SEARCH · PubMed Health

Results for “ensemble”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

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

At least 145 records · Page 8Linked to original sources

PubMed2005

Ensemble versus single-molecule protein unfolding.

Molecular dynamics (MD) simulations are the classic single-molecule "experiments," providing atomic-resolution structural and dynamic information. However, the single-molecule nature of the technique has also been its shortcoming, with frequent criticisms of sampling inadequacies and questions regarding the ensemble behavior of large numbers of molecules. Given the increase in computer power, we now address this issue by performing a large number of simulations and comparing individual and ensemble properties. One hundred independent MD simulations of the protein chymotrypsin inhibitor 2 were carried out for 20 ns each at 498 K in water to more fully describe the potentially diverse routes of protein unfolding and investigate how representative a single trajectory can be. Rapid unfolding was observed in all cases with the trajectories distributed about an average "ensemble" path in which secondary and tertiary structure was lost concomitantly, with tertiary structure loss occurring slightly faster. Individual trajectories did, however, sample conformations far from the average path with very heterogeneous time-dependent properties. Nevertheless, all of the simulations but one followed the average ensemble pathway, such that a small number of simulations (5-10) are sufficient to capture the average properties of these states and the unfolding pathway.

Hydrogen Bonding↗

PubMed2000

Description of microcolumnar ensembles in association cortex and their disruption in Alzheimer and Lewy body dementias.

The cortex of the brain is organized into clear horizontal layers, laminae, which subserve much of the connectional anatomy of the brain. We hypothesize that there is also a vertical anatomical organization that might subserve local interactions of neuronal functional units, in accord with longstanding electrophysiological observations. We develop and apply a general quantitative method, inspired by analogous methods in condensed matter physics, to examine the anatomical organization of the cortex in human brain. We find, in addition to obvious laminae, anatomical evidence for tightly packed microcolumnar ensembles containing approximately 11 neurons, with a periodicity of about 80 microm. We examine the structural integrity of this new architectural feature in two common dementing illnesses, Alzheimer disease and dementia with Lewy bodies. In Alzheimer disease, there is a dramatic, nearly complete loss of microcolumnar ensemble organization. The relative degree of loss of microcolumnar ensembles is directly proportional to the number of neurofibrillary tangles, but not related to the amount of amyloid-beta deposition. In dementia with Lewy bodies, a similar disruption of microcolumnar ensemble architecture occurs despite minimal neuronal loss. These observations show that quantitative analysis of complex cortical architecture can be applied to analyze the anatomical basis of brain disorders.

Alzheimer Disease↗

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↗

PubMedDate not supplied

Multiple views of the response of an ensemble of spectro-temporal features support concurrent classification of utterance, prosody, sex and speaker identity.

Models of auditory processing, particularly of speech, face many difficulties. These difficulties include variability among speakers, variability in speech rate and robustness to moderate distortions such as time compression. In contrast to the 'invariance of percept' (across different speakers, of different sexes, using different intonation, and so on) is the observation that we are sensitive to the identity, sex and intonation of the speaker. In previous work we have reported that a model based on ensembles of spectro-temporal feature detectors, derived from onset sensitive pre-processing of a limited class of stimuli, preserves significant information about the stimulus class. We have also shown that this is robust with respect to the exact choice of feature set, moderate time compression in the stimulus and speaker variation. Here we extend these results to show a) that by using a classifier based on a network of spiking neurons with spike-driven plasticity, the output of the ensemble constitutes an effective rate coding representation of complex sounds; and b) that the same set of spectro-temporal features concurrently preserve information about a range of qualitatively different classes into which the stimulus might fall. We show that it is possible for multiple views of the same pattern of responses to generate different percepts. This is consistent with suggestions that multiple parallel processes exist within the auditory 'what' pathway with attentional modulation enhancing the task-relevant classification type. We also show that the responses of the ensemble are sparse in the sense that a small number of features respond for each stimulus type. This has implications for the ensembles' ability to generalise, and to respond differentially to a wide variety of stimulus classes.

Acoustic Stimulation↗

PubMed2003

Ensembl 2002: accommodating comparative genomics.

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of human, mouse and other genome sequences, available as either an interactive web site or as flat files. Ensembl also integrates manually annotated gene structures from external sources where available. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. These range from sequence analysis to data storage and visualisation and installations exist around the world in both companies and at academic sites. With both human and mouse genome sequences available and more vertebrate sequences to follow, many of the recent developments in Ensembl have focusing on developing automatic comparative genome analysis and visualisation.

Animals↗

PubMed2005

Ensembl 2005.

