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PubMed1997

Nonlinear trading models through Sharpe Ratio maximization.

While many trading strategies are based on price prediction, traders in financial markets are typically interested in optimizing risk-adjusted performance such as the Sharpe Ratio, rather than the price predictions themselves. This paper introduces an approach which generates a nonlinear strategy that explicitly maximizes the Sharpe Ratio. It is expressed as a neural network model whose output is the position size between a risky and a risk-free asset. The iterative parameter update rules are derived and compared to alternative approaches. The resulting trading strategy is evaluated and analyzed on both computer-generated data and real world data (DAX, the daily German equity index). Trading based on Sharpe Ratio maximization compares favorably to both profit optimization and probability matching (through cross-entropy optimization). The results show that the goal of optimizing out-of-sample risk-adjusted profit can indeed be achieved with this nonlinear approach.

Algorithms↗

PubMed2006

[Monitoring the depth of anesthesia using a fuzzy neural network based on EEG].

In this paper, a fuzzy neural network (FNN) is proposed for fusing the anesthesia information, and realizing the monitoring of the depth of anesthesia (DOA). EEG data from 31 patients undergoing general anesthesia with different anesthetic agents, and Kc complexity (Kc), approximate entropy (ApEn) were extracted and the fuzzy neural network was trained by 25 samples, and tested by the other 6 samples. The results show that the outputs of the fuzzy neural network whose inputs were Kc and ApEn obtained under the awake state and asleep state, exist obvious difference. It can be regarded as an quantitative index to estimate DOA.

Algorithms↗

PubMedDate not supplied

Evaluation of free energy landscape for base-amino acid interactions using ab initio force field and extensive sampling.

Structural data of protein-DNA complex show redundancy and flexibility in base-amino acid interactions. To understand the origin of the specificity in protein-DNA recognition, we calculated the interaction free energy, enthalpy, entropy, and minimum energy maps for AT-Asn, GC-Asn, AT-Ser, and GC-Ser by means of a set of ab initio force field with extensive conformational sampling. We found that the most preferable interactions in these pairs are stabilized by hydrogen bonding, and are mainly enthalpy driven. However, minima in the free energy maps are not necessarily the same as those in the minimum energy map or enthalpy maps, due to the entropic effect. The effect of entropy is particularly important in the case of GC-Asn. Experimentally observed structures of base-amino acid interactions are within preferable regions in the calculated free energy maps, where there are many different interaction configurations with similar energy. The full geometry optimization procedure using ab initio molecular orbital method was applied to get the optimal interaction geometries for AT-Asn, GC-Asn, AT-Ser, and GC-Ser. We found that there are various base-amino acid combinations with similar interaction energies. These results suggest that the redundancy and conformational flexibility in the base-amino acid interactions play an important role in the protein-DNA recognition.

Adenine↗

PubMed2006

Entropic folding pathway of human epidermal growth factor explored by disulfide scrambling and amplified collective motion simulations.

Epidermal growth factor (EGF) regulates cell proliferation and differentiation by binding to the EGF receptor (EGFR) extra-cellular domains. Human EGF is a small, single-chain protein comprising three distinct loops (A, B, and C), which are connected by three disulfide bridges (Cys6-Cys20, Cys14-Cys31, and Cys33-Cys42). These disulfide bridges are essential for structural stability and biological activity. EGF was extensively studied by disulfide scrambling, an experimental technique for the conformational entrapment of intermediate states, which allows us to study the folding pathway of proteins containing disulfide bonds. The experimental results showed that there is a major 2-disulfide intermediate (denoted EGF-II) and that the native disulfide bonding pattern is less prevalent in one of the mutants. In this article, we investigated for the first time the solution conformations of wild-type EGF, EGF-II, and the mutant S9C through extensive molecular dynamics (MD) simulations in water using both the standard MD technique and a recently developed amplified-collective-motion (ACM) sampling method. Compared to standard MD simulations, we achieved a much more enhanced sampling by the ACM simulations, and the structures were sufficiently relaxed to estimate configurational entropies. The simulation results suggest a predominantly entropic folding pathway governed by the disorder of three functional loop regions. Although EGF-II exhibits two native disulfide bonds (Cys14-Cys31 and Cys33- Cys42), its large configurational entropy inhibits a direct transition to the native structure in the folding process. When Ser9 is mutated into Cys, a non-native disulfide bridge Cys9- Cys20 is slightly more favorable than the native Cys6-Cys20 because a less constrained N-terminus affords larger entropy. Isomers that are functionally less active also exhibit a more localized dynamics of the functional loop regions, which may suggest a possible mechanism for the modulation of EGF activity.

