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Results for “Entropy”

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At least 433 records · Page 24Linked to original sources

PubMed2005

CD8 T-cell responses in early HIV-1 infection are skewed towards high entropy peptides.

OBJECTIVE: To understand the mechanisms underlying the differential targeting of T-cell responses during HIV-1 disease progression. DESIGN: We performed a cross-sectional analysis of HIV specific CD8 T-cell responses in peripheral blood mononuclear cells (PBMC) obtained from 21 subjects with well characterized acute or early infection and 88 subjects with chronic HIV-1 infection. We also performed a longitudinal analysis of T-cell responses in five early infected subjects one of whom was studied extensively over a 4-year-period. METHODS: PBMC were stimulated with pools of peptides encompassing all of the HIV-1 proteins in an interferon-gamma ELISpot assay. A mean entropy score was calculated for each peptide in the HIV-1 genome. RESULTS: The early infected group preferentially targeted variable peptides with higher entropy while responses towards more conserved peptides with lower entropy predominated in the group with chronic infection. In five early infected subjects followed longitudinally, responses to variable proteins declined while those to conserved proteins increased over time. In the subject who was followed for 4 years, epitopes in Vif and Nef were targeted early and escape occurred in three of these four epitopes. During the chronic phase of his infection, the early responses waned with an associated increase in breadth of T-cell responses mainly to Gag and Pol epitopes. CONCLUSION: Taken together, these data demonstrate that HIV-specific CD8 T cells are directed preferentially to the variable peptides in early infection but diminish in frequency during chronic disease, in large part due to cytotoxic T lymphocyte escape.

Acute Disease↗

PubMed2003

A block coding method that leads to significantly lower entropy values for the proteins and coding sections of Haemophilus influenzae.

A simple statistical block code in combination with the LZW-based compression utilities gzip and compress has been found to increase by a significant amount the level of compression possible for the proteins encoded in Haemophilus influenzae, the first fully sequenced genome. The method yields an entropy value of 3.665 bits per symbol (bps), which is 0.657 bps below the maximum of 4.322 bps and an improvement of 0.452 bps over the best known to date of 4.118 bps using Matsumoto, Sadakane, and Imai's lza-CTW algorithm. Calculations based on a compact inverse genetic code show that the genome has a maximum entropy of 1.757 bps for the coding regions, with a possibly lower actual entropy. These results hint at the existence of hitherto unexplored redundancies that do not show up in Markov models and are indicative of more internal structure than suspected in both the protein and the genome.

Algorithms↗

PubMedDate not supplied

[Entropy in the assessment of diagnostic importance of changes in urine].

Entropy, as the measure of that part of the heat or energy of a system which is not available to perform work, is suitable for application in numerous medical investigations. It is determined in regard to two states of the system: states above and below the examined level of studied parameters. By application of entropy function in completed examinations sometimes it is possible to gain additional conclusions or to confirm already existing. This method of entropy determination was performed in final quantitative bacteriological and cytological examinations of samples gained from the first morning urine of 314 persons without symptoms or signs of urinary tract infection, 422 patients with symptoms and signs of bacterial infection and 31 deceased persons with autopsy confirmed pyelonephritis. Gathered results confirm the diagnostic and prognostic significance of quantitative bacteriological and cytological urine examination. However, by examination of these findings in patients with pyelonephritis, as well as the nature of bacteria, it can be concluded that the lowest of bacteriuria is between 10(3) and 10(4) in 1 ml of urine.

Entropy↗

PubMed1998

Association of prognosis in surgically treated lung cancer patients with cytometric, histometric and ligand histochemical properties: with an emphasis on structural entropy.

