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PubMedDate not supplied

Application of associative neural networks for prediction of lipophilicity in ALOGPS 2.1 program.

This article provides a systematic study of several important parameters of the Associative Neural Network (ASNN), such as the number of networks in the ensemble, distance measures, neighbor functions, selection of smoothing parameters, and strategies for the user-training feature of the algorithm. The performance of the different methods is assessed with several training/test sets used to predict lipophilicity of chemical compounds. The Spearman rank-order correlation coefficient and Parzen-window regression methods provide the best performance of the algorithm. If additional user data is available, an improved prediction of lipophilicity of chemicals up to 2-5 times can be calculated when the appropriate smoothing parameters for the neural network are selected. The detected best combinations of parameters and strategies are implemented in the ALOGPS 2.1 program that is publicly available at http://www.vcclab.org/lab/alogps.

Journal Article↗
PubMed2006

Structure and adsorption of a hard-core multi-Yukawa fluid confined in a slitlike pore: grand canonical Monte Carlo simulation and density functional study.

Because of the increasing interest in studying the phenomenon exhibited by charge-stabilized colloidal suspensions in confining geometry, we present a density functional theory (DFT) for a hard-core multi-Yukawa fluid. The excess Helmholtz free-energy functional is constructed by using the modified fundamental measure theory and Rosenfeld's perturbative method, in which the bulk direct correlation function is obtained from the first-order mean spherical approximation. To validate the established theory, grand canonical ensemble Monte Carlo (GCMC) simulations are carried out to determine the density profiles and surface excesses of multi-Yukawa fluid in a slitlike pore. Comparisons of the theoretical results with the GCMC data suggest that the present DFT gives very accurate density profiles and surface excesses of multi-Yukawa fluid in the slitlike pore as well as the radial distribution functions of the bulk fluid. Both the DFT and the GCMC simulations predict the depletion of the multi-Yukawa fluid near a nonattractive wall, while the mean-field theory fails to describe this depletion in some cases. Because the simple form of the direct correlation function is used, the present DFT is computationally as efficient as the mean-field theory, but reproduces the simulation data much better than the mean-field theory.

Journal Article↗
PubMed2004

Importance of chirality and reduced flexibility of protein side chains: a study with square and tetrahedral lattice models.

Side chains of amino acid residues are the determining factor that distinguishes proteins from other unstable chain polymers. In simple models they are often represented implicitly (e.g., by spin states) or simplified as one atom. Here we study side chain effects using two-dimensional square lattice and three-dimensional tetrahedral lattice models, with explicitly constructed side chains formed by two atoms of different chirality and flexibility. We distinguish effects due to chirality and effects due to side chain flexibilities, since residues in proteins are L residues, and their side chains adopt different rotameric states. For short chains, we enumerate exhaustively all possible conformations. For long chains, we sample effectively rare events such as compact conformations and obtain complete pictures of ensemble properties of conformations of these models at all compactness region. This is made possible by using sequential Monte Carlo techniques based on chain growth method. Our results show that both chirality and reduced side chain flexibility lower the folding entropy significantly for globally compact conformations, suggesting that they are important properties of residues to ensure fast folding and stable native structure. This corresponds well with our finding that natural amino acid residues have reduced effective flexibility, as evidenced by statistical analysis of rotamer libraries and side chain rotatable bonds. We further develop a method calculating the exact side chain entropy for a given backbone structure. We show that simple rotamer counting underestimates side chain entropy significantly for both extended and near maximally compact conformations. We find that side chain entropy does not always correlate well with main chain packing. With explicit side chains, extended backbones do not have the largest side chain entropy. Among compact backbones with maximum side chain entropy, helical structures emerge as the dominating configurations. Our results suggest that side chain entropy may be an important factor contributing to the formation of alpha helices for compact conformations.

Computer Simulation↗
PubMed2006

Two-dimensional electronic spectra of symmetric dimers: Intermolecular coupling and conformational states.

