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PubMed1990

Maximum entropy image reconstruction of DNA sequencing gel autoradiographs.

DNA sequencing gel autoradiographs become increasingly difficult to read as one moves up the gel, due to crowding and overlapping of the bands. Maximum entropy image reconstructions of the autoradiograph improve the ease with which crowded sequence data can be read, and extend the region of the gel in which reading is possible. Superior reconstructions are obtained by using nonuniform models based on the initial reconstructions.

Autoradiography↗

PubMed2001

Determination of the electron affinities of alpha- and beta-naphthyl radicals using the kinetic method with full entropy analysis. The C-H bond dissociation energies of naphthalene.

The C - H bond dissociation energies for naphthalene were determined using a negative ion thermochemical cycle involving the gas-phase acidity (Delta H (acid)) and electron affinity (EA) for both the alpha- and beta-positions. The gas-phase acidity of the naphthalene alpha- and beta-positions and the EAs of the alpha- and beta-naphthyl radicals were measured in the gas phase in a flowing after glow-triple quadrupole apparatus. A variation of the Cooks kinetic method was used to measure the EAs of the naphthyl radicals by collision-induced dissociation of the corresponding alpha- and beta-naphthylsulfinate adducts formed by reactions in the flow tube portion of the instrument. Calibration references included both pi and sigma radicals, and full entropy analysis was performed over a series of calibration curves measured at collision energies ranging from 3.5 to 8 eV (center-of-mass). The measured EAs are 33.0 +/- 1.4 and 31.4 +/- 1.0 kcal mol(-1) (1 kcal = 4.184 kJ) for the alpha- and beta-naphthyl radicals, respectively. The gas-phase acidities for naphthalene were measured by the DePuy silane cleavage method, which utilizes the relative abundances of aryldimethylsiloxides and trimethylsiloxide that result from competitive cleavages from a proposed penta coordinate hydroxysiliconate intermediate. The measured acidities are 394.0 +/- 5.0 and 397.6 +/- 4.8 kcal mol(-1) for the alpha- and beta- positions, respectively. The C - H bond dissociation energies calculated from the thermochemical cycle are 113.4 +/- 5.2 and 115.4 +/- 4.9 kcal mol(-1) for the alpha- and beta-positions, respectively. These energies are, to within experimental error, indistinguishable and are approximately the same as the first bond dissociation energy for benzene.

Journal Article↗

PubMed1987

Edited 31P brain spectra using maximum entropy data processing.

Strategies for estimating peak areas in 31P brain spectra are discussed, and the widespread convolution difference method is analyzed. The Skilling maximum entropy method (MEM) algorithm is applied to in vivo spectra and provides an estimate of the spectrum that is operator-independent, although at the expense of some negative bias. It may be possible to overcome this bias.

Animals↗

PubMed1988

Maximum entropy and 2DFT NMR images.

A comparison between contrast and signal-to-noise ratio (SNR), as obtained by both maximum entropy (ME) and 2DFT reconstruction, is reported for NMR images. Our results show that in the ME elaboration the contrast and SNR are generally increased with respect to the 2DFT elaboration. The magnitude of such an increase depends on the ME statistical parameter and also, quite strongly, on the values of contrast and SNR of the 2DFT image.

Magnetic Resonance Imaging↗

PubMed2006

Beyond the g-factor limit in sensitivity encoding using joint histogram entropy.

The maximum practical speed-up that can be achieved using parallel imaging methods is widely accepted to be limited by g-factor noise. An approximate expression for the g-factor noise as a function of the principal eigenvector of the inverse sensitivity matrix is derived. This formulation allows g-factor enhanced noise to be reduced by a constrained optimization procedure with joint image histogram entropy between a reference image and a SENSE image as an image quality metric. The reference image does not need to have identical resolution or contrast. The reference image may also be used for coil calibration. The limits of the method are explored using simulated and real array coil data with high g-factor using a variety of contrast and resolution combinations. The method preserves image structure, contrast, and lesions even when these were not observable in the reference data. In all cases g-factor was dramatically reduced.

Brain Mapping↗

PubMed1996

On the entropy of protein folding.

The failure to appreciate that the hydration of polar groups is a major contribution to the entropy of protein unfolding has led to considerable underestimates for the loss of configurational freedom when a protein chain folds.

Bacterial Proteins↗

PubMed1993

The contribution of cross-links to protein stability: a normal mode analysis of the configurational entropy of the native state.

The vibrational entropy of native BPTI, with three disulfide bonds, was determined by use of normal mode calculations and compared with that of folded variants having either one less disulfide bond or lacking a peptide bond at the trypsin-reactive site. Favorable contributions to the free energy of 2.5-5.1 kcal/mol at 300 K were calculated for the reduction of disulfide bonds in the folded state, whereas no favorable contribution was found for the hydrolysis of the peptide bond cleaved by trypsin. This is on the order of the effect of disulfides in the unfolded state. The implications of these results for the stabilization of a folded protein by the introduction of cross-links are discussed.

Aprotinin↗

PubMed2000

Assessing the degree of association in groups of animals using the concept of entropy.

