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PubMed2001

Flat histogram simulation of lattice polymer systems.

We demonstrate the use of an algorithm called the Flat Histogram sampling algorithm for the simulation of two-dimensional lattice polymer systems. Thermodynamic properties, such as the average energy or entropy and other physical quantities such as the end-to-end distance or radius of gyration can be easily calculated using this method. The ground-state energy can also be determined. We also explore the accuracy and limitations of this method.

Journal Article↗

PubMed2003

Identification of signature and primers specific to genus Pseudomonas using mismatched patterns of 16S rDNA sequences.

BACKGROUND: Pseudomonas, a soil bacterium, has been observed as a dominant genus that survives in different habitats with wide hostile conditions. We had a basic assumption that the species level variation in 16S rDNA sequences of a bacterial genus is mainly due to substitutions rather than insertion or deletion of bases. Keeping this in view, the aim was to identify a region of 16S rDNA sequence and within that focus on substitution prone stretches indicating species level variation and to derive patterns from these stretches that are specific to the genus. RESULTS: Repeating elements that are highly conserved across different species of Pseudomonas were considered as guiding markers to locate a region within the 16S gene. Four repeating patterns showing more than 80% consistency across fifty different species of Pseudomonas were identified. The sub-sequences between the repeating patterns yielded a continuous region of 495 bases. The sub-sequences after alignment and using Shanon's entropy measure yielded a consensus pattern. A stretch of 24 base positions in this region, showing maximum variations across the sampled sequences was focused for possible genus specific patterns. Nine patterns in this stretch showed nearly 70% specificity to the target genus. These patterns were further used to obtain a signature that is highly specific to Pseudomonas. The signature region was used to design PCR primers, which yielded a PCR product of 150 bp whose specificity was validated through a sample experiment. CONCLUSIONS: The developed approach was successfully applied to genus Pseudomonas. It could be tried in other bacterial genera to obtain respective signature patterns and thereby PCR primers, for their rapid tracking in the environmental samples.

Base Pair Mismatch↗

PubMed2007

Packing regularities in biological structures relate to their dynamics.

The high packing density inside proteins leads to certain geometric regularities and also is one of the most important contributors to the high extent of cooperativity manifested by proteins in their cohesive domain motions. The orientations between neighboring nonbonded residues in proteins substantially follow the similar geometric regularities, regardless of whether the residues are on the surface or buried, a direct result of hydrophobicity forces. These orientations are relatively fixed and correspond closely to small deformations from those of the face-centered cubic lattice, which is the way in which identical spheres pack at the highest density. Packing density also is related to the extent of conservation of residues, and we show this relationship for residue packing densities by averaging over a large sample or residue packings. There are three regimes: (1) over a broad range of packing densities the relationship between sequence entropy and inverse packing density is nearly linear, (2) over a limited range of low packing densities the sequence entropy is nearly constant, and (3) at extremely low packing densities the sequence entropy is highly variable. These packing results provide important justification for the simple elastic network models that have been shown for a large number of proteins to represent protein dynamics so successfully, even when the models are extremely coarse grained. Elastic network models for polymeric chains are simple and could be combined with these protein elastic networks to represent partially denatured parts of proteins. Finally, we show results of applications of the elastic network model to study the functional motions of the ribosome, based on its known structure. These results indicate expected correlations among its components for the step-wise processing steps in protein synthesis, and suggest ways to use these elastic network models to develop more detailed mechanisms, an important possibility because most experiments yield only static structures.

Amino Acid Sequence↗

PubMed2004

Entropy considerations in kinetic method experiments.

