SEARCH · PubMed Health

Results for “sample entropy”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 145 records · Page 8Linked to original sources

PubMed1996

Prediction and evaluation of side-chain conformations for protein backbone structures.

A common approach to protein modeling is to propose a backbone structure based on homology or threading and then to attempt to build side chains onto this backbone. A fast algorithm using the simple criteria of atomic overlap and overall rotamer probability is proposed for this purpose. The method was first tested in the context of exhaustive searches of side chain configuration space in protein cores and was then applied to all side chains in 49 proteins of known structure, using simulated annealing to sample space. The latter procedure obtains the correct rotamer for 57% and the correct chi 1 value for 74% of the 6751 residues in the sample. When low-temperature Monte-Carlo simulations are initiated from the results of the simulated-annealing processes, consensus configurations are obtained which exhibit slightly more accurate predictions. The Monte-Carlo procedure also allows converged side chain entropies to be calculated for all residues. These prove to be accurate indicators of prediction reliability. For example, the correct rotamer is obtained for 79% and the correct chi 1 value is obtained for 84% of the half of the sample residues exhibiting the lowest entropies. Side chain entropy and predictability are nearly completely uncorrelated with solvent-accessible area. Some precedents for and implications of this observation are discussed.

Algorithms↗

PubMed2000

Information content of protein sequences.

The complexity of large sets of non-redundant protein sequences is measured. This is done by estimating the Shannon entropy as well as applying compression algorithms to estimate the algorithmic complexity. The estimators are also applied to randomly generated surrogates of the protein data. Our results show that proteins are fairly close to random sequences. The entropy reduction due to correlations is only about 1%. However, precise estimations of the entropy of the source are not possible due to finite sample effects. Compression algorithms also indicate that the redundancy is in the order of 1%. These results confirm the idea that protein sequences can be regarded as slightly edited random strings. We discuss secondary structure and low-complexity regions as causes of the redundancy observed. The findings are related to numerical and biochemical experiments with random polypeptides.

Algorithms↗

PubMed1998

Low temperature photolysis of denatured nitrosyl hemoproteins.

Photolysis of denatured HbNO were carried out at temperatures below 26 K. The normalized kinetic curves were fitted using either two exponentials or a conformational substate energy distribution or a fractal model. The parameters are related to the protein structure. The two exponentials model assumes the existence of two fractions of photolysed molecules that rebind with slow and fast reaction rates. Only the slow reaction rate is sensitive to the denaturation process. The pre-exponential factor and the peak energy of the substate distribution values suggest an increase in the entropy and a decrease of the flexibility in the denatured samples, respectively. The fractal model parameters strengthened the functional relevance of the flexibility of the protein chain.

Electron Spin Resonance Spectroscopy↗

PubMed2002

Parsimony in protein evolution.

Pohl found the activation enthalpy and entropy for melting of his mesophilic proteins to be linear in the total number of residues and Privalov and colleagues found this same linearity for the standard heat-capacity, enthalpy and entropy changes in the overall melting equilibria. Despite the small samples these results suggest that mesophiles individually, and as a class, are related through a single standard representative. If so, very extensive convergent evolution has provided both great simplification and very sophisticated goals for genome decoding and quantitative description of protein substructures [R. Lumry, The protein primer, http://www.umn.edu.chem. /groupslumry].

Evolution, Molecular↗

PubMed2006

Layering in sedimentation of suspensions of charged colloids: simulation and theory.

We study the equilibrium sediment of a multicomponent system of charged colloids using primitive model Monte Carlo simulations, which include counterions explicitly. We find separation of the different colloidal components into almost pure layers, where colloids with large charge-to-mass ratio sediment higher in the sample. This effect appears due to a competition between ionic entropy, gravitational energy, and electrostatic energy. Our simulations provide a direct confirmation of recent theoretical predictions on the sedimentation of multicomponent mixtures of charged colloids in regimes with relatively low total densities and low colloidal charges. To explore the limitations of the theory we perform simulations at higher total densities for monodisperse and multicomponent systems and at stronger electrostatic couplings by increasing the colloidal charge for monodisperse suspensions. We find good agreement between theory and simulation when the colloidal charge is increased in the monodisperse case. However, we find deviations between simulations and theory upon increasing the total densities in the monodisperse and multicomponent systems. The density profiles obtained from simulations are more homogeneous than those predicted by theory. The spontaneous formation of layered structures predicted by the theory and found by simulation can serve as a useful tool to separate different components from a mixture of charged colloids.

