METHODS: Computed tomographic 0.625-mm sections of 10 cases with IIH and 10 control subjects were reformatted on a workstation. Globe lengths and widths were measured from axial reformats. Globe lengths and heights were measured from oblique sagittal reformats. Two masked observers took all the measurements. RESULTS: The mean axial lengths of the globes of cases with IIH were significantly shorter than those of controls (t test for independent samples, P<0.001). Both observers also found globe height to be significantly greater than globe length in oblique sagittal sections of cases with IIH compared with control subjects (Mann-Whitney U tests, P<0.01). The difference between length and width in axial sections was not different between cases with IIH and control subjects. Using a critical cutoff of 0.6-mm difference between globe height and length in oblique sagittal sections returned a sensitivity of 0.75 and a specificity of 0.75 for IIH detection from both right and left eyes. CONCLUSIONS: There are significant differences in globe shape and axial length between cases with IIH and control subjects. The differences in globe shape manifest significantly only in oblique sagittal sections. This imaging sign could be a useful marker for subclinical IIH.

Adult↗
PubMed1983

Pedigree information to predict genetic merit for type of Holstein bulls.

Three methods of computing predicted differences for type were compared for accuracy of pedigree evaluation of young Holstein bulls. Computing methods were herdmate comparison, herdmate comparison adjusted for genetic merit of herdmates, and best linear unbiased prediction. Evaluations by progeny test were available for 1298, 1293, and 1088 sons and sires for herdmate comparison, herdmate comparison adjusted for cow index of herdmates, and best linear unbiased prediction with fewer sons having more complete pedigrees. Ten regression models were used to predict eventual progeny test evaluations of sons from combinations of evaluations for sires, dams, and maternal grandsires. Negative intercepts and smaller than expected regression coefficients suggested bias in evaluations by all methods but much less bias with best linear unbiased prediction than with other methods. Multiple correlations generally were largest for equations using evaluations by best linear unbiased prediction.

Animals↗
PubMed2004

Eulerian method for computing multivalued solutions of the Euler-Poisson equations and applications to wave breaking in klystrons.

We provide methods of computing multivalued solutions to the Euler-Poisson system and test them in the context of a klystron amplifier. An Eulerian formulation capable of computing multivalued solutions is derived from a kinetic description of the Euler-Poisson system and a moment closure. The system of the moment equations may be closed due to the special structure of the solution in phase space. The Eulerian moment equations are computed for a velocity modulated electron beam, which has been shown by prior Lagrangian theories to break in a finite time and form multivalued solutions. The results of the Eulerian moment equations are compared to direct computation of the kinetic equations and a Lagrangian method also developed in the paper. We use the Lagrangian formulation for the explicit computation of wave breaking time and location for typical velocity modulation boundary conditions.

Journal Article↗
PubMed1986

A fully-automated computer-assisted method of CT brain scan analysis for the measurement of cerebrospinal fluid spaces and brain absorption density.

Computer-assisted methods of CT brain scan analysis offer considerable advantages over visual inspection, particularly in research; and several semi-automated methods are currently available. A new computer-assisted program is presented which provides fully automated processing of CT brain scans, depending on "anatomical knowledge" of where cerebrospinal fluid (CSF)-containing spaces are likely to lie. After identifying these regions of interest quantitative estimates are then provided of CSF content in each slice in cisterns, ventricles, Sylvian fissure and interhemispheric fissure. Separate measures are also provided of mean brain density in each slice. These estimates can be summated to provide total ventricular and total brain volumes. The program shows a high correlation with measures derived from mechanical planimetry and visual grading procedures, also when tested against a phantom brain of known ventricular volume. The advantages and limitations of the present program are discussed.

Absorption↗
PubMed2001

Method for computing the anisotropy of the solid-liquid interfacial free energy.

We present a method to compute accurately the weak anisotropy of the solid-liquid interfacial free energy, a parameter which influences dendritic evolution in materials with atomically rough interfaces. The method is based on monitoring interfacial fluctuations during molecular dynamics simulation and extracting the interfacial stiffness which is an order of magnitude more anisotropic than the interfacial free energy. We present results for pure Ni with interatomic potentials derived from the embedded atom method.

Journal Article↗
PubMed1984

On computer simulation methods used to study models of two-component lipid bilayers.

We show that the use of a computer simulation method introduced to calculate the equilibrium thermodynamic properties of a model of a two-component lipid bilayer membrane [Freire, E., & Snyder, B. (1980) Biochemistry 19, 88-94] is incorrect. This is done by comparing the method to that of Metropolis, which has been proven to generate equilibrium distribution of that model, and by showing that back-processes have been omitted in the implicit master equation of Freire and Snyder. We have illustrated this explicitly by first generating distributions according to the method of Freire and Snyder and then allowing the system to relax via the Kawasaki method, which uses the technique of Metropolis. We show that relaxation to a different distribution occurs. We also remark that the cluster distributions generated by the Freire-Snyder method are substantially different from those occurring in equilibrium distributions. Thus, conclusions about equilibrium thermodynamic properties such as specific heats and transition enthalpies or about transport properties or cluster properties at equilibrium cannot be drawn from the results obtained by using this method. Finally, we point out that the method of Freire and Snyder is appropriate to so-called aggregation models, which have been used to study irreversible growth; and we suggest biological systems that might be simulated by their method.

Computers↗
PubMed1993

Method for computing the oxidation of two 13C-substrates ingested simultaneously during exercise.