In extended kinetic method experiments, relative binding enthalpies ('affinities') and relative entropies are obtained based on unimolecular dissociation kinetics. A series of ion-bound dimers A-X-B(i) is formed, in which the sample (A) and structurally similar reference molecules (B(i)) are bridged by a central cation or anion (X). The branching ratios of the A-X-B(i) set to A-X and B(i)-X are determined at different internal energies, usually by subjecting A-X-B(i) to collisionally activated dissociation at various collision energies. The dependence of the natural logarithm of the branching ratios on the corresponding B(i)-X bond enthalpies (X affinities of B(i)) is evaluated as a function of internal energy to thereby deduce the A-X bond enthalpy (X affinity of A) as well as an apparent relative entropy of the competitive dissociation channels, Delta(DeltaS(app)). Experiments with proton- and Na(+)-bound dimers show that this approach can yield accurate binding enthalpies. In contrast, the derived Delta(DeltaS(app)) values do not correlate with the corresponding thermodynamic entropy differences between the channels leading to A-X and B(i)-X, even after scaling. The observed trends are reconciled by the transition state switching model. According to this model, the kinetics of barrierless dissociations, such as those encountered in kinetic method studies, are dominated by a family of tight transition states ('entropy bottlenecks') lying lower in energy than the corresponding dissociation thresholds. In general, the relative energies of these tight transition states approximately match those of the dissociation products, but their relative entropies tend to be much smaller, as observed experimentally.

Alanine↗

PubMed2003

Entropy-based gene ranking without selection bias for the predictive classification of microarray data.

BACKGROUND: We describe the E-RFE method for gene ranking, which is useful for the identification of markers in the predictive classification of array data. The method supports a practical modeling scheme designed to avoid the construction of classification rules based on the selection of too small gene subsets (an effect known as the selection bias, in which the estimated predictive errors are too optimistic due to testing on samples already considered in the feature selection process). RESULTS: With E-RFE, we speed up the recursive feature elimination (RFE) with SVM classifiers by eliminating chunks of uninteresting genes using an entropy measure of the SVM weights distribution. An optimal subset of genes is selected according to a two-strata model evaluation procedure: modeling is replicated by an external stratified-partition resampling scheme, and, within each run, an internal K-fold cross-validation is used for E-RFE ranking. Also, the optimal number of genes can be estimated according to the saturation of Zipf's law profiles. CONCLUSIONS: Without a decrease of classification accuracy, E-RFE allows a speed-up factor of 100 with respect to standard RFE, while improving on alternative parametric RFE reduction strategies. Thus, a process for gene selection and error estimation is made practical, ensuring control of the selection bias, and providing additional diagnostic indicators of gene importance.

Adenocarcinoma↗

PubMed2004

Calorimetric vs. van't Hoff binding enthalpies from isothermal titration calorimetry: Ba2+-crown ether complexation.

The 1:1 complexation reaction between Ba(2+) and 18-crown-6 ether is re-examined using isothermal titration calorimetry (ITC), with the goal of clarifying previously reported discrepancies between reaction enthalpies estimated directly (calorimetric) and indirectly, from the temperature dependence of the reaction equilibrium constant K (van't Hoff). The ITC thermograms are analyzed using three different non-linear fit models based on different assumptions about the data error: constant, proportional to the heat and proportional but correlated. The statistics of the fitting indicate a preference for the proportional error model, in agreement with expectations for the conditions of the experiment, where uncertainties in the delivered titrant volume should dominate. With attention to proper procedures for propagating statistical error in the van't Hoff analysis, the differences between Delta H(cal) and Delta H(vH) are deemed statistically significant. In addition, statistically significant differences are observed for the Delta H(cal) estimates obtained for two different sources of Ba(2+), BaCl(2) and Ba(NO(3))(2). The effects are tentatively attributed to deficiencies in the standard procedure in ITC of subtracting a blank obtained for pure titrant from the thermogram obtained for the sample.

Barium Compounds↗

PubMed1993

Disulfide bond isomerization in BPTI and BPTI(G36S): an NMR study of correlated mobility in proteins.

