Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Ensemble methods”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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

At least 217 records · Page 12Linked to original sources
PubMed1997

Non-random ionic-charge distribution responsible for the structural stability and molecular recognition of proteins.

The 'ionic-charge shuffling method' is presented to generate a complete set of electrostatic mutants for a natural protein where ionic charges on the molecular surface of the template protein are exhaustively interchanged with each other. Total Coulomb interaction energies are evaluated for all of the mutants by numerically solving the finite difference Poisson-Boltzmann equation and their distribution in the ensemble is obtained. This method has been applied to five natural proteins to reveal that they have a significantly lower Coulomb energy than the average over the ensemble of their mutants. It is also shown that these natural proteins have a significantly larger and smaller number of pairs of attractive and repulsive ionic groups, respectively, than those expected for their randomly shuffled ensemble: They have been 'designed' through molecular evolution so that a pair of ionic charges with opposite signs may have a higher tendency to be located close to each other, while a pair with the same sign are away from each other.

Ions↗
PubMed2003

[Ultrasound of acute abdomen].

Ultrasound is an important tool in the diagnosis of acute abdominal pain, which is mainly caused by gastrointestinal diseases. This article gives an overview on the important differential diagnosis related to pain localization. Sonomorphological signs and their sensitivity and specificity are discussed. In contrast to other imaging methods ultrasound is hand guided. The present article differentiates the diagnostic capability of ultrasonic diagnosis depending on technical equipment and sonographer's educational level. These facts are important to stabilize the position of ultrasound in the ensemble of other imaging methods. The use of mobile ultrasound machines and an improved training (e.g. by computer assisted sonosimulator systems) will lead to an increasing importance of ultrasound.

Abdomen↗
PubMed2004

Reaction ensemble molecular dynamics: direct simulation of the dynamic equilibrium properties of chemically reacting mixtures.

A molecular simulation method to study the dynamics of chemically reacting mixtures is presented. The method uses a combination of stochastic and dynamic simulation steps, allowing for the simulation of both thermodynamic and transport properties. The method couples a molecular dynamics simulation cell (termed dynamic cell) to a reaction mixture simulation cell (termed control cell) that is formulated upon the reaction ensemble Monte Carlo (RxMC) method, hence the term reaction ensemble molecular dynamics. Thermodynamic and transport properties are calculated in the dynamic cell by using a constant-temperature molecular dynamics simulation method. RxMC forward and reverse reaction steps are performed in the control cell only, while molecular dynamics steps are performed in both the dynamic cell and the control cell. The control cell, which acts as a sink and source reservoir, is maintained at reaction equilibrium conditions via the RxMC algorithm. The reaction ensemble molecular dynamics method is analogous to the grand canonical ensemble molecular dynamics technique, while using some elements of the osmotic molecular dynamics method, and so simulates conditions that directly relate to real, open systems. The accuracy and stability of the method is assessed by considering the ammonia synthesis reaction N2 +3 H2 <-->2N H3 . It is shown to be a viable method for predicting the effects of nonideal environments on the dynamic properties (particularly diffusion) as well as reaction equilibria for chemically reacting mixtures.

Journal Article↗
PubMed2004

Cortical cartography using the discrete conformal approach of circle packings.

Cortical flattening algorithms are becoming more widely used to assist in visualizing the convoluted cortical gray matter sheet of the brain. Metric-based approaches are the most common but suffer from high distortions. Conformal, or angle-based algorithms, are supported by a comprehensive mathematical theory. The conformal approach that uses circle packings is versatile in the manipulation and display of results. In addition, it offers some new and interesting metrics that may be useful in neuroscientific analysis and are not available through numerical partial differential equation conformal methods. In this paper, we begin with a brief description of cortical "flat" mapping, from data acquisition to map displays, including a brief review of past flat mapping approaches. We then describe the mathematics of conformal geometry and key elements of conformal mapping. We introduce the mechanics of circle packing and discuss its connections with conformal geometry. Using a triangulated surface representing a cortical hemisphere, we illustrate several manipulations available using circle packing methods and describe the associated "ensemble conformal features" (ECFs). We conclude by discussing current and potential uses of conformal methods in neuroscience and computational anatomy.

