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PubMed2002

Replica field theories, painlevé transcendents, and exact correlation functions.

Exact solvability is claimed for nonlinear replica sigma models derived in the context of random matrix theories. Contrary to other approaches reported in the literature, the framework outlined does not rely on traditional "replica symmetry breaking" but rests on a previously unnoticed exact relation between replica partition functions and Painlevé transcendents. While expected to be applicable to matrix models of arbitrary symmetries, the method is used to treat fermionic replicas for the Gaussian unitary ensemble (GUE), chiral GUE (symmetry classes A and AIII in Cartan classification) and Ginibre's ensemble of complex non-Hermitian random matrices. Further applications are briefly discussed.

Journal Article↗
PubMed2003

Quantitative evaluation of noise reduction strategies in dual-energy imaging.

In this paper we describe a quantitative evaluation of the performance of three dual-energy noise reduction algorithms: Kalender's correlated noise reduction (KCNR), noise clipping (NOC), and edge-predictive adaptive smoothing (EPAS). These algorithms were compared to a simple smoothing filter approach, using the variance and noise power spectrum measurements of the residual noise in dual-energy images acquired with an a-Si TFT flat-panel x-ray detector. An estimate of the true noise was made through a new method with subpixel accuracy by subtracting an individual image from an ensemble average image. The results indicate that in the lung regions of the tissue image, all three algorithms reduced the noise by similar percentages at high spatial frequencies (KCNR=88%, NOC=88%, EPAS=84%, NOC/KCNR=88%) and somewhat less at low spatial frequencies (KCNR=45%, NOC=54%, EPAS=52%, NOC/KCNR=55%). At low frequencies, the presence of edge artifacts from KCNR made the performance worse, thus NOC or NOC combined with KCNR performed best. At high frequencies, KCNR performed best in the bone image, yet NOC performed best in the tissue image. Noise reduction strategies in dual-energy imaging can be effective and should focus on blending various algorithms depending on anatomical locations.

Algorithms↗
PubMed2006

Influence of dementia on antithrombotic therapy prescribed before stroke in patients with atrial fibrillation.

BACKGROUND AND PURPOSE: Oral anticoagulation (OAC) decreases the risk of stroke in patients with nonvalvular atrial fibrillation (NVAF), but remains underused in practice. The aim of this study was to test the hypothesis that prestroke dementia influenced the nonprescription of OAC before stroke. METHODS: This is an ancillary study of Stroke in Atrial Fibrillation Ensemble II, an observational study conducted in patients with a previously known NVAF, consecutively admitted for an acute stroke to French and Italian centers. Prestroke dementia was evaluated by the clinical physician and validated by an Informant Questionnaire for Cognitive Decline in the Elderly score of >or=104 in patients with a reliable informant. RESULTS: Of 204 patients, 24 patients met criteria for prestroke dementia according to GP's opinion. The only variables independently associated with OAC before stroke were follow-up by a cardiologist (adjusted OR: 3.33; 95% CI: 1.47-7.53) and a younger age of patients (adjusted OR: 0.94; 95% CI: 0.89-0.99). Variables independently associated with any antithrombotic drug therapy before stroke were follow-up by a general practitioner (adjusted OR: 2.78; 95% CI: 1.09-7.11), and by a cardiologist (adjusted OR: 3.15; 95% CI: 1.48-6.69). CONCLUSION: In daily practice, the under-prescription of OAC in patients with NVAF mainly depends on co-morbidity and on characteristics of the physician, not on prestroke dementia.

Administration, Oral↗
PubMed2006

[Application of boosting-based decision tree ensemble classifiers for discrimination of thermophilic and mesophilic proteins].

In this paper, the Boosting-based decision tree ensemble classifiers were applied to discriminate thermophilic and mesophilic proteins. Three methods, namely, self-consistency test, 5-fold cross-validation and independent testing with other dataset, were used to evaluate the performance and robust of the models. Logitboost, as a novel classifier in Boosting algorithm, performed better than Adaboost. The overall accuracy of the three methods was 100%, 88.4% and 89.5%, respectively. It was demonstrated that LogitBoost performed comparably or even better than that of neural network, a very powerful classifier widely used in biological literatures. The influence of protein size on discrimination was addressed. It is anticipated that the power in predicting many bio-macromolecular attributes will be further strengthened if the Boosting and some other existing algorithms can be effectively complemented with each other.