Amino Acid Sequence↗

PubMedDate not supplied

Thermodynamic parameters for the intramolecular disordered-to-beta transition of poly(L-tyrosine) in aqueous solution.

We have examined the disordered-to-beat transition of two samples of high molecular wieght poly(L-tyrosine), a polypeptide with an ionizing side chain, by potentiometric titration of solutions of this polymer in aqueous buffer. The degree of ionization was determined spectrophotometrically from the absorption of the tyrosinate anion at 293.5 nm. By using polymer solutions of high dilution the region of the conformational transition was separated from that of aggregation. As a consequence it was possible to obtain titration data for the intramolecular transition which we believe are free of interference from aggregation. For this transition we found that deltaHO=-1330 cal/mol of residue. The two samples gave values of -3.42+/-0.14 and -3.85+/-0.10 u for the change in entropy. Possible artifactual origins for this distinction have been examined and may be dicounted. Rather, it probably reflects a difference in the beta structures formed which depends on molecular weight.

Hydrogen-Ion Concentration↗

PubMed2003

Moment analysis of retention equilibrium, mass transfer kinetics, and thermodynamic properties in reversed-phase liquid chromatography using phenyl bonded silica gel.

Information about retention equilibrium, mass transfer kinetics, and related thermodynamic properties of chromatography using phenyldimethylsilyl (Ph)-silica gel was derived by moment analysis of pulse response peak profiles. The results for the Ph-silica gel were compared with those for octadecyldimethylsilyl (C18)-silica gel. Some parameters characterizing the chromatographic behavior of the two stationary phases were correlated with the hydrophobic surface area of sample molecules. Surface diffusion had a predominant role for intraparticle diffusion. An enthalpy-entropy compensation was established for both the retention equilibrium and surface diffusion. A linear correlation was observed between the logarithm of surface diffusion coefficient (Ds) and that of retention equilibrium constant (Ka), suggesting the establishment of a linear free energy relationship. The ratio of Ds to molecular diffusivity (Dm) decreased with increasing Ka and was correlated by a single curved line. The value of Ds was of the same order of magnitude with Dm when Ka became negligible. These results suggest the presence of a sort of correlation between surface diffusion and molecular diffusion and the restriction of the molecular mobility by surface diffusion due to the retention strength.

Air Pollutants↗

PubMed2004

Age and testosterone feedback jointly control the dose-dependent actions of gonadotropin-releasing hormone in healthy men.

Healthy older men manifest combined declines in testosterone concentrations, LH secretory burst mass (amount of LH released per pulse), and feedback-sensitive regularity of unknown cause. To test a unifying hypothesis of simultaneous reductions in GnRH outflow, gonadotrope responsiveness to GnRH, and androgenic negative feedback, we monitored LH secretion 1) after bolus iv injection of a 1000-fold range of randomly ordered individual doses of GnRH on separate mornings, 2) during unmodified (eugonadal) or testosterone-withdrawn (hypoandrogenemic) negative feedback, and 3) in 16 young (age, 18-35 yr) and 15 older (age, 60-85 yr) healthy men. LH secretory burst mass and pattern regularity were quantitated by intensive blood sampling, high specificity LH beta-subunit-directed immunoradiometric assay, deconvolution analysis, and approximate entropy. GnRH dose responsiveness was assessed by four-parameter nonlinear regression analysis. We demonstrated that older men exhibit 1) delayed attainment of GnRH-evoked maximal LH secretion; 2) enhanced potency of GnRH stimulation in both the feedback-intact and feedback-withdrawn states; 3) elevated gonadotrope sensitivity to GnRH, unmasked by experimental testosterone depletion; 4) comparable young adult-like GnRH efficacy, independent of testosterone feedback milieu; and 5) diminished regularity of GnRH-induced LH release evident only during unmodified androgenic feedback. We conclude that a 3-fold interaction among GnRH dose, testosterone concentration, and age governs GnRH action, and age determines both testosterone-modulated and testosterone-independent actions of GnRH.