We study the information content of two-dimensional (2D) electronic photon-echo (PE) spectra, with special emphasis on their potential to distinguish, for waiting times T=0, between different conformations of electronically coupled symmetric dimers. The analysis is performed on the basis of an analytical formula for the frequency-domain 2D PE signal. The symmetric dimers are modeled in terms of two identical, energy-degenerate, excitonically coupled pairs of electronic states in the site representation. The spectra of conformationally weighted ensembles, composed of either two or four dimers, are compared with their one-dimensional linear absorption counterparts. In order to provide a realistic coupling pattern for the ensemble consisting of four dimers, excitonic couplings are estimated on the basis of optimized geometries and site-transition dipole moments, calculated by standard semiempirical methods for the bridged bithiophene structure 1,2-bithiophene-2-yl-ethane-1,2-dion (T2[CO]2). In the framework of our model, the highly readable 2D PE spectra can unambiguously identify spectral doublets, by relating peak heights and positions with mutual orientations of site-localized transition dipoles.

Journal Article↗
PubMed2006

Time-resolved photoelectron spectroscopy of proton transfer in the ground state of chloromalonaldehyde: wave-packet dynamics on effective potential surfaces of reduced dimensionality.

We report on a simple but widely useful method for obtaining time-independent potential surfaces of reduced dimensionality wherein the coupling between reaction and substrate modes is embedded by averaging over an ensemble of classical trajectories. While these classically averaged potentials with their reduced dimensionality should be useful whenever a separation between reaction and substrate modes is meaningful, their use brings about significant simplification in studies of time-resolved photoelectron spectra in polyatomic systems where full-dimensional studies of skeletal and photoelectron dynamics can be prohibitive. Here we report on the use of these effective potentials in the studies of dump-probe photoelectron spectra of intramolecular proton transfer in chloromalonaldehyde. In these applications the effective potentials should provide a more realistic description of proton-substrate couplings than the sudden or adiabatic approximations commonly employed in studies of proton transfer. The resulting time-dependent photoelectron signals, obtained here assuming a constant value of the photoelectron matrix element for ionization of the wave packet, are seen to track the proton transfer.

Journal Article↗
PubMed2002

Spurious interactions, and their correction, in the ensemble-Kohn-Sham scheme for excited States.

We observe that the direct Coulomb (Hartree) term appearing in the ensemble-density-functional theory for excited states contains an unphysical ("ghost") interaction which has to be corrected by the ensemble exchange and correlation functional. We propose a simple additive correction to the conventional ensemble exchange energy in the form of an orbital functional. By treating this corrected exchange energy functional self-consistently within the optimized effective potential method one finds a significant improvement of atomic excitation energies.

Journal Article↗
PubMed2004

Stroke prevention and atrial fibrillation: reasons leading to an inappropriate management. Main results of the SAFE II study.

AIMS: The aim of the Stroke and Atrial Fibrillation Ensemble (SAFE) II study was to identify the reasons underlying the under-utilization of oral anticoagulation (OAC) in patients with nonvalvular atrial fibrillation (NVAF). METHODS: We investigated from all available sources the reasons why patients hospitalized for a stroke, who had a previously known NVAF, were not receiving OAC beforehand. We interviewed general practitioners (GPs) and cardiologists with a structured questionnaire, to identify the reasons for their therapeutic choice. RESULTS: Of 370 patients, 257 were theoretically eligible for OAC according to guidelines and the presence of contra-indications, but only 82 (22.2%) of them had actually received OAC before. We found that factors independently associated with the prescription of OAC were being followed-up by a cardiologist and having a younger GP. The leading reason evoked by GPs or cardiologists to explain why patients were not treated with OAC was the presence of a 'potential contra-indication', which was often inappropriate, followed by 'there was no indication', 'low compliance' and 'fear of bleeding'. CONCLUSIONS: An important reason for not prescribing OAC was the lack of knowledge about trials and guidelines. Medical education about OAC in NVAF should therefore be improved.

Aged↗
PubMed2004

Improved hemiparetic muscle activation in treadmill versus overground walking.