Nearest-neighbour analysis is commonly used to calculate indices of aggregation in groups of animals. It has several problems, however, including lack of data independence and, when studying groups of animals penned at high densities, the difficulty of determining a given individual's nearest neighbour. We describe an entropy-based method to assess the degree of association (or segregation) of groups of animals. We show that this method gives more information and is more sensitive than the nearest-neighbour technique. An example with a particular experimental situation (mixing groups of lambs) is presented. Copyright 2000 The Association for the Study of Animal Behaviour.

Journal Article↗

PubMed1997

Effect of Mixing Entropy on the Static Yield Stress of a Liquid Dispersion of Solid Particles: Comparison between Si3 N4 and Ca3 (PO4 )2 Aqueous Suspensions

Experimental measurements of the static yield stresses tau of silicon nitride (SN, Si3 N4 ) and alpha-tricalcium phosphate (TCP, alpha-Ca3 (PO4 )2 ) aqueous dispersions have been performed for different pH values of the liquid medium and, as a result, the two tau vs pH behaviors are quite different. In agreement with the DLVO theory, the static yield stress value for silicon nitride is maximal at the isoelectric point of the slurry (pHiep (SN) = 8.0 ± 0.1) and, for higher and/or lower suspension pH values, it decreases progressively. On the other hand, in tricalcium phosphate dispersed systems, the maximum value of tau is not observed at the isoelectric point (pHiep (TCP) = 6.7 ± 0.1) but two relative maximum values, taua and taub , are observed for two suspension pH values in the acid/basic environments, namely, for pH <> pHiep (TCP) . First, displacements of the pH from the isoelectric point in both environments are accompanied by an increase in tau; second, after the maximum tau values have been reached, the static yield stress decreases with the increase in the [H+ ]/[OH+ ] ions in the solution. It is shown that this phenomenon can be interpreted as an effect of the mixing entropy relative to the solid TCP aggregates, which is very sensitive to the suspension pH. Phenomenological and theoretical explanations are developed, respectively, by a heuristic recasting of the Hamaker expression for the London-van der Waals forces and by a relationship between the static yield stress and the number of solid aggregates; this relation is based on recently proposed methods for investigating the agglomeration/adsorption phenomena in a dispersed system.

Journal Article↗

PubMed1995

Calculation of relative binding free energies and configurational entropies: a structural and thermodynamic analysis of the nature of non-polar binding of thrombin inhibitors based on hirudin55-65.

Free energy calculations were carried out on a series of exosite-binding inhibitors of thrombin. These inhibitors are based on the C-terminal fragment of hirudin and have the sequence Phe-Glu-Glu-IleH59-Pro-Glu-Glu-Tyr- Leu, where the superscript over Ile indicates its relative position in the natural sequence of hirudin. In this study, the effect of replacing IleH59 with ten other non-polar amino acids was examined. Three preferred interaction sites for methyl/methylene groups for the various XaaH59 side-chains in the complex were identified from conformational search calculations. The corresponding thermodynamic changes were determined using a combination of systematic search and energy minimization in a manner that locates the local minima in the system and in the process simultaneously builds up the partition function. The free energy, internal energy and entropic contributions are readily calculated from the partition function. Very good agreement in the resulting relative binding free energies was obtained between theory and experiment. The calculations allowed us to dissect out the enthalpic, entropic and solvation contributions to delta delta G. The contribution from desolvation was found to be relatively weak. The binding of these non-polar side-chains to thrombin is found to be driven mainly by favorable protein-ligand interactions rather than by the desire for non-polar groups to be desolvated. We also find that the configurational entropy contributes about 0.48 kcal/mol (0.81 kappa T) in average for each torsional angle "frozen" in binding.

Algorithms↗

PubMed2001

Identification Model Based on the Maximum Information Entropy Principle.

A new theoretical approach to stimulus identification is proposed through a probabilistic multidimensional model based on the maximum information entropy principle. The approach enables us to derive the multidimensional scaling (MDS) choice model, without appealing to Luce's choice rule and without defining a similarity function. It also clarifies the relationship between the MDS choice model and the optimal version of the identification model based on Ashby's general recognition theory; it is shown theoretically that the identification model derived from the new approach includes these two models as special cases. Finally, as an application of our approach, a model of similarity judgment is proposed and compared with Ashby's extended similarity model. Copyright 2001 Academic Press.

Journal Article↗

PubMed1986

Maximum-entropy approximations of stochastic nonlinear transductions: an extension of the Wiener theory.

We consider the description of a nonlinear stochastic transduction in terms of its input/output distribution. We construct a sequence of approximating maximum-entropy estimates from a finite set of input/output observations. This procedure extends the Wiener theory to the analysis of nonlinear stochastic transducers and to the analysis of transducers with multiple outputs but an inaccessible input.

Animals↗

PubMed1991

Maximum entropy and drug absorption.