Algorithms↗
PubMed2002

Assessment of the risk of heat disorders encountered during work in hot conditions.

OBJECTIVE: To co-ordinate the work of the main European research teams in the field of thermal factors in order to develop and improve significantly the methods presently available for assessing the risks of heat disorders encountered during work in hot conditions. METHOD: Each item from the required sweat rate model was reviewed on the basis of the most recent literature. A database with 1,113 laboratory and field experiments, covering the whole range of hot working conditions, was assembled and used for the validation. RESULTS: Influence of clothing ensemble on heat exchange: methods and formulas were developed that take into account the dynamic effects associated with forced convection and the pumping effect associated with body movements and exercise. Prediction of the average skin temperature: the model used in the required sweat rate standard ISO 7933 was extended to cover more severe conditions with high radiation and high humidity and different clothing and take into account the rectal temperature for the prediction of the skin temperature. Criteria for estimating acceptable exposure times in hot work environments: criteria were reviewed and updated concerning the maximum increase in core temperature and the acceptable water loss, for acclimatised and nonacclimatised subjects. These limits are intended to protect 95% of the population. Measuring strategy: a strategy was developed to assess the risks in any working situation with varying conditions of climate, metabolic rate or clothing. A detailed methodology was developed in three stages: an "observation" method for the recognition of the conditions that might lead to thermal stress; an "analysis" method for evaluating the problem and optimising the solutions; and an "expert" method for in-depth analysis of the working situation when needed. VALIDATION: the different results were used to prepare a revision of the interpretation procedure proposed in the ISO standard 7933. We validated the modified approaches using the database. This involved the whole range of conditions for which the model was extended, namely conditions with high and low radiation, humidity and air velocity as well as fluctuating conditions. Based on these results, the predicted heat strain model was developed: it is presently proposed as an ISO and CEN standard.

Biomechanical Phenomena↗
PubMed2006

Classifier ensembles for protein structural class prediction with varying homology.

Structural class characterizes the overall folding type of a protein or its domain. A number of computational methods have been proposed to predict structural class based on primary sequences; however, the accuracy of these methods is strongly affected by sequence homology. This paper proposes, an ensemble classification method and a compact feature-based sequence representation. This method improves prediction accuracy for the four main structural classes compared to competing methods, and provides highly accurate predictions for sequences of widely varying homologies. The experimental evaluation of the proposed method shows superior results across sequences that are characterized by entire homology spectrum, ranging from 25% to 90% homology. The error rates were reduced by over 20% when compared with using individual prediction methods and most commonly used composition vector representation of protein sequences. Comparisons with competing methods on three large benchmark datasets consistently show the superiority of the proposed method.

Algorithms↗
PubMed2001

2-D motion estimation using two parallel receive beams.

We describe a method for estimating 2-D target motion using ultrasound. The method is based on previous ensemble tracking techniques, which required at least four parallel receive beams and 2-D pattern matching. In contrast, the method described requires only two parallel receive beams and 1-D pattern matching. Two 1-D searches are performed, one in each lateral direction. The direction yielding the best match indicates the lateral direction of motion. Interpolation provides sub-pixel magnitude resolution. We compared the two beam method with the four beam method using a translating speckle target at three different parallel beam steering angles and transducer angles of 0, 45, and 90 degrees. The largest differences were found at 90 degrees, where the two beam method was generally more accurate and precise than the four beam method and also less prone to directional errors at small translations. We also examined the performance of both methods in a laminar flow phantom. Results indicated that the two beam method was more accurate in measuring the flow angle when the flow velocity was small. Computer simulations supported the experimental findings. The poorer performance of the four beam method was attributed to differences in correlation among the parallel beams. Specifically, center beams 2 and 3 correlated better with each other than with the outer beams. Because the four beam method used a comparison of a kernel region in beam pair 2-3 with two different beam pairs 1-2 and 3-4, the 2-to-1 and 3-to-4 components of this comparison increased the incidence of directional errors, especially at small translations. The two beam method used a comparison between only two beams and so was not subject to this source of error. Finally, the two beam method did not require amplitude normalization, as was necessary for the four beam method, when the two beams were chosen symmetric to the transmit axis. We conclude that two beam ensemble tracking can accurately estimate motion using only two parallel receive beams.

