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PubMed2006

A study of hearing aid gain functions based on a nonlinear nonlocal feedforward cochlea model.

A model based sound amplification method is proposed and studied to enhance the ability of the hearing impaired. The model consists of mechanical equations on basilar membrane and outer hair cell (OHC). The OHC is described by a nonlinear nonlocal feedforward model. In addition, a perceptive correction is defined to account for the lumped effect of higher level auditory processing, motivated by the intelligibility function of the hearing impaired. The gain functions are computed by matching the impaired model output to the perceptively weighted normal output, and qualitative agreement is achieved with NAL-NL1 prescription on clean signals. For noisy signals, an adaptive gain strategy is proposed based on the signal to noise ratios (SNR) computed by the model. The adaptive gain functions provide less gain as SNRs decrease so that the intelligibility can be higher with the adaptivity.

Basilar Membrane↗
PubMed1998

DNA computing on surfaces: encoding information at the single base level.

The feasibility of encoding a bit (0 or 1) of information for DNA-based computations at the single nucleotide level is evaluated, particularly with regard to the efficiency and specificity of hybridization discrimination. Hybridization experiments are performed on addressed arrays of 32 (2(5)) distinct oligonucleotides immobilized on chemically modified glass and gold surfaces with information encoded in a binary (base 2) format. Similar results are obtained on both glass and gold surfaces and the results are generally consistent with thermodynamic calculations of matched and mismatched duplex stabilities. It is found that under the conditions required to obtain single nucleotide specificity in the hybridization process, hybridization efficiency is low, compromising the utility of single nucleotide encoding for DNA computing applications in the absence of some additional mechanism for increasing specificity. Several methods are suggested to provide such increased discrimination.

Base Composition↗
PubMed1994

Calculation of the molecular weight of proteins from electrophoretic and gel exclusion chromatographic experiments.

The molecular weights of proteins or protein subunits are frequently estimated from the electrophoretic mobility in the presence of sodium dodecyl sulphate, or from the elution volume in gel filtration chromatography. Using a series of standards of known size, a calibration curve is prepared which often yields a straight line in a semilogarithmic plot; interpolation from this line then gives the size of the sample. While this method is simple to apply, it does not give any estimate of the accuracy of the determined size. Furthermore there is no objective criterion for deciding if the calibration curve is linear, or a procedure for dealing with non-linear calibration curves. Here I report a method and a computer program which uses appropriate statistical methods to select the best straight or curved calibration line. The size of the unknown is then interpolated and an estimate or the error in this value is calculated.

Calibration↗
PubMed1990

[Study on the estimation theory of genetic parameters--the estimation method when the parents were relative].

By decomposing the expected mean squares in variance analysis, the estimation methods of genetic parameters are suggested in sib analysis when the parents of the sibs are relatives. Two estimation examples are also given. The results indicate that the estimation values are greater than those estimated by supposing that the parents are not relatives. The closer relative the parents are, the bigger the biased would be. The computer programme PARESTH and PARESTF made it easy to apply the methods. Furthermore, the methods can also be used in variance analysis when the relationships between the levels of each factors are determined.

Analysis of Variance↗
PubMed1993

Testing random number generators for Monte Carlo applications.

Central to any system for modelling radiation transport phenomena using Monte Carlo techniques is the method by which pseudo random numbers are generated. This method is commonly referred to as the Random Number Generator (RNG). It is usually a computer implemented mathematical algorithm which produces a series of numbers uniformly distributed on the interval [0,1). If this series satisfies certain statistical tests for randomness, then for practical purposes the pseudo random numbers in the series can be considered to be random. Tests of this nature are important not only for new RNGs but also to test the implementation of known RNG algorithms in different computer environments. Six RNGs have been tested using six statistical tests and one visual test. The statistical tests are the moments, frequency (digit and number), serial, gap, and poker tests. The visual test is a simple two dimensional ordered pair display. In addition the RNGs have been tested in a specific Monte Carlo application. This type of test is often overlooked, however it is important that in addition to satisfactory performance in statistical tests, the RNG be able to perform effectively in the applications of interest. The RNGs tested here are based on a variety of algorithms, including multiplicative and linear congruential, lagged Fibonacci, and combination arithmetic and lagged Fibonacci. The effect of the Bays-Durham shuffling algorithm on the output of a known "bad" RNG has also been investigated.

Algorithms↗
PubMed1993

Comparison of the crystal structures of genetically engineered human manganese superoxide dismutase and manganese superoxide dismutase from Thermus thermophilus: differences in dimer-dimer interaction.