Journal Article↗

PubMed2004

Growth hormone secretion in primary adrenal Cushing's syndrome is disorderly and inversely correlated with body mass index.

To evaluate the impact on the somatotropic axis of endogenous cortisol excess in the absence of primary pituitary disease, we investigated spontaneous 24-h growth hormone (GH) secretion in 12 adult patients with ACTH-independent hypercortisolism. Plasma GH concentration profiles (10-min samples) were analyzed by deconvolution to reconstruct secretion and approximate entropy to quantitate orderliness of the release process. Comparisons were made with a body mass index (BMI)-, age-, and gender-matched control group and an age- and gender-matched lean control group. GH secretion rates did not differ from BMI-matched controls but were twofold lower compared with lean subjects, mainly due to a 2.5-fold attenuation of the mean secretory burst mass (P = 0.001). In hypercortisolemic patients, GH secretion was negatively correlated with BMI (R = -0.55, P = 0.005) but not cortisol secretion. Total serum IGF-I concentrations were similar in the three groups. Approximate entropy (ApEn) was increased in patients with Cushing's syndrome compared with both control groups (vs. BMI-matched, P = 0.04; vs. lean, P = 0.001), denoting more irregular GH secretion patterns. ApEn in patients correlated directly with cortisol secretion (R = 0.77, P = 0.003). Synchrony between cortisol and GH concentration series was analyzed by cross-correlation, cross-ApEn, and copulsatility analyses. Patients showed loss of pattern synchrony compared with BMI-matched controls, but copulsatility was unchanged. We conclude that hyposomatotropism in primary adrenal hypercortisolism is only partly explained (approximately 30%) by increased body weight and that increased GH secretory irregularity and loss of synchrony suggest altered coordinate regulation of GH release.

Adenoma↗

PubMed2006

Dehydroepiandrosterone secretion in healthy older men and women: effects of testosterone and growth hormone administration in older men.

CONTEXT: Aging is associated with diminished gonadal steroid and GH/IGF-I axis activity; whether these changes contribute to the parallel declines of dehydroepiandrosterone (DHEA) and DHEA sulfate (DHEAS) production is unknown, as are the effects of sex steroid and/or GH administration on DHEA and DHEAS production. OBJECTIVE: Our objective was to evaluate morning DHEAS concentrations and nocturnal DHEA secretory dynamics in healthy older men and women, before and after chronic administration of sex steroid(s) alone, GH alone, sex steroid(s) combined with GH, or placebo alone. DESIGN: We compared nocturnal DHEA secretory dynamics (2000 h to 0800 h, sampling every 20 min, analyzed by multiparameter deconvolution and approximate entropy algorithms) in healthy older (65-88 yr) men (n = 68) and women (n = 36), both before and after 26 wk of administration of sex steroid(s) alone [testosterone (T) in men or estrogen/progesterone in women], GH alone, sex steroid(s) combined with GH, or placebo alone. RESULTS: Morning concentrations of DHEAS were lower; nocturnal DHEA pulsatile production rate, burst frequency, and amplitude were higher; and half-life was shorter in women (P < 0.05). Nocturnal integrated DHEA concentrations, total production rate, and approximate entropy did not differ significantly by sex. Because of small treatment group sizes in women, only hormone intervention results in men are presented. In men, T and T plus GH administration significantly decreased nocturnal integrated DHEA but not morning DHEAS concentrations. GH alone exerted no significant effects on nocturnal DHEA secretion or morning DHEAS. CONCLUSIONS: Spontaneous nocturnal DHEA secretion is sexually dimorphic in healthy older individuals, and T administration decreases nocturnal DHEA secretion in older men. The clinical significance of sex steroid modulation of DHEA secretion in older persons remains to be elucidated.