Algorithms↗
PubMed1993

Occupational needs and evaluation methods for cold protective clothing.

The aim of the study was to evaluate the needs for and properties of the occupational cold protective clothing with different methods and the risks related to work in cold conditions from the point of view of occupational hygiene and clothing physiology. The thermal insulation of textile materials and clothing was investigated with the equipment, methods and parameters developed especially in cold and windy conditions in dynamic and steady states. Also the simulation and calculation of results were done and compared to the measurements. The cold exposure from the point of occupational hygiene was evaluated in working life to evaluate the risk of cooling and frostbite and utility ranges of clothing. The function of the sweating hot plate constructed and cylinder in the wind tunnel could be regarded adequate for the evaluation of winter clothing with good precision, stability and repeatability. The measured total thermal resistance was mainly dependent on, and operative thermal resistance independent of, temperature. The operative thermal resistance was also very sensitive to errors in measurement procedures. The heat flow usually evaluated by thermal and water vapour resistance could be substituted for total thermal resistance. Both the measurements and theories showed that, in addition to air permeability, also the ambient temperature, air gaps, contact layers and thickness of clothing were important parameters. Increase of wind (1...8 m/s) decreased the total thermal resistance and mass transfer up to 60% depending on conditions. The comparison of calculation models with material measurements proved the value of the simulation models. The reason for differences between the methods was mainly due to changes in water vapour resistance in the cold. The heat flux method was exact enough in the evaluation of the insulation of clothing in the field but in sweating conditions the condensation and evaporation must be taken into consideration. In the case of heat debt in the cold the heat flux method gave smaller values than the thermometric method. The material measurements diverged logically from the clothing measurements but material methods had a better capability to analyze the differences of material ensembles. In the evaluation of body cooling and performance degradation in outdoor work the physiological recommendations given were temporarily exceeded in 70% of the cases measured (N = 143). The cold problems already occurred in temperatures from 0 to 10 degrees C. The reasons for the cold problems were related to the type of work e.g. wind to the face and long exposure to the feet caused frostbite.(ABSTRACT TRUNCATED AT 400 WORDS)

Body Temperature↗
PubMed2004

Targacept active conformation search: a new method for predicting the conformation of a ligand bound to its protein target.

Targacept active conformation search (TACS) is a novel variation of well-established three-dimensional quantitative structure--activity relationship methodologies that seeks to determine probable conformation(s) of ligands bound to their protein targets. A combination of affinity or activity data and energetically accessible conformational ensembles, each conformer described by three-dimensional (3-D) sensitive descriptors, forms the basis of the TACS data model. Recursive pruning is used to reduce the size of both the conformational ensemble and the descriptor space until the TACS data model contains just enough information to determine probable conformation(s) of ligands bound to their protein targets. The TACS algorithm is comprised of five components: (1) conformational ensemble generation, (2) 3-D sensitive descriptor calculation, (3) ensemble descriptor preprocessing, (4) model generation, and (5) prediction of bound conformation(s). Significantly, this method precludes the need for subjective or objective molecular alignment. We report the application of this technique to five benchmark protein-ligand couples where the conformation of a bound ligand has been previously established using X-ray crystallography: 9-cis-retinoic (1) and 9-trans-retinoic acid (2), both agonists for the retinoic acid receptor gamma, compounds KH1060 (3) and MC1288 (4), which bind to the vitamin D3 receptor, and R04 (5), an inhibitor bound to human rhinovirus 14 thermolysin. The binding conformations predicted by TACS were compared to the crystallographic structures extracted from their respective binding sites using root-mean-squared deviation (rmsd) criteria. Three of the conformations found using TACS were within crystallographic error. 9-cis-Retinoic acid, 9-trans-retinoic acid, and MC1288, when superimposed on their crystallographic structures, gave rmsd values of 0.22, 0.17, and 0.34 A, respectively. The rmsd values for KH1060 (1.54 A) and R04 (1.01 A) were larger but still reasonable.