Adolescent↗

PubMed2006

Folding, misfolding, and amyloid protofibril formation of WW domain FBP28.

We study the folding mechanism of a triple beta-strand WW domain from the Formin binding protein 28 (FBP28) at atomic resolution with explicit water model using replica exchange molecular dynamics computer simulations. Extended sampling over a wide range of temperatures to obtain the free energy, enthalpy, and entropy surfaces as a function of structural coordinates has been performed. Simulations were started from different configurations covering the folded and unfolded states. In the free energy landscape a transition state is identified and its structures and -values are compared with experimental data from a homologous protein, the prolyl-isomerase Pin1 WW domain. A stable intermediate state is found to accumulate during the simulation characterized by the carboxyl-terminal beta-strand 3 having misregistered hydrogen bonds and where the structural heterogeneity is due to nonnative turn II formation. Furthermore, the aggregation behavior of the FBP28 WW domain may be related to one such misfolded structure, which has a much lower free energy of dimer formation than that of the native dimer. Based on the misfolded dimer, aggregation to form protofibril structure is discussed.

Amyloid↗

PubMed2002

A correction algorithm for undersampled images using dynamic segmentation and entropy based focus criterion.

A post-processing technique is presented for correcting images undersampled in k-space. The method works by taking advantage of the image's background zeros (dynamically segmented through the application of a threshold) to extrapolate the missing k-space samples. The algorithm can produce good quality images from a small set of k-space frequencies with only a few iterations of simple matrix operations, using the image entropy as the focus criterion. It does not require any special patient preparation, extra pulse sequences, complex gradient programming or specialized hardware. This makes it a good candidate for any application that requires short scan times or where only few frequencies can be sampled.

Algorithms↗

PubMed2003

Heuristic charge assignment for deconvolution of electrospray ionization mass spectra.

We propose a new algorithm for deconvolution of electrospray ionization mass spectra based on direct assignment of charge to the measured signal at each mass-to-charge ratio (m/z). We investigate two heuristics for charge assignment: the entropy-based heuristic is adapted from a deconvolution algorithm by Reinhold and Reinhold;10 the multiplicative-correlation heuristic is adapted from the multiplicative-correlation deconvolution algorithm of Hagen and Monnig.6 The entropy-based heuristic is insensitive to overestimates of z(max), the maximum ion charge. We test the deconvolution algorithm on two single-component samples: the measured spectrum of human beta-endorphin has two prominent and one very weak line whereas myoglobin has a well-developed quasi-gaussian envelope of 17 peaks. In both cases, the deconvolution algorithm gives a clean deconvoluted spectrum with one dominant peak and very few artefacts. The relative heights of the peaks due to the parent molecules in the deconvoluted spectrum of a mixture of two peptides, which are expected to ionize with equal efficiency, give an accurate measure of their relative concentration in the sample.

Algorithms↗

PubMedDate not supplied

Semisupervised learning for molecular profiling.

Class prediction and feature selection are two learning tasks that are strictly paired in the search of molecular profiles from microarray data. Researchers have become aware how easy it is to incur a selection bias effect, and complex validation setups are required to avoid overly optimistic estimates of the predictive accuracy of the models and incorrect gene selections. This paper describes a semisupervised pattern discovery approach that uses the by-products of complete validation studies on experimental setups for gene profiling. In particular, we introduce the study of the patterns of single sample responses (sample-tracking profiles) to the gene selection process induced by typical supervised learning tasks in microarray studies. We originate sample-tracking profiles as the aggregated off-training evaluation of SVM models of increasing gene panel sizes. Genes are ranked by E-RFE, an entropy-based variant of the recursive feature elimination for support vector machines (RFE-SVM). A Dynamic Time Warping (DTW) algorithm is then applied to define a metric between sample-tracking profiles. An unsupervised clustering based on the DTW metric allows automating the discovery of outliers and of subtypes of different molecular profiles. Applications are described on synthetic data and in two gene expression studies.

Algorithms↗

PubMed1999

Hormone pulsatility discrimination via coarse and short time sampling.