Two conformational isomers were observed in the 1H nuclear magnetic resonance (NMR) spectra of the basic pancreatic trypsin inhibitor (BPTI) and of a mutant protein with Gly 36 replaced by Ser, BPTI(G36S). The less abundant isomer differs from the major conformation by different chirality of the Cys 14-Cys 38 disulfide bond. In BPTI, the population of the minor conformer increases from about 1.5% at 4 degrees C to 8% at 68 degrees C. In BPTI(G36S), the population of the minor conformation is about 15% of the total protein, so that a detailed structural study was technically feasible; a trend toward increasing population of the minor conformer at higher temperatures was observed also for this mutant protein. The activation parameters for the exchange between the two conformations were measured in the temperature range 4-68 degrees C, using uniformly 15N-enriched protein samples. Below room temperature the exchange rate of the disulfide flip follows an Arrhenius-type temperature dependence, with negative activation entropy in both proteins. At higher temperatures the exchange rates are governed by a different set of activation parameters, which are similar to those for the ring flips of Tyr 35 about the C beta-C gamma bond. Although the equilibrium enthalpy and entropy were found to be largely temperature independent, the activation entropy changes sign and is positive at higher temperatures. These results suggest that, above room temperature, the disulfide flips are coupled to the same protein structure fluctuations as the ring flips of Tyr 35.

Amino Acid Sequence↗

PubMed2005

Kinetics of model energy landscapes: an approach to complex systems.

An idealized potential energy surface (PES), simply a PES-like network of stationary points, is demonstrated to be a useful tool to study kinetic relaxation of complex energy landscapes. Combined with a master equation, we show that if constructed with proper regularity, the kinetics of the PES is easy to predict and understand by carefully examining the eigenmodes of the master equation. By modifying the idealized PES model to make it more and more complicated, we demonstrate a systematic method to study the complex kinetics on large PES. The idealized PES model is used to explore the feasibility and the robustness of statistical sampling of large PES. We develop several sampling strategies, such as the "rough topography sampling" and the "low barrier saddle sampling" in the idealized PES model and find they are also applicable to a realistic PES of the 13-atom Morse cluster with range parameter rho= 6. To measure the robustness of the sampling methods, we compare the eigenvalue spectra, the eigenvector similarity and the relaxation times of the total energy of the full and sample PESs.

Algorithms↗

PubMed1986

A vacuum microbalance technique for studies on the wettability of powders.

A vacuum microbalance technique has been used to evaluate the wettability of powders. The rate of uptake, and equilibrium weight of uptake, of water vapour onto outgassed powder samples, of differing wettabilities, were determined at different known temperatures. Standard techniques of data analysis were used to establish the enthalpy, entropy and Gibb's free energy of the activation and adsorption processes. The values obtained appeared to be in the correct order of magnitude and those for activation clearly reflected the relative wettability of the powders. Tests for compensation demonstrated that with the exception of phenobarbitone, there was probably a common mechanism producing the adsorption.

Adsorption↗

PubMed2003

Octreotide represses secretory-burst mass and nonpulsatile secretion but does not restore event frequency or orderly GH secretion in acromegaly.

Octreotide is a potent somatostatin analog that inhibits growth hormone (GH) release and restricts somatotrope cell growth. The long-acting octreotide formulation Sandostatin LAR is effective clinically in approximately 60% of patients with acromegaly. Tumoral GH secretion in this disorder is characterized by increases in pulse amplitude and frequency, nonpulsatile (basal) release, and irregularity. Whether sustained blockade by octreotide can restore physiological secretion patterns in this setting is unknown. To address this question, we studied seven patients with GH-secreting tumors during chronic receptor agonism. Responses were monitored by sampling blood at 10-min intervals for 24 h, followed by analyses of secretion and regularity by multiparameter deconvolution and approximate entropy (ApEn). The somatostatin agonist suppressed GH secretory-burst mass, nonpulsatile (basal) GH release, and pulsatile secretion, thereby decreasing total GH secretion by 86% (range 70-96%). ApEn decreased from 1.203 +/- 0.129 to 0.804 +/- 0.141 (P = 0.032), denoting greater regularity. None of GH pulse frequency, basal GH secretion rates, or ApEn normalized. In summary, chronic somatostatin agonism is able to repress amplitude-dependent measures of excessive GH secretion in acromegaly. Presumptive tumoral autonomy is inferred by continued elevations of event frequency, overall pattern disruption (irregularity), and nonsuppressible basal GH secretion.

Acromegaly↗

PubMed2002

Hypophyseal-portal somatostatin (SRIH) and jugular venous growth hormone secretion in the conscious unrestrained ewe.