The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of large genome sequences. Over the last year the number of genomes available from the Ensembl site has increased by 7 to 16, with the addition of the six vertebrate genomes of chimpanzee, dog, cow, chicken, tetraodon and frog and the insect genome of honeybee. The majority have been annotated automatically using the Ensembl gene build system, showing its flexibility to reliably annotate a wide variety of genomes. With the increased number of vertebrate genomes, the comparative analysis provided to users has been greatly improved, with new website interfaces allowing annotation of different genomes to be directly compared. The Ensembl software system is being increasingly widely reused in different projects showing the benefits of a completely open approach to software development and distribution.

Animals↗

PubMed2004

The Ensembl automatic gene annotation system.

As more genomes are sequenced, there is an increasing need for automated first-pass annotation which allows timely access to important genomic information. The Ensembl gene-building system enables fast automated annotation of eukaryotic genomes. It annotates genes based on evidence derived from known protein, cDNA, and EST sequences. The gene-building system rests on top of the core Ensembl (MySQL) database schema and Perl Application Programming Interface (API), and the data generated are accessible through the Ensembl genome browser (http://www.ensembl.org). To date, the Ensembl predicted gene sets are available for the A. gambiae, C. briggsae, zebrafish, mouse, rat, and human genomes and have been heavily relied upon in the publication of the human, mouse, rat, and A. gambiae genome sequence analysis. Here we describe in detail the gene-building system and the algorithms involved. All code and data are freely available from http://www.ensembl.org.

Animals↗

PubMed2000

Online learning with ensembles.

Supervised online learning with an ensemble of students randomized by the choice of initial conditions is analyzed. For the case of the perceptron learning rule, asymptotically the same improvement in the generalization error of the ensemble compared to the performance of a single student is found as in Gibbs learning. For more optimized learning rules, however, using an ensemble yields no improvement. This is explained by showing that for any learning rule f a transform f exists, such that a single student using f has the same generalization behavior as an ensemble of f students.

Humans↗

PubMed2001

Structure of wave functions in (1+2)-body random matrix ensembles.

Random matrix ensembles defined by a mean-field one body plus a chaos generating random two-body interaction [called embedded ensembles of (1+2)-body interactions] predict for wave functions, in the chaotic domain, an essentially one-parameter Gaussian forms for the energy dependence of the number of principal components (NPC) and the localization length l(H) (defined by information entropy), which are two important measures of chaos in finite interacting many-particle systems. Numerical embedded ensemble calculations and nuclear shell-model results, for NPC and l(H), are compared with the theory. These analyses clearly point out that for realistic finite interacting many-particle systems, in the chaotic domain, wave-function structure is given by (1+2)-body embedded random matrix ensembles.

Journal Article↗

PubMed2001

Statistical ensemble of scale-free random graphs.

A thorough discussion of the statistical ensemble of scale-free connected random tree graphs is presented. Methods borrowed from field theory are used to define the ensemble and to study analytically its properties. The ensemble is characterized by two global parameters, the fractal and the spectral dimensions, which are explicitly calculated. It is discussed in detail how the geometry of the graphs varies when the weights of the nodes are modified. The stability of the scale-free regime is also considered: when it breaks down, either a scale is spontaneously generated or else, a "singular" node appears and the graphs become crumpled. A new computer algorithm to generate these random graphs is proposed. Possible generalizations are also discussed. In particular, more general ensembles are defined along the same lines and the computer algorithm is extended to arbitrary (degenerate) scale-free random graphs.

Journal Article↗

PubMed2003

Dynamical mean-field theory of spiking neuron ensembles: response to a single spike with independent noises.

A semianalytical dynamical mean-field theory has been developed for a study of dynamics of an ensemble of N-unit FitzHugh-Nagumo neurons subject to white noises. Assuming weak noises and the Gaussian distribution of state variables, we have driven equations of motions for moments of local and global variables. Dynamical mean-field approximation (DMA) has replaced original, 2N-dimensional stochastic differential equations (DEs) by eight-dimensional deterministic DEs, whereas the conventional moment method yields N(2N+3)-dimensional deterministic DEs for local variables. We have discussed the dependence of the spike firing precision and the synchronization on the noise intensity, synaptic coupling, and the size of the neuron ensemble. The spike timing precision is shown to be improved by increasing the size of the neuron ensemble, even when there are no couplings among neurons. When the coupling is introduced, neurons in ensembles respond to an input spike with a partial synchronization. Results calculated by our DMA theory are in good agreement with those obtained by direct simulations. DMA theory is extended to a large cluster which can be divided into multiple subclusters according to their functions. A model calculation has demonstrated that when the noise intensity is moderate, the spike propagation with a fairly precise timing is possible among noisy subclusters with feed-forward couplings, as in the synfire chain. We have compared DMA theory with the conventional moment method, showing that the former may be alternatively derived from the latter by a reduction in the number of moments with the mean-field approximation.