OBJECTIVE: To explore new tumor features for refined category formation that permits the tailoring of individualized treatment schemes in lung cancer. STUDY DESIGN: Survival data on patients from six independent studies on cases with surgically treated lung cancer, primary lung carcinoids or metastasizing breast carcinoma (including data on primary breast carcinoma) were analyzed by nonhierarchic multivariant discriminant analysis with respect to a set of cytometric/histometric and immunohistochemical/ligand histochemical parameters. The number of stem lines, S-phase-related tumor cell fraction and the extent of structural entropy and its current were measured. In addition, the expression of binding capacities for histo-blood group trisacharides, galectins, the alpha/beta-interferon antagonist sarcolectin, the lymphokine macrophage migration inhibitory factor and a monoclonal antibody to the Le(y) epitope was monitored for insight into aspects of immunologic and biologic behavior. RESULTS: In all studies, a correlation between tumor parameters, according to TNM stage and survival, was seen. In order to refine this category formation, at least certain selected features should provide an even more stringent association than TNM stages. Indeed, statistical correlation of the cytometric and histometric parameters as well as the expression of receptors for the two histo-blood group trisaccharides, ligands for the galectins (CL-16, CL-14) and macrophage migration inhibitory factor was stronger than that of TNM stage. A large amount of the current of structural entropy was especially highly significantly associated with poor survival. This observation could be verified in each of the different studies. CONCLUSION: The obtained data strongly support the notion that thermodynamic evaluation of tumor growth focusing on the "entropy distance" of the tumor from its environment is a promising perspective warranting extended studies. Additionally, glycohistochemical features, including binding capacities for histo-blood group trisaccharides, have the potential to aid in establishment of a biologic marker set for tumor staging.

Biomarkers, Tumor↗

PubMed2002

Pure component spectral reconstruction from mixture data using SVD, global entropy minimization, and simulated annealing. Numerical investigations of admissible objective functions using a synthetic 7-species data set.

A combination of singular value decomposition, entropy minimization, and simulated annealing was applied to a synthetic 7-species spectroscopic data set with added white noise. The pure spectra were highly overlapping. Global minima for selected objective functions were obtained for the transformation of the first seven right singular vectors. Simple Shannon type entropy functions were used in the objective functions and realistic physical constraints were imposed in the penalties. It was found that good first approximations for the pure component spectra could be obtained without the use of any a priori information. The present method out performed the two widely used routines, namely Simplisma and OPA-ALS, as well as IPCA. These results indicate that a combination of SVD, entropy minimization, and simulated annealing is a potentially powerful tool for spectral reconstructions from large real experimental systems.

Journal Article↗

PubMed2004

Accuracy of enthalpy and entropy determination using the kinetic method: are we approaching a consensus?

There is an emerging consensus regarding the applicability of the kinetic method. All parties acknowledge that it is an approximate quantitative technique, capable of yielding not only enthalpy, but also entropy values. Opinions differ mainly on the accuracy of the results but it is agreed that the energy (effective temperature) dependence of kinetic method plots needs to be checked in all but the simplest of cases. When the 'apparent basicity' is found to depend on collision energy (and hence effective temperature), the extended kinetic method must be used. We have performed a large-scale modeling study, involving thousands of randomly selected molecular systems and a variety of experimental conditions, using exact calculations and realistic data sets. The results show that when the measured entropy difference between the two competing reaction channels is less than approximately 35 J mol(-1) K(-1), overall errors (standard deviations) of DeltaH(298) determined by the kinetic method are +/-5 kJ mol(-1); those of DeltaS(298) are +/-10 J mol(-1) K(-1). These include not only inherent errors of the kinetic method, but also errors in ion abundance measurement (5%) and inaccurate knowledge of reference compound thermochemistry (+/-2 kJ mol(-1), on average). We recommend, in general, that these errors be reported in kinetic method studies. When the measured entropy difference between the two competing fragmentation channels is large (>35 J mol(-1) K(-1)), it is likely to be significantly underestimated and errors of the kinetic method increase significantly.

Journal Article↗

PubMed1995

Empirical evaluation of the influence of side chains on the conformational entropy of the polypeptide backbone.