OBJECTIVE: Treadmill training is a promising tool for retraining gait after stroke. The treadmill induces an immediate shift toward symmetry and longer paretic stance times due to altered muscle activation (active) or the motorized belt (passive). The authors investigated vastus lateralis and medial hamstrings activation differences between treadmill and overground walking in participants with stroke. METHODS: Vastus lateralis and medial hamstrings surface electromyography was recorded during velocity-matched overground and treadmill walking in 19 chronically hemiparetic subjects. Variables from ensemble averages of electromyography included burst onset and offset times (% cycle), duration (% cycle), integrated amplitude (mV.% cycle), and onset relative to foot strike (% cycle). Conditions were compared using paired t-tests (alpha = 0.05). RESULTS: Paretic vastus lateralis onset occurred earlier in the treadmill condition (overground: 47.1%, treadmill: 41.9%, P = 0.01). For nonparetic vastus lateralis in the treadmill condition, onset occurred later (overground: 85.2%, treadmill: 87.6%, P = 0.09), offset occurred earlier (overground: 54.7%, treadmill: 47.8%, P = 0.03), duration was shorter (overground: 69.1%, treadmill: 61.2%, P = 0.01), and integrated amplitude was lower (overground: 14.1, treadmill: 10.6, P = 0.05). Within limbs, paretic vastus lateralis onset occurred earlier relative to paretic foot strike. Nonparetic vastus lateralis onset occurred later relative to nonparetic foot strike. CONCLUSIONS: Treadmill walking induces immediate changes in vastus lateralis, but not medial ham-strings, activation patterns. These alterations (earlier paretic vastus lateralis onset and later nonparetic vastus lateralis onset) during treadmill versus overground walking parallel the increased symmetry in gait patterning.

Electromyography↗
PubMed2002

A new hydrostatic anti-G suit vs. a pneumatic anti-G system: preliminary comparison.

HYPOTHESIS: A newly developed hydrostatic anti-G suit is now commercially available. The suit is said to offer a high level of protection against +Gz acceleration. However, past experience shows that it is difficult to produce a hydrostatic suit with effective high-G protection. Careful testing is, therefore, needed to verify its efficacy. METHODS: The G-protective properties of the hydrostatic anti-G suit (Libelle; L) were compared with those of a pneumatic anti-G ensemble (AGE-39) used in the Swedish JAS 39 Cripen aircraft. Three pilots were studied during vertical (+Gz) acceleration in a centrifuge using the following: 1) the L-suit with varied straining maneuvers; 2) the AGE-39 in combination with full anti-G straining maneuvers (AGSM) throughout each high-G exposure (full maneuver; FM); and 3) the AGE-39 in combination with AGSM during the initial part of each high-G exposure (reduced maneuver; RM). G-intensity tolerance was established during exposures to rapid onset rate (ROR) profiles with G-plateau levels ranging from +6.0 to +9.0 Gz. G-endurance was studied during simulated aerial combat maneuvers (SACM) consisting of 10 cycles of 5.5 to 7.5 G. RESULTS: All three pilots tolerated 9.0 G with the pneumatic system both in the RM and FM conditions; their tolerances averaged 6.3 G (range 6.0 to 7.0 G) for the L suit. Thus, during the ROR exposures only the 6.0 G profile was completed by all subjects in all three conditions. At this G-load both muscle straining (as indicated by electromyographic activity in thigh and abdomen) and heart rate were higher in the L than in the RM condition. Mean arterial pressure at eye level was higher in the FM than in the L and RM conditions. Only one subject was able to complete the SACM profile in the L condition. In the RM condition all subjects completed the SACM profile and in the FM condition two subjects completed the SACM. CONCLUSIONS: Whether the AGE-39 was used in combination with maximal AGSM throughout the duration of each high-G exposure or with AGSM only during the initial part of the high-G exposure, G-intensity tolerance was 9.0 G. While wearing the L-suit, G-tolerance was 6.3 G. Thus, under the conditions tested, the G-protection afforded by the L-suit is not adequate for use in a 9-G aircraft.

Acceleration↗
PubMed2003

Rapid protein fold determination using unassigned NMR data.