Somatostatin (SRIH) release into hypophyseal portal blood varies reciprocally with growth hormone (GH) pulse generation in the male rat. However, few studies have directly evaluated this relationship in the female of any species. To address this issue, we carried out intensive (5 min) and extended (240 min) simultaneous monitoring of hypophyseal portal SRIH and internal jugular GH secretion in 7 unanesthetized ewes. Bihormonal synchrony was assessed by three statistically independent but complementary analyses: (i) cross-approximate entropy (X-ApEn) analysis to appraise the conditional regularity of SRIH/GH release patterns; (ii) cross-correlation analysis of paired sample SRIH and GH release rates, and (iii) probability analysis of random versus nonrandom SRIH and GH discrete pulse concordance. From a one-variable perspective, ApEn analysis documented consistently more irregular patterns of SRIH than GH release (94 +/- 4.3 and 72 +/- 8.1%, respectively, of the mean irregularity of 1,000 individual random-shuffled cognate series, p = 0.034). From a two-variable perspective, X-ApEn analysis revealed a nearly mean random relationship between SRIH and GH release patterns (group mean +/- SEM, 94 +/- 4.5% of the mean asynchrony of 1,000 randomly shuffled SRIH/GH pairs). Cross-correlation analysis disclosed highly variable linkages between SRIH and GH secretion; viz, negative cross-correlations in 5 sheep, positive relationships in 4, and both positive and negative SRIH/GH associations in 2 animals, wherein changes in SRIH secretion either preceded or followed those of GH. Peak detection by model-free cluster analysis quantified a total of 28 SRIH and 31 GH release episodes. Corresponding interpulse intervals (min) were comparable (37 +/- 4 (SRIH) and 43 +/- 12 (GH)), but the mean fractional (%) amplitude of SRIH peaks was 3.5-fold lower (60 +/- 10%) than that for GH (225 +/- 50%) (p = 0.024). Pulse-concordance probability testing showed that discrete peaks of SRIH and GH secretion coincided only 33% of the time, although this value exceeded chance expectation (p < 10(-4)). In summary, the present analysis applies intensive (5 min) and extended (240 min) simultaneous sampling of hypophyseal-portal and jugular venous blood to quantitate the degree of coordinate SRIH and GH secretion in the unanesthetized ovariectomized ewe. Thereby, we unmask highly irregular SRIH release patterns, and nearly random SRIH and GH associations. We conclude that, to the extent that in vivo sampling reflects physiological SRIH/somatotrope activity, the female sheep maintains complex time-varying interactions between SRIH and GH release.

Animals↗

PubMed2005

Thermodynamic functions of water and ice confined to 2 nm radius pores.

The heat capacity C(p) of the liquid state of water confined to 2 nm radius pores in Vycor glass was measured by temperature modulation calorimetry in the temperature range of 253-360 K, with an accuracy of 0.5%. On nanoconfinement, C(p) of water increases, and the broad minimum in the C(p) against T plot shifts to higher temperature. The increase in the C(p) of water is attributed to an increase in the phonon and configurational contributions. The apparent heat capacity of the liquid and partially frozen state of confined water was measured by temperature scanning calorimetry in the range of 240-280 K with an accuracy of 2%, both on cooling or heating at 6 K h(-1) rate. The enthalpy, entropy, and free energy of nanoconfined liquid water have been determined. The apparent heat capacity remains higher than that of bulk ice at 240 K and it is concluded that freezing is incomplete at 240 K. This is attributed to the intergranular-water-ice equilibrium in the pores. The nanoconfined sample melts over a 240-268 K range. For 9.6 wt % nanoconfined water concentration ( approximately 50% of the maximum filling) at 280 K, the enthalpy of water is 81.6% of the bulk water value and the entropy is 88.5%. For 21.1 wt % (100% filling) the corresponding values are 90.7% and 95.0%. The enthalpy decrease on nanoconfinement is a reflection of the change in the H-bonded structure of water. The use of the Gibbs-Thomson equation for analyzing the data has been discussed and it is found that a distribution of pore size does not entirely explain our results.

Journal Article↗

PubMed1981

Optimal sampling for pedigree analysis: sequential schemes for sibships.