Binding Sites↗
PubMed2004

Ensemble quantum computation with atoms in periodic potentials.

We show how to perform universal quantum computation with atoms confined in optical lattices which works both in the presence of defects and without individual addressing. The method is based on using the defects in the lattice, wherever they are, both to "mark" different copies on which ensemble quantum computation is carried out and to define pointer atoms which perform the quantum gates. We also show how to overcome the problem of scalability in this system.

Journal Article↗
PubMed1996

Energy functions that discriminate X-ray and near native folds from well-constructed decoys.

This study generates ensembles of decoy or test structures for eight small proteins with a variety of different folds. Between 35,000 and 200,000 decoys were generated for each protein using our four-state off-lattice model together with a novel relaxation method. These give compact self-avoiding conformations each constrained to have native secondary structure. Ensembles of these decoy conformations were used to test the ability of several types of empirical contact, surface area and distance-dependent energy functions to distinguish between correct and incorrect conformations. These tests have shown that none of the functions is able to distinguish consistently either the X-ray conformation or the near-native conformations from others which are incorrect. Certain combinations of two of these energy functions were able, however, consistently to identify X-ray structures from amongst the decoy conformations. These same combinations are better also at identifying near-native conformations, consistently finding them with a hundred-fold higher frequency than chance. The fact that these combination energy functions perform better than generally accepted energy functions suggests their future use in folding simulations and perhaps threading predictions.

Crystallography, X-Ray↗
PubMed1999

Improved modeling of side-chains in proteins with rotamer-based methods: a flexible rotamer model.

Side-chain modeling has a widespread application in many current methods for protein tertiary structure determination, prediction, and design. Of the existing side-chain modeling methods, rotamer-based methods are the fastest and most efficient. Classically, a rotamer is conceived as a single, rigid conformation of an amino acid sidechain. Here, we present a flexible rotamer model in which a rotamer is a continuous ensemble of conformations that cluster around the classic rigid rotamer. We have developed a thermodynamically based method for calculating effective energies for the flexible rotamer. These energies have a one-to-one correspondence with the potential energies of the rigid rotamer. Therefore, the flexible rotamer model is completely general and may be used with any rotamer-based method in substitution of the rigid rotamer model. We have compared the performance of the flexible and rigid rotamer models with one side-chain modeling method in particular (the self-consistent mean field theory method) on a set of 20 high quality crystallographic protein structures. For the flexible rotamer model, we obtained average predictions of 85.8% for chi1, 76.5% for chi1+2 and 1.34 A for root-mean-square deviation (RMSD); the corresponding values for core residues were 93.0%, 87.7% and 0.70 A, respectively. These values represent improvements of 7.3% for chi1, 8.1% for chi1+2 and 0.23 A for RMSD over the predictions obtained with the rigid rotamer model under otherwise identical conditions; the corresponding improvements for core residues were 6.9%, 10.5% and 0.43 A, respectively. We found that the predictions obtained with the flexible rotamer model were also significantly better than those obtained for the same set of proteins with another state-of-the-art side-chain placement method in the literature, especially for core residues. The flexible rotamer model represents a considerable improvement over the classic rigid rotamer model. It can, therefore, be used with considerable advantage in all rotamer-based methods commonly applied to protein tertiary structure determination, prediction, and design and also in predictions of free energies in mutational studies.

Amino Acids↗
PubMed1995

Transfer of radiative heat through clothing ensembles.

A mathematical model was designed to calculate the temperature and dry heat transfer in the various layers of a clothing ensemble, and the total heat loss of a human who is irradiated for a certain fraction of his or her area. The clothing ensemble that is irradiated by an external heat source is considered to be composed of underclothing, trapped air, and outer fabric. The model was experimentally tested with heat balance methods, using subjects, varying the activity, wind, and radiation characteristics of the outer garment of two-layer ensembles. In two experiments the subjects could only give off dry heat because they were wrapped in plastic foil. The model appeared to be correct within about 1 degree C (rms error) and 10 Wm-2 (rms error). In a third experiment, sweat evaporation was also taken into account, showing that the resulting physiological heat load of 10 to 30% of the intercepted additional radiation is compensated by additional sweating. The resulting heat strain was rather mild. It is concluded that the mathematical model is a valid tool for the investigation of heat transfer through two-layer ensembles in radiant environments.