Changes in amino acid side chains have long been recognized to alter the range and distribution of phi, psi angles found in the main chain of polypeptides. Altering the range and distribution of phi, psi angles also alters the conformational entropy of the flexible denatured state and may thus stabilize or destabilize it relative to the comparatively conformationally rigid native state. A database of 12,320 residues from 61 nonhomologous, high resolution crystal structures was examined to determine the phi, psi conformational preferences of each of the 20 amino acids. These observed distributions in the native state of proteins are assumed to also reflect the distributions found in the denatured state. The distributions were used to approximate the energy surface for each residue, allowing the calculation of relative conformational entropies for each residue relative to glycine. In the most extreme case, replacement of glycine by proline, conformational entropy changes will stabilize the native state relative to the denatured state by -0.82 +/- 0.08 kcal/mol at 20 degrees C. Surprisingly, alanine is found to be the most ordered residue other than proline. This unexpected result is a result of the high percentage of alanines found in helical conformations. This either indicates that the observed distributions in the native state do not reflect the distributions in the denatured state, or that alanine is much more likely to adopt a helical conformation in the denatured state than residues with longer side chains.(ABSTRACT TRUNCATED AT 250 WORDS)

Alanine↗

PubMed1999

Enthalpy-Entropy Compensation Phenomenon Observed for Different Surfactants in Aqueous Solution.

Based on previously reported thermodynamic data such as changes of the Gibbs energy (DeltaG(m)( degrees )), the enthalpy (DeltaH(m)( degrees )), and the entropy (DeltaS(m)( degrees )) on micelle formation of more than 15 species of surfactants (including nonionic, anionic, and cationic surfactants), plots of DeltaH(m)( degrees ) vs DeltaS(m)( degrees ) (not of DeltaS(m)( degrees ) vs DeltaH(m)( degrees ), as is usually done) were made. For each surfactant, a linear relation having almost the same slope (1/307 K(-1)) within a small error (+/-2.3%) but a different intercept (varsigma) depending on the surfactant species was obtained, i.e., DeltaS(m)( degrees ) = (1/307)DeltaH(m)( degrees ) + varsigma, where 1/307 (K(-1)) means that the so-called compensation temperature (T(C)) is 307 K. Strictly speaking, T(C) ranges from 299 to 315 K, depending on the species. The intercept corresponds to the entropy change at a specific temperature giving DeltaH(m)( degrees ) = 0, at which the driving force of micelle formation comes only from the entropy term; this temperature is characteristic of the surfactant species. On the other hand, the compensation temperature has no significant meaning other than a mean temperature studied. Copyright 1999 Academic Press.

Journal Article↗

PubMed1993

The free energy, enthalpy and entropy of native and of partially denatured closed circular DNA.

We have used gel electrophoresis to measure the progress of local denaturation in closed circular pBR322 DNA as a function of temperature and linking deficiency, delta Lk. Local denaturation is closely coupled to supercoiling in closed DNA, requiring statistical mechanical methods for analysis. We have applied these methods to the experimental data to evaluate the free energies for three associated molecular processes. These processes are changes in the residual linking deficiency, delta Lkr, initiation of local denaturation, and twisting of denatured strands about one another. Our results confirm the quadratic dependence of the supercoiling free energy upon delta Lk, with a free energy coefficient of 740/N kcal/mol at 37 degrees C, where N is the number of base-pairs. The free energy of initiation of denaturation is 10.2(+/- 0.7) kcal/mol. The free energy of interstrand twisting of denatured regions varies with the square of the twist density, with proportionality coefficient C tau = 1.62 (+/- 0.11) kcal/rad2 at 37 degrees C. We have also calculated the entropy and enthalpy of these three processes, using the temperature dependence of the respective free energies. We find that both the entropy and the enthalpy of supercoiling are positive and vary quadratically with delta Lk. The free energy of initiation of denaturation is independent of temperature, hence arises primarily from a change in enthalpy. The entropy and enthalpy of interstrand twisting of denatured regions are both positive, and the twisting force constant decreases with temperature. These results differ considerably from expectations based solely upon considerations of chain configuration in vacuo, indicating the importance of solvent-dependent factors in determining the structure of closed circular DNA.