Aged↗

PubMed2000

Image deconvolution for protein crystals.

The image deconvolution technique developed for non-biological samples, which is based on the weak-phase-object approximation and principle of maximum entropy, was applied to simulated images of the biotin-binding protein streptavidin. A slight modification of the technique was introduced to solve the problem caused by the special image formation condition for biological samples. It has been shown that the modified technique is effective.

Crystallography↗

PubMed2005

New combinatorial approach for the investigation of kinetics and temperature dependence of surface reactions in thin organic films.

In this paper we present a new, simple, and reproducible method for the rapid determination of the temperature dependence of solution phase surface reactions of organic thin films on solid supports. Instead of estimating the extent of reaction for many separate samples for many different temperatures sequentially, we exploit in our new high throughput combinatorial approach surface reactions carried out under a thermal gradient followed by position-resolved contact angle (CA) measurements. The reaction kinetics, activation energies, and entropies are, thus, accessible on the basis of measurements on a very limited set of samples that differ in reaction times. The kinetics and temperature dependence of surface reactions of the previously studied alkaline hydrolysis of 11,11'-dithiobis(N-hydroxysuccinimidylundecanoate) (NHS-C10) self-assembled monolayers (SAMs) on gold, as well as the ester hydrolysis in SAMs of the novel disulfide 11,11-dithiobis(tert-butylundecanoate) (t-Bu-C10), were investigated in detail using the conventional sequential and the new combinatorial approach. The reaction kinetics, corresponding apparent rate constants k, and activation energies Ea, as well as activation entropies deltaS double dagger, determined according to both approaches agree well with each other to within the experimental error. Hence, these parameters can be quantitatively determined using the described combinatorial approach. A comparison of the reactions of the two model systems indicated that the transition state is tighter for the acid-catalyzed ester hydrolysis in SAMs of the novel disulfide t-Bu-C10 compared to the hydrolysis of the ester groups in SAMs of NHS-C10 on gold.

Journal Article↗

PubMed2003

Thermodynamic resolution of periosteal reaction and taphonomic change.

New bone formation (e.g., periosteal reaction) is one component of bone and joint disease diagnosis. Its application in the archeologic record has been compromised by lack of standardization. An objective technique for validating observations seems especially valuable when visual examination of a single data set results in widely disparate perspectives. Such discrepancies as to presence or absence of periosteal reaction are amenable to objective analysis. Bone, as any other form of matter, has a variety of properties. Some are characterized by weight or volume and are referred to as colligative. Some are related to its intrinsic nature, independent of mass. The latter are referred to as non-colligative. Non-colligative properties of matter provide an opportunity to assess structure, independent of quantity. Study of one such property, entropy, revealed that taphonomic changes can confidently be distinguished from bone surface reaction. Contrasted with the homogeneous entropy of normal bone, the loss of surface bone inherent in taphonomy results in reduced entropy. Contrasted with the homogenous patterns of normal bone, specific non-homogenous patterns allow periosteal reaction to be recognized, independent of variety of periosteal reaction or its origin. Thermographic approach allows observational techniques to be independently validated. Such validation allows for greater facility in interobserver archeologic site sample comparisons.

Bone Remodeling↗

PubMed1997

Novel modalities for appraising individual and coordinate pulsatile hormone secretion: the paradigm of luteinizing hormone and testosterone release in the aging male.