The three-dimensional X-ray structure of a recombinant human mitochondrial manganese superoxide dismutase (MnSOD) (chain length 198 residues) was determined by the method of molecular replacement using the related structure of MnSOD from Thermus thermophilus as a search model. This tetrameric human MnSOD crystallizes in space group P2(1)2(1)2 with a dimer in the asymmetric unit (Wagner, U.G., Werber, M.M., Beck, Y., Hartman, J.R., Frolow, F., & Sussman, J.L., 1989, J. Mol. Biol. 206, 787-788). Refinement of the protein structure (3,148 atoms with Mn and no solvents), with restraints maintaining noncrystallographic symmetry, converged at an R-factor of 0.207 using all data from 8.0 to 3.2 A resolution and group thermal parameters. The monomer-monomer interactions typical of bacterial Fe- and Mn-containing SODs are retained in the human enzyme, but the dimer-dimer interactions that form the tetramer are very different from those found in the structure of MnSOD from T. thermophilus. In human MnSOD one of the dimers is rotated by 84 degrees relative to its equivalent in the thermophile enzyme. As a result the monomers are arranged in an approximately tetrahedral array, the dimer-dimer packing is more intimate than observed in the bacterial MnSOD from T. thermophilus, and the dimers interdigitate. The metal-ligand interactions, determined by refinement and verified by computation of omit maps, are identical to those observed in T. thermophilus MnSOD.

Amino Acid Sequence↗
PubMed1991

A method of non-parametric back-projection and its application to AIDS data.

The method of back-projection has been used to estimate the unobserved past incidence of infection with the human immunodeficiency virus (HIV) and to obtain projections of future AIDS incidence. Here a new approach to back-projection, which avoids parametric assumptions about the form of the HIV infection intensity, is described. This approach gives the data greater opportunity to determine the shape of the estimated intensity function. The method is based on a modification of an EM algorithm for maximum likelihood estimation that incorporates smoothing of the estimated parameters. It is easy to implement on a computer because the computations are based on explicit formulae. The method is illustrated with applications to AIDS data from Australia, U.S.A. and Japanese haemophiliacs.

Acquired Immunodeficiency Syndrome↗
PubMed1990

A macro-driven Lotus 1-2-3 template for calculating and plotting receiver-operator characteristic curves for clinical laboratory tests.

Receiver-operator characteristic (ROC) curve analysis has become an accepted method of evaluating the efficiency of clinical laboratory tests. The calculations necessary to plot such curves are not difficult, but are repetitive and time consuming. Such calculations are easily done by computers. The availability, ease of use and graphics capabilities of spreadsheet programs such as Lotus 1-2-3 lend themselves to these applications. In this article, we describe such an application.

Clinical Laboratory Techniques↗
PubMed1989

Assessment of autonomic response by broad-band respiration.

We present a technique for introducing broad-band respiratory perturbations so that the response characteristics of the autonomic nervous system can be determined noninvasively over a wide range of physiologically relevant frequencies. A subject's respiratory bandwidth was broadened by breathing on cue to a sequence of audible tones spaced by Poisson intervals. The transfer function between the respiratory input and the resulting instantaneous heart rate was then computed using spectral analysis techniques. Results using this method are comparable to those found using traditional techniques, but are obtained with an economy of data collection.

Autonomic Nervous System↗
PubMed1994

[Rapid temperature measurement by calculating the final temperature within the response time].

For the early detection of an epidemic among animals in mass production, rapid information about the temperature of the animals is important. The response time of conventional thermometers is too long to permit rapid measurement. For adequate accuracy the measuring time required is about five times the response time. Using a microcomputer and regression computation, measurement of the final temperature can be effected within the period of a single response time. In addition, several thousand data can be stored for evaluation at a later date.

Animal Husbandry↗
PubMedDate not supplied

[Statistico-mathematical appraisal of the length of the pretherapeutic interval in the prognosis of tubercular meningitis in children].

The data obtained concerning the two main parameters for the prognosis of tuberculous meningitis: onset-admission interval, assessed anamnestically and electtoencephalogram performed on admission, were processed mathematically by computer. The EEG is a more reliable parameter for assessing the gravity of the lesions on admission that the anammestic data regarding the onset, at a signficance threshold of 10.48% as against 5.23%. For 11.3 days there was a close correspondence between the two parameters, after which the onset-admission variable became aleatory, the only objective index of gravity being the EEG. Statistico-mathematical processing increases the objectivity and precision of the prognosis.

Adolescent↗
PubMed1989

Systematic procedure for indexing HOLZ lines in convergent beam electron diffraction patterns of cubic crystal.