The application of maximum entropy to the calculation of drug absorption rates was introduced in an earlier paper. Here it is developed further, and the whole procedure is presented as a problem in scientific inference to be solved using Bayes' theorem. Blood samples do not need to be taken at equally spaced intervals, and no smoothing, interpolation, extrapolation, or other preprocessing of the data is necessary. The resulting input rate estimates are smooth and physiologically realistic, even with noisy data, and their accuracy is quantified. Derived quantities such as the proportion of the dose absorbed, and the mean and median absorption times, are also obtained, together with their error estimates. There are no arbitrarily valued parameters in the analysis, and no specific functional form, such as an exponential or polynomial, is assumed for the input rate functions.

Biological Availability↗

PubMed1987

Maximum entropy and its application to the calculation of drug absorption rates.

A new method is presented for calculating the rate at which a drug enters the bloodstream after dosing, given the concentration of the drug in blood at various times. The method is based on the principle of maximum entropy, which has not been applied previously to pharmacokinetic problems. The resulting input rate functions are smooth and physiologically realistic, free of spurious oscillations yet still showing small-scale structure where there is evidence for it in the data. Blood samples do not need to be taken at equal intervals, and no preliminary smoothing or interpolation of the data is required.

Acetaminophen↗

PubMed1993

Measurement of fetal movements using multichannel ultrasound pulsed Doppler: autorecognition of fetal movements by maximum entropy method.

Changes in fetal movements indicate biophysical conditions and functional development. The precise evaluation of fetal movements in clinical medicine requires the development of a continuous automated monitoring technique. A basic study of the measurement of fetal movements was carried out by modifying the Doppler ultrasound module of a cardiotocograph to produce low-frequency Doppler signals and five simultaneous outputs at various depths. These outputs represent displacement inside tissue at the various depths. Signal processing was executed on a 32-bit computer with a high-accuracy displacement estimation technique using the arctangent method. Results showed successful tracking of minute movements, such as fetal breathing movements (FBM), while rejecting other movements derived from maternal breathing etc. Using spectral analysis by the maximum entropy method (MEM), fetal movements were classified in three groups (FBM, fetal gross movements (FGM) and fetal heart movements (FHM), based on the character of their special peak frequencies. The order of movement recognition was first FGM, then FBM and lastly FHM. FBM were more successfully recognised by MEM than by conventional B-mode observation methods. Small body movements were difficult to recognise as FGM by MEM in some cases. Although further studies are required for clinical application, it appears that automated assessments of fetal movements should be possible with this technique.

Female↗

PubMed1992

Frequency domain analysis of highly amplified ECG on the basis of maximum entropy spectral estimation.

Recognition of patients with high risk for ventricular tachycardia (VT) or sudden cardiac death is of high clinical importance. We have investigated the efficiency of maximum entropy spectral estimation (MES) to detect such risk patients on the basis of highly amplified surface ECG. In comparison with the traditionally applied periodogram (fast Fourier transform), the MES produces sharper and more pronounced peaks in the power density spectrum (PS). The main problem is the influence of residual noise (after averaging), which often leads to additional components in the PS. To completely avoid this negative noise influence we developed a new algorithm, called the variance subtraction method. In a first clinical investigation 86 per cent of patients with myocardial infarction and ventricular tachycardia have shown frequency components above 80 Hz in the PS compared with healthy persons where no frequency components above this 80 Hz level could be detected.

Algorithms↗

PubMed1995

Deconvolution of STM images using entropy as a regularization functional.

The Maximum Entropy approach is applied to restore and sharpen scanning tunneling microscopy (STM) images with atomic resolution. Based on the STM theory of Tersoff and Hamann the process of data acquisition can be approximated by the convolution of a localised atomic density of states (i.e. narrow spots in the reconstruction) of the sample and a Gaussian resolution function which limits the resolution. In STM practice a good and robust estimation of the atomic core positions is necessary for different reasons, such as to be able to calculate the characteristics of the atomic lattice or to study non-periodicities.

Journal Article↗

PubMed1985

Entropy-driven polymerization of ribgrass virus protein.

Holmes ribgrass virus (HRV), because of serological results, is regarded as a distantly related strain of tobacco mosaic virus (TMV). HRV protein differs substantially in amino acid sequence from TMV protein, especially in that it contains one histidine residue and three methionine residues, compared to none of either for TMV protein. Ultracentrifugation and hydrogen ion titration data on HRV protein, similar to those obtained previously for the early stage polymerization of TMV and E66 proteins, demonstrated some similarities and more distinct differences from those of the other two proteins. The major similarities are that the early polymerization of HRV protein is entropy driven and the first major polymerized product is a 20 S component, presumably a double disk or two-turn helix, as in the case of the other proteins. The major differences are that the unpolymerized HRV protein sediments at 3 S rather than at the 4 S for the others; it is presumably a dimer of the polypeptide chain. The enthalpy of polymerization per mole of A protein, delta H*, is 18,400 cal for HRV protein, compared to about 30,000 for TMV protein. One mol of H+ ion/mol HRV A protein, compared to 1.5 for TMV and E66 proteins, is bound during polymerization to the 20 S state. Contrasted with the other proteins, very little if any electrical work contribution was detected for the HRV protein. A major difference was found in hydrogen ion titration. Unpolymerized HRV protein binds hydrogen ions significantly in the unpolymerized A protein state, unlike the A proteins from the other two viruses.

Hydrogen Bonding↗