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At least 1,207 records · Page 67Linked to original sources
PubMed1994

[Use of an index of migration, indicators for surname diversity, entropy and redundancy for surname distribution in describing the population structure].

The index of migration, the parameter of surname diversity, and the values of entropy and redundancy of the distribution of surnames, proposed by Barrai et al. [1], were determined for populations of Kirovskaya and Kostromskaya oblasts. The relationship of these indices with previously used population characteristics, such as the Wright's F st parameter, the index of endogamy, and the burden of autosomal recessive and autosomal dominant Mendelian pathology, was determined. Further use of these parameters in population genetic research is considered.

Genes, Dominant↗
PubMed1994

Enthalpy-entropy balance and convergence temperatures in protein unfolding.

We find that isoenthalpic and isoentropic temperatures characterizing the unfolding of small globular proteins are linked by a simple relationship, which takes into account the occurrence of common values of specific unfolding enthalpy and entropy changes. The difference between these temperatures implies that the hydration effect favors protein folding over a quite large range of temperatures.

Models, Theoretical↗
PubMed2006

Direct evaluation of a kinetic model for RecA-mediated DNA-strand exchange: the importance of nucleic acid dynamics and entropy during homologous genetic recombination.

The Escherichia coli RecA protein is the prototype of a class of proteins that play central roles in genomic repair and recombination in all organisms. The unresolved mechanistic strategy by which RecA aligns a single strand of DNA with a duplex DNA and mediates a DNA strand switch is central to understanding homologous recombination. We explored the mechanism of RecA-mediated DNA-strand exchange using oligonucleotide substrates with the intrinsic fluorophore 6-methylisoxanthopterin. Pre-steady-state spectrofluorometric analysis elucidated the earliest transient intermediates formed during recombination and delineated the mechanistic strategy by which RecA facilitates this process. The structural features of the first detectable intermediate and the energetic characteristics of its formation were consistent with interactions between a few bases of the single-stranded DNA and the minor groove of a locally melted or stretched duplex DNA. Further analysis revealed RecA to be an unusual enzyme in that entropic rather than enthalpic contributions dominate its catalytic function, and no unambiguously active role for the protein was detected in the earliest molecular events of recombination. The data best support the conclusion that the mechanistic strategy of RecA likely relies on intrinsic DNA dynamics.

DNA↗
PubMed2005

Generalized scalar measures for diffusion MRI using trace, variance, and entropy.

This paper details the derivation of rotationally invariant scalar measures from higher-rank diffusion tensors (DTs) and functions defined on a unit sphere. This was accomplished with the use of an expression that generalizes the evaluation of the trace operator to tensors of arbitrary rank, and even to functions whose domains are the unit sphere. It is shown that the mean diffusivity is invariant to the selection of tensor rank for the model used. However, this rank invariance does not apply to the anisotropy measures. Therefore, a variance-based, general anisotropy measure is proposed. Also an information theoretical parametrization of anisotropy is introduced that is frequently more consistent with the meaning attributed to anisotropy. We accomplished this by associating anisotropy with the amount of orientational information present in the data, regardless of the imaging technique used. Using a simplified model of fibrous tissue, we simulated anisotropy values with varying orientational complexity and tensor models. Simulations suggested that a lower-rank tensor model may produce artificially low anisotropy values in voxels with complex structure. This was confirmed with a spin-echo experiment performed on an excised rat brain.

Animals↗
PubMed2005

Stochastic entropy QSAR for the in silico discovery of anticancer compounds: prediction, synthesis, and in vitro assay of new purine carbanucleosides.

A Markov model based QSAR is introduced for the rational selection of anticancer compounds. The model discriminates 90.3% of 226 structurally heterogeneous anticancer/non-anticancer compounds in training series. External validation series were used to validate the model; the 91.8% containing 85 compounds, not considered to fit the model, were correctly classified. The model developed is afterwards used in a simulation of a virtual search for anticancer compounds never considered either in training or in predicting series. The 87.7% of the 213 anticancer compounds used in this simulated search were correctly classified. The model also shows high values for specificity (0.89), sensitivity (0.91), and Mathews correlation coefficient (0.79). In addition, the present model compares better-to-similar with respect to other four models elsewhere reported if one takes into consideration 26 comparison parameters. Finally, we exemplify the use of the model in practice with the design of a new series of carbanucleosides. The compounds evaluated with the model were synthesized and experimentally assayed for their antitumor effects on the proliferation of murine leukemia cells (L1210/0) and human T-lymphocyte cells (CEM/0 and Molt4/C8). The more interesting activity was detected for the compound 5a with a predicted probability of 80.2% and IC(50) = 27.0, 27.2, and 29.4 microM, respectively, against the above-mentioned cellular lines. These values are comparable to those for the control compound Ara-A.

Animals↗
PubMed2006

Concepts of EEG processing: from power spectrum to bispectrum, fractals, entropies and all that.