Biomedical Engineering↗
PubMedDate not supplied

MIMUMBA revisited: torsion angle rules for conformer generation derived from X-ray structures.

A method has been developed which automatically generates SMARTS patterns for four-atomic torsional fragments, searches experimental structures in the Cambridge Crystallographic Database, and obtains rules for preferred torsion angles in drug-size molecules. These rules can be used for exhaustive conformational analysis using the popular conformer generator OMEGA. This approach results in an overall improvement of quality and coverage of conformational space when comparing conformer ensembles generated by this method with results obtained by using the default OMEGA setup. In particular, the percentage of structures with at least one conformation closer than 0.5 A to the X-ray structure improves from 84% to 92% in a test set of 11 027 experimental structures from the CSD. Moreover, the average RMS distance of the closest conformation to the X-ray structure improves from 0.30 to 0.22 A.

Chemistry↗
PubMed2000

Landscape approaches for determining the ensemble of folding transition states: success and failure hinge on the degree of frustration.

We present a method for determining structural properties of the ensemble of folding transition states from protein simulations. This method relies on thermodynamic quantities (free energies as a function of global reaction coordinates, such as the percentage of native contacts) and not on "kinetic" measurements (rates, transmission coefficients, complete trajectories); consequently, it requires fewer computational resources compared with other approaches, making it more suited to large and complex models. We explain the theoretical framework that underlies this method and use it to clarify the connection between the experimentally determined Phi value, a quantity determined by the ratio of rate and stability changes due to point mutations, and the average structure of the transition state ensemble. To determine the accuracy of this thermodynamic approach, we apply it to minimalist protein models and compare these results with the ones obtained by using the standard experimental procedure for determining Phi values. We show that the accuracy of both methods depends sensitively on the amount of frustration. In particular, the results are similar when applied to models with minimal amounts of frustration, characteristic of rapid-folding, single-domain globular proteins.

Kinetics↗
PubMedDate not supplied

Ensemble of linear models for predicting drug properties.

We propose a new classification method for the prediction of drug properties, called random feature subset boosting for linear discriminant analysis (LDA). The main novelty of this method is the ability to overcome the problems with constructing ensembles of linear discriminant models based on generalized eigenvectors of covariance matrices. Such linear models are popular in building classification-based structure-activity relationships. The introduction of ensembles of LDA models allows for an analysis of more complex problems than by using single LDA, for example, those involving multiple mechanisms of action. Using four data sets, we show experimentally that the method is competitive with other recently studied chemoinformatic methods, including support vector machines and models based on decision trees. We present an easy scheme for interpreting the model despite its apparent sophistication. We also outline theoretical evidence as to why, contrary to the conventional AdaBoost ensemble algorithm, this method is able to increase the accuracy of LDA models.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2005

Density-functional theory-based chemical reactivity indices in the Hartree-Fock method. I. Unrestricted Hartree-Fock method for a noninteger number of electrons.

Correct evaluation of the reactivity indices, such as chemical potential, hardness, and Fukui function demands for the extension of the formalism beyond the integer particle picture. An ensemble approach is used as an extension of the unrestricted Hartree-Fock (UHF) method for noninteger electron number systems. A prescription is given for the construction of an ensemble Fock operator for a system with partially filled spin-orbitals. The comparison between the ensemble HF method and the hyper-HF method in terms of density matrices and spin-orbitals is presented. The equivalence of the equiensemble case and the ensemble UHF case with unequal weight factors is shown.