Methods for inferring the mode of inheritance of a trait from familial data are becoming widely used. It is therefore important to assess alternative procedures for the collection of the relevant data. Cannings and Thompson (1977, Clinical Genetics 12, 208-212) and Thompson and Cannings (1979. In Genetic Analysis of Common Diseases, 363-382, New York: Liss) have advocated sequential schemes on the grounds that these admit simple methods for the correction of the likelihood function for ascertainment bias. Here it is shown that sequential procedures may also greatly increase efficiency, as measured by (statistical) information gained per individual sampled. Although attention is restricted to sampling sibships, and to a simple genetic model, the measures introduced are more widely applicable. A practical procedure for the construction of schemes, via a relationship between expected log likelihood and entropy, is also presented. This too is more widely applicable. A numerical example demonstrates the gains which can be achieved in practice, relative to alternative hypotheses which have been considered in several medical-genetic studies.

Data Collection↗

PubMed1998

Measuring regularity by means of a corrected conditional entropy in sympathetic outflow.

A new method for measuring the regularity of a process over short data sequences is reported. This method is based on the definition of a new function (the corrected conditional entropy) and on the extraction of its minimum. This value is taken as an index in the information domain quantifying the regularity of the process. The corrected conditional entropy is designed to decrease in relation to the regularity of the process (like other estimates of the entropy rate), but it is able to increase when no robust statistic can be performed as a result of a limited amount of available samples. As a consequence of the minimisation procedure, the proposed index is obtained without an a-priori definition of the pattern length (i.e. of the embedding dimension of the reconstructed phase space). The method is validated on simulations and applied to beat-to-beat sequences of the sympathetic discharge obtained from decerebrate artificially ventilated cats. At control, regular, both quasiperiodic and periodic (locked to ventilation) dynamics are observed. During the sympathetic activation induced by inferior vena cava occlusion, the presence of phase-locked patterns and the increase in regularity of the sympathetic discharge evidence an augmented coupling between the sympathetic discharge and ventilation. The reduction of complexity of the neural control obtained by spinalization decreases the regularity in the sympathetic outflow, thus pointing to a weaker coupling between the sympathetic discharge and ventilation.

Animals↗

PubMed2007

Nearest-neighbor nonparametric method for estimating the configurational entropy of complex molecules.

A method for estimating the configurational (i.e., non-kinetic) part of the entropy of internal motion in complex molecules is introduced that does not assume any particular parametric form for the underlying probability density function. It is based on the nearest-neighbor (NN) distances of the points of a sample of internal molecular coordinates obtained by a computer simulation of a given molecule. As the method does not make any assumptions about the underlying potential energy function, it accounts fully for any anharmonicity of internal molecular motion. It provides an asymptotically unbiased and consistent estimate of the configurational part of the entropy of the internal degrees of freedom of the molecule. The NN method is illustrated by estimating the configurational entropy of internal rotation of capsaicin and two stereoisomers of tartaric acid, and by providing a much closer upper bound on the configurational entropy of internal rotation of a pentapeptide molecule than that obtained by the standard quasi-harmonic method. As a measure of dependence between any two internal molecular coordinates, a general coefficient of association based on the information-theoretic quantity of mutual information is proposed. Using NN estimates of this measure, statistical clustering procedures can be employed to group the coordinates into clusters of manageable dimensions and characterized by minimal dependence between coordinates belonging to different clusters.

Computer Simulation↗

PubMed2000

Assessment of insulin secretion in relatives of patients with type 2 (non-insulin-dependent) diabetes mellitus: evidence of early beta-cell dysfunction.