Over the past two decades, methods of processing the EEG for monitoring anaesthesia have greatly expanded. Whereas power spectral analysis was once the most important tool for extracting EEG monitoring variables, higher-order spectra, wavelet decomposition and especially methods used in the analysis of complex dynamical systems such as non-linear dissipative systems are nowadays attracting much attention. This chapter reviews some of these methods in brief. However, a comparison of some of the newer approaches with the more traditional ones with respect to clinical end-points by association measures and to the signal-to-noise ratio raises some doubt over whether the newer EEG-processing techniques really do better than the more traditional ones.

Electroencephalography↗
PubMed2005

Protein targeting: entropy, energetics and modular machines.

New light is being shed on the mechanism of protein import into mitochondria. The inner membrane translocase can switch between modes of translocation, and assists what might be an entropic device to drive the initial entry of substrate proteins across the outer membrane.

Entropy↗
PubMed2004

A family of evolution-entropy hybrid methods for ranking protein residues by importance.

In order to identify the amino acids that determine protein structure and function it is useful to rank them by their relative importance. Previous approaches belong to two groups; those that rely on statistical inference, and those that focus on phylogenetic analysis. Here, we introduce a class of hybrid methods that combine evolutionary and entropic information from multiple sequence alignments. A detailed analysis in insulin receptor kinase domain and tests on proteins that are well-characterized experimentally show the hybrids' greater robustness with respect to the input choice of sequences, as well as improved sensitivity and specificity of prediction. This is a further step toward proteome scale analysis of protein structure and function.

Amino Acid Sequence↗
PubMed2005

Entropy analysis of neuronal spike train synchrony.

Although vector strength (VS) and the Rayleigh tests are widely used to quantify neuronal firing synchrony to cyclic events, their use is valid only for singly peaked, unimodal distributions. In this report, we propose a new method to quantify synchrony, applicable to both unimodal and multimodal distributions. We also propose a statistical test to examine temporal structure under a null hypothesis of no synchrony.

Action Potentials↗
PubMed2004

Study of DNA binding sites using the Rényi parametric entropy measure.

Shannon's definition of uncertainty or surprisal has been applied extensively to measure the information content of aligned DNA sequences and characterizing DNA binding sites. In contrast to Shannon's uncertainty, this study investigates the applicability and suitability of a parametric uncertainty measure due to Rényi. It is observed that this measure also provides results in agreement with Shannon's measure, pointing to its utility in analysing DNA binding site region. For facilitating the comparison between these uncertainty measures, a dimensionless quantity called "redundancy" has been employed. It is found that Rényi's measure at low parameter values possess a better delineating feature of binding sites (of binding regions) than Shannon's measure. The critical value of the parameter is chosen with an outlier criterion.

Animals↗
PubMed2001

Entropy as the predominant driving force of binding to human recombinant alpha(x)beta(3)gamma(2) GABA(A) receptors.

In order to study the correlation of the thermodynamic driving forces of binding with the efficacies of displacing ligands, the specific binding of [3H]SR 95531 [2-(3-carboxypropyl)3-amino-6-p-methoxyphenylpyridazinium bromide], a GABA(A) receptor antagonist, was studied in cell lines stably expressing human alpha(1)beta(3)gamma(2) and alpha(2)beta(3)gamma(2) GABA(A) receptors. Displacing potencies for the agonists with different efficacies (muscimol, 4,5,6,7-tetrahydroisoxazolo[5,4-c]pyridin-3-ol (THIP) and piperidine-4-sulfonic acid) and for antagonists (SR 95531 and 5-(4-piperidyl)isothiazol-3-ol) were determined at 0 degrees C, 20 degrees C and 37 degrees C. Displacing potencies were temperature-nearly independent for alpha(1)beta(3)gamma(2) receptors. At alpha(2)beta(3)gamma(2), receptor binding of the antagonists was exothermic, endothermic for the agonists THIP and piperidine-4-sulfonic acid and isothermic for muscimol. The free energy increments of displacement for the binding of the antagonist [3H]SR 95531 versus the agonist [3H]muscimol approach saturation as a function of the efficacies of the displacers only for alpha(1)beta(3)gamma(2) receptors. This suggests that, for binding to alpha(1)beta(3)gamma(2) GABA(A) receptors, displacement is an efficacy-dependent interaction predominantly driven by entropic increases.

Animals↗
PubMed2003

Folding rates and low-entropy-loss routes of two-state proteins.

We develop a simple model for computing the rates and routes of folding of two-state proteins from the contact maps of their native structures. The model is based on the graph-theoretical concept of effective contact order (ECO). The model predicts that proteins fold by "zipping up" in a sequence of small-loop-closure events, depending on the native chain fold. Using a simple equation, with a few physical rate parameters, we obtain a good correlation with the folding rates of 24 two-state folding proteins. The model rationalizes data from Phi-value analysis that have been interpreted in terms of delocalized or polarized transition states. This model indicates how much of protein folding may take place in parallel, not along a single reaction coordinate or with a single transition state.

Animals↗