Journal Article↗
PubMed2006

Computing the starting state for Gibbs-Duhem integration.

Gibbs-Duhem integration implies the numerical integration of a Clapeyron equation. To start the numerical integration, an initial coexistence point and a corresponding initial slope of the Clapeyron equation are needed. In order to apply Gibbs-Duhem integration to all kinds of systems at diverse physical conditions, one has to investigate and assess the available methods that can be used to compute these initial values. This publication focuses on vapor-liquid equilibria in binary mixtures comprising chain molecules. The initial coexistence point is either computed with the NVbeta Gibbs ensemble or with the Npbeta+test molecule method with overlapping distributions, which is introduced in this publication. Although computationally demanding, the Npbeta+test molecule method with overlapping distributions is applicable at conditions where the NVbeta Gibbs ensemble fails. We investigated three methods that can be employed to compute the initial slope of the Clapeyron equation. The Widom method and the overlapping-distributions difference method provide correct values for the initial slope. The difference method does only provide the correct answer in special cases. The possibility to judge the reliability of the results makes the overlapping-distributions difference method the safest route to the initial slope. Gibbs-Duhem integration requires the frequent computation of the slope of the Clapeyron equation. This slope depends on ensemble averages of the composition. A new bias method for efficient sampling of the composition in a semigrand-canonical simulation of chain molecules is presented. This bias method considerably enhances the composition sampling in systems comprising chain molecules of different sizes.

Journal Article↗
PubMed1992

Identification of time-varying biological systems from ensemble data.

The theory underlying a new method for the identification of time-varying systems is described. The method uses singular value decomposition to obtain least-squares estimates of time-varying impulse response functions from an ensemble of input-output realizations. No a priori assumptions regarding the system structure or form of the time-variation are required and there are few restrictions on the input signal. Simulation studies, using a model of time-varying joint dynamics, show that the method can track rapid changes in system dynamics accurately and is robust in the presence of output noise. An application of the method is demonstrated by using it to track dynamic ankle stiffness during a rapid, voluntary, isometric contraction. During the transient phase of the contraction, low-frequency ankle stiffness gain decreased in a manner which could not be described with the second-order model of joint dynamics often used under stationary conditions.

Adult↗
PubMed2003

Rare fluctuations of native proteins sampled by equilibrium hydrogen exchange.

We present a method for determining the ensembles of native protein structures that result from the large fluctuations of low probability revealed by hydrogen-exchange experiments. The measured protection factors are used to bias Monte Carlo simulations to sample the structures of the exchange competent species. The approach is illustrated by its application to the case of alpha-lactalbumin.

Humans↗
PubMed1986

[Structural organization and connections of cell ensembles of the olfactory bulb of the cat brain].

The cat cerebral olfactory tubercle (OT) includes into its composition certain cellular ensembles distinguished by means of morphological criteria. The ensembles consist of three cellular components: clusters of granular neurons (islands of Calleja), pyramid-like neurons of the layer II, situating along the periphery of the islands, and groupings made by polygonal and spindle-like neurons of the layer III. Morphometrical analysis of every of the three cellular complex components has been carried out. About 7-10 islands of Calleja are situated on the OT territory, which makes nearly 75% of the whole surface of the OT. Neuronal composition of the cellular ensembles has been studied by Golgi method. Varieties of long and short axonal neurons, included into the ensemble composition, have been characterized. Presence of projections of the macrocellular neurons of the layer III (a part of the third component of the ensemble) has been revealed in the posterior part of the lateral hypothalamus and in the field of Forel H1. Possible role of the cellular ensembles is discussed for ensuring various functions of the OT.

Animals↗
PubMed1993

Representing an ensemble of NMR-derived protein structures by a single structure.