Adolescent↗
PubMed2000

A fast method to sample real protein conformational space.

A fast computer program, FOLDTRAJ, to generate plausible random protein structures is reported. All-atom proteins are made directly in continuous three-dimensional space starting from primary sequence with an N to C directed build-up method. The method uses a novel pipelined residue addition approach in which the leading edge of the protein is constructed three residues at a time for optimal protein geometry, including the placement of cis proline. Build-up methods represent a classic N-body problem, expected to scale as N(2). When proteins become more collapsed, build-up methods are susceptible to backtracking problems which can scale exponentially with the number of residues required to back out of a trapped walk. We have provided solutions to both these problems, using a multiway binary tree that makes the N-body problem of bump-checking scale as NlogN, and speeding up backtracking by varying the number of tries before backtracking based on available conformational space. FOLDTRAJ is independent of energy potentials, other than that implicit in the geometrical properties derived by statistical studies of known structures, and in atomic Van der Waals radii. WHAT-CHECK shows that the program generates chirally and physically valid proteins with all bond lengths, angles and dihedrals within allowable tolerances. Random structures built using sequences from PDB files 1SEM, 2HPR, and 1RTP typically have 5-15% alpha-helical content (according to DSSP) and on the order of 20% beta-strand/extended content. Ensembles of random structures are compared with polymer theory and with experimentally determined fluorescence resonance energy transfer distances. Reasonably sized structure ensembles do sample most of the conformational space available to proteins. The method is also capable of protein reconstruction using Calpha--Calpha direction vectors, and it compares favorably with methods that reconstruct protein backbones based on alpha-carbon coordinates, having an average backbone and Cbeta root mean square deviation of 0.63 A for nine different protein folds. Proteins 2000;39:112-131.

Algorithms↗
PubMed2000

Artificial selection of microbial ecosystems for 3-chloroaniline biodegradation.

We present a method for selecting entire microbial ecosystems for bioremediation and other practical purposes. A population of ecosystems is established in the laboratory, each ecosystem is measured for a desired property (in our case, degradation of the environmental pollutant 3-chloroaniline), and the best ecosystems are used as 'parents' to inoculate a new generation of 'offspring' ecosystems. Over many generations of variation and selection, the ecosystems become increasingly well adapted to produce the desired property. The procedure is similar to standard artificial selection experiments except that whole ecosystems, rather than single individuals, are the units of selection. The procedure can also be understood in terms of complex system theory as a way of searching a vast combinatorial space (many thousands of microbial species and many thousands of genes within species) for combinations that are especially good at producing the desired property. Ecosystem-level selection can be performed without any specific knowledge of the species that comprise the ecosystems and can select ensembles of species that would be difficult to discover with more reductionistic methods. Once a 'designer ecosystem' has been created by ecosystem-level selection, reductionistic methods can be used to identify the component species and to discover how they interact to produce the desired effect.

Aniline Compounds↗
PubMed2000

Effects of Pore-Pore Correlations on Capillary Condensation in an Ensemble of Slit-like Pores: Application of a Density Functional Theory.

Using a density functional method we study how the correlations between particles adsorbed in neighboring pores, forming a network of slit-like pores, influence the capillary condensation and the structure of adsorbed Lennard-Jones fluid. The calculations indicate that if the distance between two pores is small enough, these correlations lead to pronounced changes in the density profiles, to an increase of the critical temperature, and to the modifications in the coexistence envelope. Copyright 2000 Academic Press.

Journal Article↗
PubMed1995

Rapid non-empirical approaches for estimating relative binding free energies.

Rapid non-empirical methods for estimating binding free energies are reviewed. A novel approach based on the application of the free energy perturbation formula to a biased ensemble is presented. Preliminary results demonstrating the applicability of this approach in protein systems are shown and the potential of this method in structure-based drug design is discussed.

Models, Theoretical↗
PubMed1993

A Monte Carlo method for conformational analysis of saccharides.