Experimental structure determination by x-ray crystallography and NMR spectroscopy is slow and time-consuming compared with the rate at which new protein sequences are being identified. NMR spectroscopy has the advantage of rapidly providing the structurally relevant information in the form of unassigned chemical shifts (CSs), intensities of NOESY crosspeaks [nuclear Overhauser effects (NOEs)], and residual dipolar couplings (RDCs), but use of these data are limited by the time and effort needed to assign individual resonances to specific atoms. Here, we develop a method for generating low-resolution protein structures by using unassigned NMR data that relies on the de novo protein structure prediction algorithm, rosetta [Simons, K. T., Kooperberg, C., Huang, E. & Baker, D. (1997) J. Mol. Biol. 268, 209-225] and a Monte Carlo procedure that searches for the assignment of resonances to atoms that produces the best fit of the experimental NMR data to a candidate 3D structure. A large ensemble of models is generated from sequence information alone by using rosetta, an optimal assignment is identified for each model, and the models are then ranked based on their fit with the NMR data assuming the identified assignments. The method was tested on nine protein sequences between 56 and 140 amino acids and published CS, NOE, and RDC data. The procedure yielded models with rms deviations between 3 and 6 A, and, in four of the nine cases, the partial assignments obtained by the method could be used to refine the structures to high resolution (0.6-1.8 A) by repeated cycles of structure generation guided by the partial assignments, followed by reassignment using the newly generated models.

Algorithms↗
PubMed2004

Practicality of performing medical procedures in chemical protective ensembles.

OBJECTIVE: To determine whether certain life saving medical procedures can be successfully performed while wearing different levels of personal protective equipment (PPE), and whether these procedures can be performed in a clinically useful time frame. METHODS: We assessed the capability of eight medical personnel to perform airway maintenance and antidote administration procedures on manikins, in all four described levels of PPE. The levels are: Level A--a fully encapsulated chemically resistant suit; Level B--a chemically resistant suit, gloves and boots with a full-faced positive pressure supplied air respirator; Level C--a chemically resistant splash suit, boots and gloves with an air-purifying positive or negative pressure respirator; Level D--a work uniform. Time in seconds to inflate the lungs of the manikin with bag-valve-mask, laryngeal mask airway (LMA) and endotracheal tube (ETT) were determined, as was the time to secure LMAs and ETTs with either tape or linen ties. Time to insert a cannula in a manikin was also determined. RESULTS: There was a significant difference in time taken to perform procedures in differing levels of personal protective equipment (F21,72 = 1.75, P = 0.04). Significant differences were found in: time to lung inflation using an endotracheal tube (A vs. C mean difference and standard error 75.6 +/- 23.9 s, P = 0.03; A vs. D mean difference and standard error 78.6 +/- 23.9 s, P = 0.03); time to insert a cannula (A vs. D mean difference and standard error 63.6 +/- 11.1 s, P < 0.001; C vs. D mean difference and standard error 40.0 +/- 11.1 s, P = 0.01). CONCLUSIONS: A significantly greater time to complete procedures was documented in Level A PPE (fully encapsulated suits) compared with Levels C and D. There was however, no significant difference in times between Level B and Level C. The common practice of equipping hospital and medical staff with only Level C protection should be re-evaluated.

Antidotes↗
PubMed2001

Virtual interaction profiles of proteins.

We have developed a new method for the prediction of peptide sequences that bind to a protein, given a three-dimensional structure of the protein in complex with a peptide. By applying a recently developed sequence prediction algorithm and a novel ensemble averaging calculation, we generate a diverse collection of peptide sequences that are predicted to have significant affinity for the protein. Using output from the simulations, we create position-specific scoring matrices, or virtual interaction profiles (VIPs). Comparison of VIPs for a collection of binding motifs to sequences determined experimentally indicates that the prediction algorithm is accurate and applicable to a diverse range of structures. With these VIPs, one can scan protein sequence databases rapidly to seek binding partners of potential biological significance. Overall, this method can significantly enhance the information contained within a protein- peptide crystal structure, and enrich the data obtained by experimental selection methods such as phage display.

Algorithms↗
PubMed1993

Dependence of the multiplicities of secondary particles on the impact parameter in collisions of high-energy neon and iron nuclei with photoemulsion nuclei.

A method is proposed for finding the dependence of mean multiplicities of secondaries on the nucleus-collision impact parameter from the data on the total interaction ensemble. The impact parameter has been shown to completely define the mean characteristics of an individual interaction event. A difference has been found between experimental results and the data calculated in terms of the cascade-evaporation model at impact-parameter values below 3 fm.

Elementary Particles↗
PubMed2005

Ligand-based prediction of active conformation by 3D-QSAR flexibility descriptors and their application in 3+3D-QSAR models.