To quantify aging- and disease-associated alterations in the integrative and interactive components of a pulsatile neuroendocrine axis, novel biomathematical strategies are required. Here, I illustrate as an investigative paradigm otherwise subtle aging-dependent disturbances of the gonadotropin-releasing-hormone (GnRH)-luteinizing hormone (LH)-testosterone feedback axis in men, in whom strong age-related contrasts become evident via any of four strategies applied alone or in combination: (1) intensified blood sampling schedules to capture the temporal structure of episodic hormone (LH and testosterone) secretion; (2) deconvolution analysis as a technique to quantify underlying pituitary and gonadal hormone secretory rates from the observed plasma hormone concentration profiles; (3) approximate entropy as a scale- and model-independent measure of the serial regularity or orderliness of the hormone release process over time; and (4) cross-approximate entropy (cross-ApEn) to quantify joint asynchrony between two concurrent pulse trains without confounding by variable lag. These new methodologies are introduced and reviewed briefly, a stochastic differential equation feedback construct alluded to, and the resultant insights into distinct alterations of the aging male gonadotropic axis highlighted. In summary, the new experimental strategies of intensified venous sampling, multiparameter deconvolution analysis, approximate entropy, and cross-approximate entropy unveil new mechanisms underlying dynamic neuroendocrine-axis activity, as exemplified by aging-associated disruption of the human male reproductive axis.

Aging↗

PubMed2005

Calculation of the entropy of random coil polymers with the hypothetical scanning Monte Carlo method.

Hypothetical scanning Monte Carlo (HSMC) is a method for calculating the absolute entropy S and free energy F from a given MC trajectory developed recently and applied to liquid argon, TIP3P water, and peptides. In this paper HSMC is extended to random coil polymers by applying it to self-avoiding walks on a square lattice--a simple but difficult model due to strong excluded volume interactions. With HSMC the probability of a given chain is obtained as a product of transition probabilities calculated for each bond by MC simulations and a counting formula. This probability is exact in the sense that it is based on all the interactions of the system and the only approximation is due to finite sampling. The method provides rigorous upper and lower bounds for F, which can be obtained from a very small sample and even from a single chain conformation. HSMC is independent of existing techniques and thus constitutes an independent research tool. The HSMC results are compared to those obtained by other methods, and its application to complex lattice chain models is discussed; we emphasize its ability to treat any type of boundary conditions for which a reference state (with known free energy) might be difficult to define for a thermodynamic integration process. Finally, we stress that the capability of HSMC to extract the absolute entropy from a given sample is important for studying relaxation processes, such as protein folding.

Biopolymers↗

PubMed2005

Data-robust tight lower bounds to the information carried by spike times of a neuronal population.

We develop new data-robust lower-bound methods to quantify the information carried by the timing of spikes emitted by neuronal populations. These methods have better sampling properties and are tighter than previous bounds based on neglecting correlation in the noise entropy. Our new lower bounds are precise also in the presence of strongly correlated firing. They are not precise only if correlations are strongly stimulus modulated over a long time range. Under conditions typical of many neurophysiological experiments, these techniques permit precise information estimates to be made even with data samples that are three orders of magnitude smaller than the size of the response space.

Action Potentials↗

PubMed2004

Selection of patient samples and genes for outcome prediction.

Gene expression profiles with clinical outcome data enable monitoring of disease progression and prediction of patient survival at the molecular level. We present a new computational method for outcome prediction. Our idea is to use an informative subset of original training samples. This subset consists of only short-term survivors who died within a short period and long-term survivors who were still alive after a long follow-up time. These extreme training samples yield a clear platform to identify genes whose expression is related to survival. To find relevant genes, we combine two feature selection methods -- entropy measure and Wilcoxon rank sum test -- so that a set of sharp discriminating features are identified. The selected training samples and genes are then integrated by a support vector machine to build a prediction model, by which each validation sample is assigned a survival/relapse risk score for drawing Kaplan-Meier survival curves. We apply this method to two data sets: diffuse large-B-cell lymphoma (DLBCL) and primary lung adenocarcinoma. In both cases, patients in high and low risk groups stratified by our risk scores are clearly distinguishable. We also compare our risk scores to some clinical factors, such as International Prognostic Index score for DLBCL analysis and tumor stage information for lung adenocarcinoma. Our results indicate that gene expression profiles combined with carefully chosen learning algorithms can predict patient survival for certain diseases.