DNA, Circular↗

PubMed1995

Entropy, irreversibility and evolution.

The Second Law of Thermodynamics is investigated with respect to its value as an indicator of the direction of the evolutionary process. Non-thermodynamic entropy concepts and possible errors in the use of thermodynamic entropy are discussed. The importance of genuine thermodynamic potentials and their correct application for understanding processes is emphasized. There is no direct connection between evolutionary events such as speciation and thermodynamic entropy changes; the irreversibility of evolution is not a consequence of thermodynamic irreversibility.

Animals↗

PubMed1995

Limitations of the maximum entropy principle in devising drug input rate.

A computer program applying the principle of maximum entropy to the analysis of drug absorption rate has been developed. Plasma concentrations of amoxicillin obtained after oral and intravenous dosing have been analysed, together with simulated data corresponding to a complex input. Amoxicillin absorption rates devised by the program were similar to those obtained by a standard deconvolution method, although they were displayed as an almost continuous profile. However, improbable fluctuations were obtained with some data sets and the fraction absorbed was underestimated by 13%. With the simulated data, the maximum entropy program did not provide a better solution than the standard deconvolution procedure, and it was sensitive to the addition of random error and to the number of samples. The maximum entropy principle, as implemented in our computer program, may not have a better performance than standard deconvolution procedures, especially in human experiments where the number of blood samples is usually limited.

Administration, Oral↗

PubMed1991

The estimation of the Kolmogorov entropy from a time series and its limitations when performed on EEG.

A method to estimate a lower bound of the Kolmogorov entropy-the so called K2-entropy-from a time series is presented which avoids use of the generalized correlation integral. The influence of the norm is studied. The method is demonstrated on some standard examples. The entropy of the attractor apparent in the EEG of the foetal sheep is estimated and the results are compared with results obtained from synthesized data featuring some basic properties of EEG. This gives an insight into the limitations of the procedure.

Animals↗

PubMed1990

Thermodynamics of the interaction of aristololactam-beta-D-glucoside with DNA. Ionic strength dependence of enthalpy and entropy.

The interaction of aristololactam-beta-D-glucoside with calf thymus DNA has been studied by measuring the changes in the absorbance of the alkaloid over a wide range of temperatures and sodium chloride concentrations. The binding parameters obtained are best fit by the neighbour exclusion model. The salt and temperature dependence of the binding constants are used to estimate the thermodynamic parameters involved in the interaction of the alkaloid with DNA. It is observed that aristololactam-beta-D-glucoside binding to DNA is an exothermic process over the entire range of salt and temperature, and the estimated values of enthalpy and entropy change are strongly dependent on the ionic strength of the solution. The enthalpy and entropy changes compensate one another to produce a relatively small Gibbs' free energy change. The possibility that aristololactam-beta-D-glucoside exists as a monovalent cation at neutral pH and the possible molecular contribution to the enthalpy and entropy changes of the aristololactam-beta-D-glucoside-DNA complex are discussed.

Alkaloids↗

PubMed1991

Quantification of EEG irregularity by use of the entropy of the power spectrum.

A new method for quantifying irregularity of EEGs is proposed in this study. The entropy, an information measure, determines the uniformity of proportion distribution. The peakedness or flatness of the distribution of the EEG power spectrum, representing EEG rhythmicity, can be measured by the entropy, because the power spectrum consists of proportions of power at each frequency. The irregularity of the EEG was measured by the entropy of the power spectrum, called an irregularity index (II). The II was obtained from the power spectrum at F3, F4, C3, C4, P3, P4, O1 and O2 during rest and mental arithmetic in 10 normal subjects. Relative band powers of delta, theta, alpha and beta bands and alpha peak frequency were also obtained. EEGs during rest were significantly more irregular anteriorly than in the occipital areas. Alpha activity was also more irregular in the anterior region. A greater degree of EEG desynchronization during mental arithmetic was found over the left hemisphere and the right occipital area. The II was more sensitive to such desynchronization than alpha band power and alpha peak frequency. The differences in spectral structures between rest and mental arithmetic conditions, mainly over the left hemisphere, were also confirmed by the Kullback-Leibler information.