This study presents a method for computing the respective amounts of two simultaneously ingested exogenous substrates (A and B) that are oxidized during a period of prolonged exercise by use of 13C labeling. This method is based on the observation that the total volume of 13CO2 produced (V13CO2tot) is the sum of 1) V13CO2 arising from the oxidation of endogenous substrates (V13CO2endo), 2) V13CO2 arising from the oxidation of substrate A (V13CO2A), and 3) V13CO2 arising from the oxidation of substrate B (V13CO2B). The equation, V13CO2tot = V13CO2endo+V13CO2A+V13CO2B, with three unknowns, can be solved from the results of three experiments conducted under the same conditions but with at least two values for the isotopic composition of A and B. This method has been used on five healthy male subjects to compute the amounts of glucose and fructose oxidized when a mixture of 15 g of glucose and 15 g of fructose is ingested (in 300 ml of water) over 60 min of cycle ergometer exercise at 65% of maximal O2 uptake. Results from three experiments indicated that 9.8 +/- 3.1 and 5.7 +/- 2.1 g of glucose and fructose, respectively, were oxidized. The total amount of exogenous carbohydrates oxidized (15.5 +/- 4.3 g) is in agreement with the oxidation rates of exogenous glucose computed in similar conditions when 30 g of glucose were ingested (13 g; Péronnet et al. Med. Sci. Sports Exercise 25: 297-302, 1993). The difference between the oxidation rates of exogenous glucose and fructose is also in line with data from the literature.

Adult↗
PubMed1990

Improved method for computing potential doubling time from flow cytometric data.

Relative movement methods use the timed progression of the mean fluorescence of cells which have been labeled with monoclonal antibodies against bromodeoxyuridine and displayed with bivariate flow cytometry according to DNA and label content to compute duration of DNA synthesis, TS. The relative movement is the difference of the mean DNA fluorescence of the labeled undivided cells from the G1 channel relative to the difference between the G1 and G2M channels. In this communication, we show how to extend this method to compute the potential doubling time, Tpot, the time required for a population of cells to double, given quiescent cells but no cell loss. A quantity v is introduced that is a function of the fraction of labeled divided cells and the fraction of labeled undivided cells. We show that v is independent of time and is equal to ln(2)Ts/Tpot so that Tpot (equal to ln(2)Ts/v) can be directly found from the information available in computing the relative movement. The method is applied to Chinese hamster ovary cells to demonstrate its utility.

Animals↗
PubMedDate not supplied

An algorithmic synthesis of the deterministic and stochastic paradigms via computer intensive methods.

In this paper, an approach to synthesizing the deterministic and stochastic paradigms, via computer intensive methods, is presented within the framework of a stochastic model of a HIV/AIDS epidemic in a population of homosexuals. Because of dependence among members of a population, the problem of determining threshold conditions was approached by systematically embedding a system of differential equations in a stochastic process and determining if the Jacobian matrix of this system is stable or not stable, when evaluated at a disease free equilibrium. It has been shown in numerous Monte Carlo simulation experiments that if this matrix is not stable, then an epidemic will develop in a population with positive probability, following the introduction of infectives into a population of susceptibles. This technique was used to search for points in the parameter space such that an epidemic would develop in a population of susceptibles, following the entrance of one or more infectious recruits during any time interval with small probability. Such recurrent rare events are of interest in the studying the emergence of new diseases, involving the transmission of a virus from a species that has evolved resistance to it to another species that lacks resistance.

Acquired Immunodeficiency Syndrome↗
PubMed2002

Why do we need so many chemical similarity search methods?

Computational tools to search chemical structure databases are essential to finding leads early in a drug discovery project. Similarity methods are among the most diverse and most useful. We will present some lessons we have gathered over many years experience with in-house methods on several therapeutic problems. The effectiveness of any similarity method can vary greatly from one biological activity to another in a way that is difficult to predict. Also, any two methods tend to select different subsets of actives from a database, so it is advisable to use several search methods where possible.

Decision Support Techniques↗
PubMed1978

A computer assisted method for the determination of restriction enzyme recognifion sites.

A computer program has been developed which aids in the determination of restriction enzyme recognition sequences. This is achieved by cleaving DNAs of known sequence with a restriction endonuclease and comparing the fragmentation pattern with a computer-generated set of patterns. The feasibility of this approach has been tested using fragmentation patterns of 0X174 DNA produced by enzymes of both known and unknown specificity. Recognition sequences are predicted for two restriction endonucleases (BbvI and SfaNI) using this method. In addition, recognition sequences are predicted for two other new enzymes (PvuI and MstI) using another computer-assisted method.

Base Sequence↗
PubMed2002

Theoretical study of amplitude and phase filtering of guided waves.

The design of integrated optics filters by use of refinement software based on the Abelès thin-film computation method and the film mode matching method is studied. The results obtained with the two computation methods are compared. Good agreement is obtained provided that the fill factor of the guided mode in the component is high and that modal losses between waveguide sections are simulated by absorption with the Abelès computation method. Integrated optics devices that manage either the amplitude of guided waves such as a dense wavelength division multiplexing narrow-bandpass filter and a gain-flattening filter or the phase of guided waves such as a broadband dispersion compensator are

Journal Article↗
PubMed1990

Computational simulation method of intraluminal velocity profile proved by laser Doppler velocimeter.

Measurement of the intraluminal velocity profile within an artery may provide insight into predicting the prognosis of arterial reconstruction. To confirm the results of the computer simulation method a laser Doppler velocimeter using an optical fiber was applied to canine femoral arteries with good or poor runoff, and the intraluminal velocity profile was measured directly. Under normal flow conditions, remarkable fluctuation was obtained at the layer adjacent to the wall, whereas under poor runoff conditions, stagnation of flow was seen at the layer adjacent to the wall. These results showed that our computational simulation method which calculates the intraluminal velocity profile was a reliable, valid method of on-line analysis of the intraluminal velocity profile.

Animals↗