A conceptionally new 3D molecular descriptor type and methodology are deduced by simple statistical thermodynamic reasoning, based on the free energy change encountered during a transformation of a conformational ensemble of the ligand to an active conformation. The performance of the descriptor was first tested on 37 endomorphin analogues with mu-opiate activity. The method resulted in predictive 3D-QSAR models, and the active conformation was also predicted. Generally, the methodology can be combined with the traditional 3D-QSAR techniques in a 3+3D-QSAR manner. This feature was tested on a series of 38 PGF2alphaprostaglandin analogues with antinidatory activity; the extent to which the molecular flexibility explains the variation in the biological activity was estimated and the active conformation was predicted. The novel descriptors in combination with the grid-based SOMFA descriptors resulted in 3+3D-QSAR models with good levels of predictivity leading to the approach of separation of the effect of the molecular interaction field of the active conformation and the effect of the conformational free energy loss.

Amino Acids↗
PubMed2004

Single-ensemble nonequilibrium path-sampling estimates of free energy differences.

We introduce a straightforward, single-ensemble, path sampling approach to calculate free energy differences based on Jarzynski's relation. For a two-dimensional "toy" test system, the new (minimally optimized) method performs roughly one hundred times faster than either optimized "traditional" Jarzynski calculations or conventional thermodynamic integration. The simplicity of the underlying formalism suggests the approach will find broad applicability in molecular systems.

Biopolymers↗
PubMed2002

Psychiatric genetics in silico: databases and tools for psychiatric geneticists.

Bioinformatics can significantly impact the laboratory genetics process from the study design phase to conclusive identification of a disease gene. The present review will highlight key databases to enhance psychiatric genetic study design, based on full use of genomics data and the golden path sequence. It will address methods to ensure comprehensive genetic data mining, using the best available genomic and genetic databases such as the University of California Santa Cruz human genome browser, Ensembl, Mapview, dbSNP and GDB, and locus-specific databases such as Online Mendelian Inheritance In Man. Using the golden path sequence as a template, with the necessary quality checks, it is possible to design detailed genetic studies from sequence information alone. Drawing together this diverse information, it is possible to characterize a locus or gene in silico to a very detailed level. This in turn can have real cost and efficiency benefits by assisting in the identification of markers that are most likely to be informative, or by highlighting the best candidate genes for study.

Databases, Bibliographic↗
PubMed2004

Response variance prediction in the statistical energy analysis of built-up systems.

In the statistical energy analysis (SEA) of high frequency noise and vibration, a complex engineering structure is represented as an assembly of subsystems. The response of the system to external excitation is expressed in terms of the vibrational energy of each subsystem, and these energies are found by employing the principle of power balance. Strictly the computed energy is an average taken over an ensemble of random structures, and for many years there has been interest in extending the SEA prediction to the variance of the energy. A variance prediction method for a general built-up structure is presented here. Closed form expressions for the variance are obtained in terms of the standard SEA parameters and an additional set of parameters alpha(k) that describe the nature of the power input to each subsystem k, and alpha(ks) that describe the nature of the coupling between subsystems k and s. The theory is validated by comparison with Monte Carlo simulations of plate networks and structural-acoustic systems.

Journal Article↗
PubMed2006

Optimized analysis of surface electromyograms of the scalenes during quiet breathing in humans.

Studying the inspiratory recruitment of the scalenes is clinically relevant, but the interpretation of surface electromyographic (EMG) recordings is difficult. The aim of this study was to optimize an averaging method to analyze the surface EMG activity of the scalenes. Ten healthy subjects were studied. Nasal flow and surface EMG of the right scalene were recorded during 15 min epochs of quiet breathing. In four subjects, needle scalene EMG was also recorded. The flow signal was used to trigger the ensemble averaging of the ventilatory wave forms from 80 consecutive breaths. In eight cases, this evidenced a phasic inspiratory activation of the scalenes and permitted the determination of the electromechanical inspiratory delay (134+/-55 ms) and post-inspiratory activity (811+/-233 ms). When simultaneously available, surface and intramuscular recordings provided identical results. An averaging method triggered from a respiratory flow signal can identify and characterize a low phasic inspiratory activity of the scalenes within a noisy surface signal.

Adult↗