To examine beta-cell function in glucose-tolerant offspring of type 2 diabetic families, 41 insulin-resistant (hyperinsulinemic-euglycemic clamp, P < .001) first-degree relatives and 32 controls underwent oral (OGTT) and intravenous (IVGTT) glucose tolerance tests and a constant intravenous glucose infusion (4.0 or 4.5 mg/kg/min) with blood sampling every minute for insulin determinations. Insulin concentration time-series were analyzed with complementary mathematical models (deconvolution and autocorrelation analysis, approximate entropy [ApEn], and coefficient of variation [CV] for a 6-point moving average, together with a combined index for regularity and stationarity [RaS] based on the last 2 measures). During the OGTT, the area under the curve (AUC) for plasma glucose was moderately (11%) but significantly (P < .01) elevated in the relatives despite a trend for increased serum insulin (AUC, P = .14). The acute-phase serum insulin response (IVGTT) did not differ between groups (2,055 +/- 330 v 1,766 +/- 229 pmol/L x 10 min, P = .84) but was inappropriately low (individually, P < .05 v control group) for the degree of insulin resistance in 16 relatives. Deconvolution analysis of the insulin time-series did not uncover differences in either the intersecretory pulse interval (5.8 +/- 0.2 v5.7 +/- 0.2 min/pulse) or the fractional secretory burst amplitude (133% +/- 10% v 116% +/- 7% over basal) between the 2 groups. Similarly, significant autocorrelation coefficients were observed in a comparable number of relatives and control subjects (P = .74). In contrast, the RaS index was significantly higher (ie, insulin time-series was more irregular and nonstationary) in the relatives (0.221 +/- 0.194) than in the controls (-0.318 +/- 0.176, P < .05), primarily attributed to the pattern of insulin secretion in relatives with a strong genetic burden. In conclusion, nonstationary and disorderly insulin secretion patterns during glucose stimulation and a low acute-phase serum insulin response associated with significant insulin resistance suggest early beta-cell regulatory dysfunction in individuals genetically predisposed to type 2 diabetes mellitus prior to any evident alterations in insulin secretory burst frequency or mass.

Adult↗

PubMed1996

Classification of cardiac arrhythmias using fuzzy ARTMAP.

We have investigated the QRS complex, extracted from electrocardiogram (ECG) data, using fuzzy adaptive resonance theory mapping (ARTMAP) to classify cardiac arrhythmias. Two different conditions have been analyzed: normal and abnormal premature ventricular contraction (PVC). Based on MIT/BIH database annotations, cardiac beats for normal and abnormal QRS complexes were extracted from this database, scaled, and Hamming windowed, after bandpass filtering, to yield a sequence of 100 samples for each ORS segment. From each of these sequences, two linear predictive coding (LPC) coefficients were generated using Burg's maximum entropy method. The two LPC coefficients, along with the mean-square value of the QRS complex segment, were utilized as features for each condition to train and test a fuzzy ARTMAP neural network for classification of normal and abnormal PVC conditions. The test results show that the fuzzy ARTMAP neural network can classify cardiac arrhythmias with greater than 99% specificity and 97% sensitivity.

Algorithms↗

PubMed1997

Disorderly and nonstationary insulin secretion in relatives of patients with NIDDM.

To further explore the role of the beta-cell as a pathogenic factor behind non-insulin-dependent diabetes mellitus (NIDDM), insulin secretion at modest hyperglycemia was examined in 15 healthy first-degree relatives of NIDDM patients and 13 anthropometrically and age-matched controls. The oral glucose tolerance test was normal in all, but the relatives had impaired insulin-stimulated glucose uptake (P < 0.05). During a constant intravenous glucose infusion we performed a time-series analysis of serum insulin in samples obtained at 1-min intervals for 75 min (60-135 min). The recently introduced scale- and model-independent statistic approximate entropy (ApEn) and the coefficient of variation for a 6- (9 and 15) point moving average (MA) were applied to test regularity and stationarity, respectively, of insulin secretion. Both ApEn and 6-point MA were able to significantly discern the insulin time series of the two groups (P < 0.05), demonstrating a higher degree of irregularity and nonstationarity among the offspring. Moreover, when the two complementary sets of statistics were combined into a single "index of nonpulsatility," an even more notable distinction was available (P < 0.01). No relationship was found between altered insulin secretion and insulin resistance. In conclusion, this experimental and statistical model demonstrates that the stimulated insulin secretion of glucose-tolerant relatives of NIDDM patients is characterized by disorderliness. Whether the model can predict the risk for developing a clinically important beta-cell dysfunction remains to be clarified.

Adult↗