Pulsatile hormonal secretion is a ubiquitous finding in endocrinology. However, typical protocols employed to generate data sets suitable for "pulsatility analysis" have required 60-300 samples, rendering such studies largely research methodologies, due primarily to considerable assay expense. One successful mathematical strategy in calibrating changes in pulsatility modalities is approximate entropy (ApEn), a quantification of sequential irregularity. Given the degree of differences between ApEn values in pathophysiological subjects vs. healthy controls reported in several recent studies, we queried to what extent coarser (less frequent) and shorter duration time sampling would still retain significant ApEn differences between clinically distinct cohorts. Accordingly, we reanalyzed data from two studies of 24-h profiles of healthy vs. tumoral hormone secretion: 1) growth hormone comparisons of normal subjects vs. acromegalics, originally sampled every 5 min; and 2) ACTH and cortisol comparisons of normal subjects vs. Cushing's disease patients, originally sampled every 10 min. By multiple statistical analyses, we consistently and highly significantly (P < 0.0001) established that serum concentration patterns in tumor patients are more irregular than those of controls, with high sensitivity and specificity, even at very coarse (e.g., 60 min) sampling regimens and over relatively short (2-4 h) time intervals. The consistency of these findings suggests a broadly based utility of such shorter and/or coarser sampling methodologies. Substantial reduction in sampling requirements holds the potential to move analysis of pulsatile hormone release from a primarily research tool to a clinically applicable protocol, in appropriate diagnostic and therapeutic contexts.

Acromegaly↗

PubMed2005

Strategies for selecting subsets of single-nucleotide polymorphisms to genotype in association studies.

In genetic association studies, linkage disequilibrium (LD) within a region can be exploited to select a subset of single-nucleotide polymorphisms (SNPs) to genotype with minimal loss of information. A novel entropy-based method for selecting SNPs is proposed and compared to an existing method based on the coefficient of determination (R2) using simulated data from Genetic Analysis Workshop 14. The effect of the size of the sample used to investigate LD (by estimating haplotype frequencies) and hence select the SNPs is also investigated for both measures. It is found that the novel method and the established method select SNP subsets that do not differ greatly. The entropy-based measure may thus have value because it is easier to compute than R2. Increasing the sample size used to estimate haplotype frequencies improves the predictive power of the subset of SNPs selected. A smaller subset of SNPs chosen using a large initial sample to estimate LD can in some instances be more informative than a larger subset chosen based on poor estimates of LD (using a small initial sample). An initial sample size of 50 individuals is sufficient in most situations investigated, which involved selection from a set of 7 SNPs, although to select a larger number of SNPs, a larger initial sample size may be required.

Genetic Loci↗

PubMed2005

Improvement of duty-cycle heating compensation in NMR spin relaxation experiments.

To reliably measure NMR relaxation properties of macromolecules is a prerequisite for precise experiments that identify subtle variations in relaxation rates, as required for the determination of rotational diffusion anisotropy, CSA tensor determination, advanced motional modeling or entropy difference estimations. An underlying problem with current NMR relaxation measurement protocols is maintaining constant sample temperature throughout the execution of the relaxation series especially when rapid data acquisition is required. Here, it is proposed to use a combination of a heating compensation and a proton saturation sequence at the beginning of the NMR relaxation pulse scheme. This simple extension allows reproducible, robust and rapid acquisition of NMR spin relaxation data sets. The method is verified with (15)N spin relaxation measurements for human ubiquitin.

Algorithms↗

PubMed1995

Diurnal variations in blood chemical items in Sprague-Dawley rats.

Diurnal variations in 23 blood chemical items were investigated in Sprague-Dawley rats of both sexes at 6 weeks of age. Blood samples were obtained every two hours. One to three periodic components detected by the maximum entropy method from the observed time-series and the optimum fitting parameters were calculated by the least squares method. The fitting curves were compared with the observed data for the evaluation of systematic and fluctuating parts of the time domain as circadian variations. The periodic components were detected from all the blood chemical items examined. This suggests that all items have systematic parts as basic rhythmic changes. The optimum fitting curves corresponded to the observed time-series in the following items: glucose, total protein, A/G ratio, alkaline phosphatase, Na, K, Cl and BUN of both sexes and total cholesterol, triglyceride, cholinesterase, CPK, inorganic phosphorus, direct and total bilirubin, creatinine and uric acid in males. Others showed insufficient correspondence to many fluctuating parts. This randomness was more frequently seen in females than in males.