This article has been written for experimenters who are beginning to work with convergent beam electron diffraction patterns (CBED). The indexing of the higher-order Laue zone (HOLZ) lines inside the central spot of a CBED pattern is the first step towards studying variations in lattice parameter and three-dimensional (3D) symmetry. To index the HOLZ lines one must construct and index the HOLZ, find its interplanar spacing and the location of its projection on the zero order Laüe zone (ZOLZ) for a given zone axis, and finally find the radius of the HOLZ ring. A computer program has been developed to perform all these tasks for cubic crystals and is very useful, especially when one varies parameters such as operating voltage, zone axis, lattice parameter, and crystalline structure.

Crystallography↗
PubMed2001

Numerical bifurcation analysis of delay differential equations arising from physiological modeling.

This paper has a dual purpose. First, we describe numerical methods for continuation and bifurcation analysis of steady state solutions and periodic solutions of systems of delay differential equations with an arbitrary number of fixed, discrete delays. Second, we demonstrate how these methods can be used to obtain insight into complex biological regulatory systems in which interactions occur with time delays: for this, we consider a system of two equations for the plasma glucose and insulin concentrations in a diabetic patient subject to a system of external assistance. The model has two delays: the technological delay of the external system, and the physiological delay of the patient's liver. We compute stability of the steady state solution as a function of two parameters, compare with analytical results and compute several branches of periodic solutions and their stability. These numerical results allow to infer two categories of diabetic patients for which the external system has different efficiency.

Blood Glucose↗
PubMed1987

EGTA.

A method is described to compute the free calcium concentration in a solution buffered by EGTA. The effects of solution pH and [Mg] are fully taken into account. A sample program in the C programming language is described.

Calcium↗
PubMed1990

MIC-III--an integrated software package to support experiments using the radioactive microsphere technique.

MIC-III is a versatile program system to support gamma spectrometry data management and data collection for experiments using the radioactive microsphere technique. It is mainly written in PASCAL and running on a minicomputer. Hierarchical organ dissection schemes are used for unique classification and identification of samples. For each series of experiments, up to 12 different nuclides and up to 20 different organ dissection schemes can be handled simultaneously. Sample weights are collected on-line and sample radioactivities are measured automatically by gamma spectrometry under process control. The spectra with a resolution of 1022 channels are analyzed using a modified linear regression technique and a strategy to compensate for global spectrum shifts. The spectrum deconvolution algorithm was evaluated by calculating the recovery indices for known nuclide mixtures and compared to the stripping method, matrix method and a linear regression technique using window counts. Recovery values produced by MIC-III are better balanced than those of the other methods. MIC-III showed the smallest dispersion of the recovery index and exhibited least error accumulation in case of spectrum shift. MIC-III computes regional blood flow and arterio-venous shunt, and provides interfaces to customized programs or statistical software packages for further analysis. It has successfully been employed in more than 140 experiments.

Animals↗
PubMed1991

Randomization tests: statistics for experimenters.

Randomization (permutation) tests free the experimenter from the constraints of random sampling, a known error distribution and equal variances, to give a direct answer to the question "how likely is such a large (or small) result if the applied treatments had no effect?" The "result" may be the difference in mean responses, a correlation coefficient or any other value of interest. A randomization test is not a different statistical test but a different, and always valid, method of determining statistical significance. The familiar t-test and F-test can be carried out by data permutation without any parametric assumptions being fulfilled. A particular advantage of this method is that unbalanced designs and missing values are easily accommodated. Even with only a small number of subjects the number of permutations will be large and a computer is necessary if the randomization test is to be of practical value. To make this method of determining statistical significance generally available an interactive microcomputer program, forming a comprehensive package for the design and analysis of experiments, has been prepared.

Mathematical Computing↗
PubMed2004

Equilibrium concentrations for pyruvate dehydrogenase and the citric acid cycle at specified concentrations of certain coenzymes.

It is of interest to calculate equilibrium compositions of systems of biochemical reactions at specified concentrations of coenzymes because these reactants tend to be in steady states. Thermodynamic calculations under these conditions require the definition of a further transformed Gibbs energy G" by use of a Legendre transform. These calculations are applied to the pyruvate dehydrogenase reaction plus the citric acid cycle, but steady-state concentrations of CoA, acetyl-CoA and succinyl-CoA cannot be specified because they are involved in the conservation of carbon atoms. These calculations require the use of linear algebra to obtain further transformed Gibbs energies of formation of reactants and computer programs to calculate equilibrium compositions. At specified temperature, pH, ionic strength and specified concentrations of several coenzymes, the equilibrium composition depends on the specified concentrations of the coenzymes and the initial amounts of reactants.

Citric Acid Cycle↗

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