The usefulness of representing an ensemble of NMR-derived protein structures by a single structure has been investigated. Two stereochemical properties have been used to assess how a single structure relates to the ensemble from which it was derived, namely the distribution of phi psi torsion angles and the distribution of chi 1 torsion angles. The results show that the minimized average structure derived from the ensemble (a total of 11 ensembles from the Brookhaven Protein Data Bank were analyzed) does not always correspond well with this ensemble, particularly for those ensembles generated with a smaller number of experimentally derived restraints per residue. An alternative method that selects the member of the ensemble which is closest to the "average" of the ensemble has been investigated (a total of 23 ensembles from the Brookhaven Protein Data Bank were analyzed). Although this method selected a structure that on the whole corresponded more closely to the ensemble than did the minimized average structure, this is still not a totally reliable means of selecting a single structure to represent the ensemble. This suggests that it is advisable to study the ensemble as a whole. A study has also been made of the practice of selecting the "best" rather than the most representative member of the ensemble. This too suggests that the ensemble should be studied as a whole. A study of the conformational space occupied by the ensemble also suggests the need to consider the ensemble as a whole, particularly for those ensembles generated with a smaller number of experimentally derived restraints per residue.

Animals↗
PubMed2006

Chain conformation and solvent partitioning in reversed-phase liquid chromatography: Monte Carlo simulations for various water/methanol concentrations.

Many structural models for the stationary phase in reversed-phase liquid chromatography (RPLC) systems have been suggested from thermodynamic and spectroscopic measurements and theoretical considerations. To provide a molecular picture of chain conformation and solvent partitioning in a typical RPLC system, a particle-based Monte Carlo simulation study is undertaken for a dimethyl octadecyl (C(18)) bonded stationary phase on a model siliceous substrate in contact with mobile phases having different methanol/water concentrations. Following upon previous simulations for gas-liquid chromatography and liquid-liquid phase equilibria, the simulations are conducted using the configurational-bias Monte Carlo method in the Gibbs ensemble and the transferable potentials for phase equilibria force field. The simulations are performed for a chain surface density of 2.9 micromol/m(2), which is a typical bonded-phase coverage for mono-functional alkyl silanes. The solvent concentrations used here are pure water, approximately 33 and 67% mole fraction of methanol and pure methanol. The simulations show that the chain conformation depends only weakly on the solvent composition. Most chains are conformationally disordered and tilt away from the substrate normal. The interfacial width increases with increasing methanol content and, for mixtures, the solvent shows an enhancement of the methanol concentration in a 10 Angstrom region outside the Gibbs dividing surface. Residual surface silanol groups are found to provide hydrogen bonding sites that lead to the formation of substrate bound water and methanol clusters, including bridging clusters that penetrate from the solvent/chain interfacial region all the way to the silica surface.

Chromatography, Liquid↗
PubMed1996

Analysis of topological and nontopological structural similarities in the PDB: new examples with old structures.

We have developed a new method and program, SARF2, for fast comparison of protein structures, which can detect topological as well as nontopological similarities. The method searches for large ensembles of secondary structure elements, which are mutually compatible in two proteins. These ensembles consist of small fragments of C alpha-trace, similarly arranged in three-dimensional space in two proteins, but not necessarily equally-ordered along the polypeptide chains. The program SARF2 is available for everyone through the World-Wide Web (WWW). We have performed an exhaustive pairwise comparison of all the entries from a recent issue of the Protein Data Bank (PDB) and report here on the results of an automated hierarchical cluster analysis. In addition, we report on several new cases of significant structural resemblance between proteins. To this end, a new definition of the significance of structural similarity is introduced, which effectively distinguishes the biologically meaningful equivalences from those occurring by chance. Analyzing the distribution of sequence similarity in significant structural matches, we show that sequence similarity as low as 20% in structurally-prealigned proteins can be a strong indication for the biological relevance of structural similarity.

Algorithms↗