Animals↗

PubMed2000

Conformational features of a hexapeptide model Ac-TGAAKA-NH2 corresponding to a hydrated alpha helical segment from glyceraldehyde 3-phosphate dehydrogenase: implications for the role of turns in helix folding.

Recent analysis of alpha helices in protein crystal structures, available in literature, revealed hydrated alpha helical segments in which, water molecule breaks open helix 5-->1 hydrogen bond by inserting itself, hydrogen bonds to both C=O and NH groups of helix hydrogen bond without disrupting the helix hydrogen bond, and hydrogen bonds to either C=O or NH of helix hydrogen bond. These hydrated segments display a variety of turn conformations and are thought to be 'folding intermediates' trapped during folding-unfolding of alpha helices. A role for reverse turns is implicated in the folding of alpha helices. We considered a hexapeptide model Ac-1TGAAKA6-NH2 from glyceraldehyde 3-phosphate dehydrogenase, corresponding to a hydrated helical segment to assess its role in helix folding. The sequence is a site for two 'folding intermediates'. The conformational features of the model peptide have been investigated by 1H 2D NMR techniques and quantum mechanical perturbative configuration interaction over localized orbitals (PCILO) method. Theoretical modeling largely correlates with experimental observations. Based upon the amide proton temperature coefficients, the observed d alpha n(i, i + 1), d alpha n(i, i + 2), dnn(i, i + 1), d beta n(i, i + 1) NOEs and the results from theoretical modeling, we conclude that the residues of the peptide sample alpha helical and neck regions of the Ramachandran phi, psi map with reduced conformational entropy and there is a potential for turn conformations at N and C terminal ends of the peptide. The role of reduced conformational entropy and turn potential in helix formation have been discussed. We conclude that the peptide sequence can serve as a 'folding intermediate' in the helix folding of glyceraldehyde 3-phosphate dehydrogenase.

Amino Acid Sequence↗

PubMed1994

Side-chain entropy and packing in proteins.

What role does side-chain packing play in protein stability and structure? To address this question, we compare a lattice model with side chains (SCM) to a linear lattice model without side chains (LCM). Self-avoiding configurations are enumerated in 2 and 3 dimensions exhaustively for short chains and by Monte Carlo sampling for chains up to 50 main-chain monomers long. This comparison shows that (1) side-chain degrees of freedom increase the entropy of open conformations, but side-chain steric exclusion decreases the entropy of compact conformations, thus producing a substantial entropy that opposes folding; (2) there is side-chain "freezing" or ordering, i.e., a sharp decrease in entropy, near maximum compactness; and (3) the different types of contacts among side chains (s) and main-chain elements (m) have different frequencies, and the frequencies have different dependencies on compactness. mm contacts contribute significantly only at high densities, suggesting that main-chain hydrogen bonding in proteins may be promoted by compactness. The distributions of mm, ms, and ss contacts in compact SCM configurations are similar to the distributions in protein structures in the Brookhaven Protein Data Bank. We propose that packing in proteins is more like the packing of nuts and bolts in a jar than like the pairwise matching of jigsaw puzzle pieces.

Drug Stability↗

PubMed2005

Estimation of the absolute internal-rotation entropy of molecules with two torsional degrees of freedom from stochastic simulations.

A method of statistical estimation is applied to the problem of evaluating the absolute entropy of internal rotation in a molecule with two torsional degrees of freedom. The configurational part of the entropy is obtained as that of the joint probability density of an arbitrary form represented by a two-dimensional Fourier series, the coefficients of which are statistically estimated using a sample of the torsional angles of the molecule obtained by a stochastic simulation. The internal rotors in the molecule are assumed to be attached to a common frame, and their reduced moments of inertia are initially calculated as functions of the two torsional angles, but averaged over all the remaining internal degrees of freedom using the stochastic-simulation sample of the atomic configurations of the molecule. The torsional-angle dependence of the reduced moments of inertia can be also averaged out, and the absolute internal-rotation entropy of the molecule is obtained in a good approximation as the sum of the configurational entropy and a kinetic contribution fully determined by the averaged reduced moments of inertia. The method is illustrated using Monte Carlo simulations of isomers of stilbene and halogenated derivatives of propane. The two torsional angles in cis-stilbene are found to be much more strongly correlated than those in trans-stilbene, while the degree of the angular correlation in propane increases strongly on substitution of hydrogen atoms with chlorine.

Journal Article↗