Biomarkers, Tumor↗

PubMed2004

Kinetics of interaction of three carbamate pesticides with Indian soils: Aligarh district.

The kinetics of interaction with soil of three carbamate pesticides (I, II, III) used as nematicides and herbicides was studied at four different temperatures from solutions of six soil samples of Aligarh district. The values obtained for rate constants for adsorption and desorption were in good agreement with those obtained from the Lindstrom model, which proved useful in the simultaneous evaluation of adsorption (k1) and desorption (k2) rate constants. The rate constants for pesticides were in the order III > I > II on all the six soil samples. The data for rate constants, activation energies, heats of activation, entropy of activation and thermodynamic parameters indicated a partly physical and partly chemical adsorption of pesticide on the soil surfaces. Adsorption occurred via coordination and/or protonation of the exchangeable cations with the amidic carbonyl group, and hydrogen bonding and dipole association at the crystal edge and basal surfaces. The adsorptivity of the soils may be attributed to the organic matter content and percentage clay content.

Adsorption↗

PubMed2000

Influence of the modification conditions of alkyl bonded ligands on the characteristics of reversed-phase liquid chromatography.

The parameters characterizing retention and the mass transfer mechanisms in reversed-phase liquid chromatography were derived from data acquired for a series of compounds on a silica gel bonded to alkyl ligands of various lengths and ligand densities. The adsorption equilibrium constant, the absolute value of the isosteric heat of adsorption, and the activation energy of surface diffusion increase while the surface diffusion coefficient decreases with increasing length of the alkyl chain and density of the C18 ligand. These results are consistent with increasing restriction of the mobility of an increasingly adsorbable molecule. There is a critical level of carbon content above which the four parameters just listed no longer change with increasing alkyl ligand density. This level is likely to depend on the sizes of the alkyl ligand and the sample molecule. Even at high densities of C18 chains, there may be a limitation in the contact area of the sample molecule and the alkyl ligand. The retention behavior on the stationary phases studied is explained by assuming that the sample molecules penetrate into the layer of alkyl ligands. Enthalpy-entropy compensation was demonstrated for surface diffusion. Its mechanism is probably similar on the different stationary phases studied, irrespective of the length and density of the bonded ligand.

Chromatography, Liquid↗

PubMed1992

Light scattering study of irradiated lipid bilayer.

Vesicular phospholipid bilayer membranes in the form of giant unilamellar vesicles (GUVs) of dipalmitoylphosphatidylcholine (DPPC) were irradiated with fast neutron fluences ranging from 10(4) to 10(7) n cm-2. The phase behaviour of both non-irradiated and irradiated GUVs was investigated using an angular light scattering technique. A model independent size distribution of the samples and their optical anisotropy (delta) were determined using a maximum entropy technique and the theory of light scattering from spherical shells composed of anisotropic cylindrical molecules arranged radially in the shells. The structural changes in the lipid bilayer exposed to fission neutrons are discussed on the basis of the damaging mechanisms of fast neutrons to both the hydrophobic and hydrophilic regions of the lipid bilayer.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed2005

Characterization of digital waveforms using thermodynamic analogs: applications to detection of materials defects.

We describe characterization of digital signals using analogs of thermodynamic quantities: the topological entropy, Shannon entropy, thermodynamic energy, partition function, specific heat at constant volume, and an idealized version of Shannon entropy in the limit of digitizing with infinite dynamic range and sampling rate. We show that analysis based on these quantities is capable of detecting differences between digital signals that are undetectable by conventional methods of characterization based on peak-to-peak amplitude or signal energy. We report the results of applying thermodynamic quantities to a problem from nondestructive materials evaluation: detection of foreign objects (FO) embedded near the surface of thin graphite/epoxy laminates using backscattered waveforms obtained by C-scanning the laminate. The characterization problem was to distinguish waveforms acquired from the region containing the FO from those acquired outside. In all cases the thermodynamic analogs exhibit significant increases (up to 20-fold) in contrast and for certain types of FO materials permit detection when energy or amplitude methods fail altogether.

Journal Article↗