Animals↗

PubMed2003

Statistical mechanics in the extended Gaussian ensemble.

The extended Gaussian ensemble (EGE) is introduced as a generalization of the canonical ensemble. This ensemble is a further extension of the Gaussian ensemble introduced by Hetherington [J. Low Temp. Phys. 66, 145 (1987)]. The statistical mechanical formalism is derived both from the analysis of the system attached to a finite reservoir and from the maximum statistical entropy principle. The probability of each microstate depends on two parameters beta and gamma which allow one to fix, independently, the mean energy of the system and the energy fluctuations, respectively. We establish the Legendre transform structure for the generalized thermodynamic potential and propose a stability criterion. We also compare the EGE probability distribution with the q-exponential distribution. As an example, an application to a system with few independent spins is presented.

Journal Article↗

PubMed2004

Augmented moment method for stochastic ensembles with delayed couplings. II. FitzHugh-Nagumo model.

Dynamics of FitzHugh-Nagumo (FN) neuron ensembles with time-delayed couplings subject to white noises, has been studied by using both direct simulations and a semianalytical augmented moment method (AMM) which has been proposed in a preceding paper [H. Hasegawa, Phys. Rev. E 70, 021911 (2004)]. For N-unit FN neuron ensembles, AMM transforms original 2N-dimensional stochastic delay differential equations (SDDEs) to infinite-dimensional deterministic DEs for means and correlation functions of local and global variables. Infinite-order recursive DEs are terminated at the finite level m in the level-m AMM (AMMm), yielding 8(m+1)-dimensional deterministic DEs. When a single spike is applied, the oscillation may be induced if parameters of coupling strength, delay, noise intensity and/or ensemble size are appropriate. Effects of these parameters on the emergence of the oscillation and on the synchronization in FN neuron ensembles have been studied. The synchronization shows the fluctuation-induced enhancement at the transition between nonoscillating and oscillating states. Results calculated by AMM5 are in fairly good agreement with those obtained by direct simulations.

Action Potentials↗

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↗

PubMed2005

Analysis of ensemble learning using simple perceptrons based on online learning theory.

Ensemble learning of K nonlinear perceptrons, which determine their outputs by sign functions, is discussed within the framework of online learning and statistical mechanics. One purpose of statistical learning theory is to theoretically obtain the generalization error. This paper shows that ensemble generalization error can be calculated by using two order parameters, that is, the similarity between a teacher and a student, and the similarity among students. The differential equations that describe the dynamical behaviors of these order parameters are derived in the case of general learning rules. The concrete forms of these differential equations are derived analytically in the cases of three well-known rules: Hebbian learning, perceptron learning, and AdaTron (adaptive perceptron) learning. Ensemble generalization errors of these three rules are calculated by using the results determined by solving their differential equations. As a result, these three rules show different characteristics in their affinity for ensemble learning, that is "maintaining variety among students." Results show that AdaTron learning is superior to the other two rules with respect to that affinity.

Journal Article↗

PubMed2005

Level density for deformations of the Gaussian orthogonal ensemble.

Formulas are derived for the average level density of deformed, or transition, Gaussian orthogonal random matrix ensembles. After some general considerations about Gaussian ensembles, we derive formulas for the average level density for (i) the transition from the Gaussian orthogonal ensemble (GOE) to the Poisson ensemble and (ii) the transition from the GOE to m GOEs.

Journal Article↗

PubMed2005

Family of solvable generalized random-matrix ensembles with unitary symmetry.

We construct a very general family of characteristic functions describing random matrix ensembles (RME) having a global unitary invariance, and containing an arbitrary, one-variable probability measure, which we characterize by a "spread function." Various choices of the spread function lead to a variety of possible generalized RMEs, which show deviations from the well-known Gaussian RME originally proposed by Wigner. We obtain the correlation functions of such generalized ensembles exactly and show examples of how particular choices of the spread function can describe ensembles with arbitrary eigenvalue densities as well as critical ensembles with multifractality.

Journal Article↗

PubMed2005

Creation-annihilation processes in the ensemble of constant particle number.

We study, in the ensemble of constant particle number, processes in which a cluster of particles is annihilated and particles are created catalytically in active sites. In this ensemble, particles belonging to a cluster of l particles jump to l distinct active sites. As examples of our prescription, we analyze numerically three nonequilibrium systems that annihilate cluster of particles that are identified as conserved versions of the pair annihilation contact model, triplet annihilation contact model, and pair contact process. We show also how to set up the constant particle number ensemble from the constant rate ensemble.

Journal Article↗