A Metropolis Monte Carlo (MMC) algorithm was applied to explore conformational spaces spanned by the exocyclic dihedral angles of four disaccharides alpha-D-Man(1-->3)-alpha-D-Man(1-->O)Me (1), alpha-D-Man(1-->2)-alpha-D-Man(1-->O)Me (2), methyl beta-cellobioside (3), and methyl beta-maltoside (4). The simulation method uses the HSEA force field and randomly samples the conformational space with an automatic preference for low-energy states. In comparison to a systematic grid search, MMC offers a much more convenient and efficient protocol for the computation of ensemble average values of experimentally accessible NMR parameters such as NOE effects or 3J coupling constants. Energy barriers of a few kcal/mol were found to be surmounted easily when running the simulations with the temperature parameter set at room temperature, whereas passing significantly higher barriers required elevated temperature parameters. Ensemble average NOE values were calculated using the MMC technique and a conventional systematic grid search showing that the MMC method adequately samples the conformational spaces of 1-4. Theoretical NOEs derived for global or local minimum conformations are different from ensemble average values, and it is shown that averaged NOEs agree significantly better with experimental data. Ensemble average NOEs for 1 derived from MMC/HSEA, and previously reported MM2CARB and AMBER calculations all showed good agreement with experimental data, with MMC/HSEA giving the closest fit.

Algorithms↗
PubMed2004

Ensemble dynamics of hippocampal regions CA3 and CA1.

Computational models based on hippocampal connectivity have proposed that CA3 is uniquely positioned as an autoassociative memory network, capable of performing the competing functions of pattern completion and pattern separation. Recently, three independent studies, two using parallel neurophysiological recording methods and one using immediate-early gene imaging, have examined the responses of CA3 and CA1 ensembles to alterations of environmental context in rats. The results provide converging evidence that CA3 is capable of performing nonlinear transformations of sensory input patterns, whereas CA1 may represent changes in input in a more linear fashion.

Animals↗
PubMed2005

A simulation method for the calculation of chemical potentials in small, inhomogeneous, and dense systems.

We present a modification of the gauge cell Monte Carlo simulation method [A. V. Neimark and A. Vishnyakov, Phys. Rev. E 62, 4611 (2000)] designed for chemical potential calculations in small confined inhomogeneous systems. To measure the chemical potential, the system under study is set in chemical equilibrium with the gauge cell, which represents a finite volume reservoir of ideal particles. The system and the gauge cell are immersed into the thermal bath of a given temperature. The size of the gauge cell controls the level of density fluctuations in the system. The chemical potential is rigorously calculated from the equilibrium distribution of particles between the system cell and the gauge cell and does not depend on the gauge cell size. This scheme, which we call a mesoscopic canonical ensemble, bridges the gap between the canonical and the grand canonical ensembles, which are known to be inconsistent for small systems. The ideal gas gauge cell method is illustrated with Monte Carlo simulations of Lennard-Jones fluid confined to spherical pores of different sizes. Special attention is paid to the case of extreme confinement of several molecular diameters in cross section where the inconsistency between the canonical ensemble and the grand canonical ensemble is most pronounced. For sufficiently large systems, the chemical potential can be reliably determined from the mean density in the gauge cell as it was implied in the original gauge cell method. The method is applied to study the transition from supercritical adsorption to subcritical capillary condensation, which is observed in nanoporous materials as the pore size increases.

Journal Article↗
PubMed2004

Absence of charge inversion on rodlike polyelectrolytes with excess divalent counterions.

Filamentous viruses such as fd and M13 are highly charged rodlike polyelectrolytes. In this study, we employ fd virus to test the recent prediction of charge inversion [Nguyen, Rouzina, and Shklovskii, J. Chem. Phys. 112, 2562 (2000)]. Light scattering measurements show bundle formation and resolubilization of fd viruses when MgCl(2) was added from 0 to 600 mM. The effective charge of fd was studied by measuring their electrophoretic mobility using a filament tracking method uniquely suited for the system. Monte Carlo simulations were performed under canonical ensemble to predict the charge distribution around the rodlike virus. Charge inversion, which has been suggested theoretically to accompany with bundle resolubilization, was not observed in either experiments or simulations. A modified analysis of force balance is called upon to account for these new findings.

Bacteriophage M13↗