Adolescent↗

PubMed1989

Growth rate, population entropy, and perturbation theory.

This paper is concerned with the connection between two classes of population variables: measures of population growth rate--the Malthusian parameter, the net reproduction rate, the gross reproduction rate, and the mean life expectancy; and measures of demographic heterogeneity--population entropy. It is shown that the entropy functions predict the response of the growth rate parameters to perturbations in the age-specific fecundity and mortality schedule. These results are invoked to introduce the notion of environmental intensity. The intensity function, expressed in terms of the entropy parameters, is applied to give a comparative study of the effect of environmental factors on the dynamics of Swedish and French populations.

Age Factors↗

PubMed1977

Morphology of branching trees related to entropy.

Analyses of river systems by geomorphologists have suggested that for minimal entropy production in the movement of water down the river the fall in altitude should be equal in each order of branching of the tributaries. In this paper the same concepts have been applied to the bronchial tree and pulmonary arterial tree, assuming that the energy associated with pressure difference is analogous to that associated with altitude difference in rivers. The morphology of the bronchial tree is such that, given laminar flow or air, the calculated pressure difference across each order is equal. This may indicate that the bronchial tree is designed for minimal entropy production. In the arterial tree, however, this result is not obtained, probably because we do not know how to calculate the pressure drop in blood flowing through a branching system. It is therefore not currently possible, on the basis of this approach, to say whether the pulmonary arterial tree is designed for minimal entropy production or not.

Airway Resistance↗

PubMed1986

Natural selection, fitness entropy, and the dynamics of coevolution.

The coevolutionary dynamics of interacting populations were studied by combining continuous time Lotka-Volterra models of population growth with single-locus genetic models of weak selection. The effects of natural selection on population growth were evaluated using Ginzburg's fitness entropy function as a measure of the deviation of a population's initial allele frequencies from their polymorphic equilibrium values. This entropy measure was used to relate the dynamics of a community composed of evolving populations to the dynamics of a "reference community" whose populations are initially in genetic equilibrium. Specifically, a quantity called the "selective difference area" was defined as the total difference between the population size trajectories of a reference and evolving population. The selective difference area represents the amount of extra life a species would realize if the entire community were at genetic equilibrium. It was shown that this selective difference area is a simple linear function of the initial fitness entropies of each species. This prediction is independent of the strength of selection and holds for any arbitrary set of initial population densities. Numerical examples were presented to illustrate the results. Under the assumption of weak selection, a generalization for arbitrary population growth models was outlined.

Biological Evolution↗

PubMed1991

Aging as a multi-step process characterized by a lowering of entropy production leading the cell to a sequence of defined stages.

The principles of the thermodynamics of irreversible processes which occur in biological cells considered as open systems, have been reviewed and applied in order to describe a possible evolution of cells during aging. The main feature of such an approach is that cells operating in a steady state, optimize their free energy production by lowering their entropy production which is kept to a minimum. Instabilities can however occur which can lead the cell from one steady state to another characterized by a lower production of entropy. Concomitantly, the level of errors or entropy of the system will increase. The process will continue and the cell will go from one state to another until a critical level is attained where the cell can not cope any more with keeping its organization and will die. The effect of stresses and mitosis have been also considered in this model. Such an approach stresses that cells can only subsist as a whole in certain states which are the result of the genetic constitution but also of the optimalization of cellular functions given their requirement in energy and the fluctuations from the environmental changes. In this respect, it reconciles both programmed and stochastic theories of aging.

Aging↗