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At least 451 records · Page 25Linked to original sources
PubMed2002

Effective time averaging of multiplexed measurements: a critical analysis.

Multiplexing and time averaging of signal are effective noise reduction protocols applied in many analytical measurement systems. The efficacy of these protocols may be reduced by random occurrences of high-magnitude noise that do not conform to the statistical distribution of noise for all other measurements in the data set. This high-magnitude noise, which may have an insignificant probability of occurrence for a single measurement, almost certainly affects data collected in a multichannel, multiplexed modality, such as Fourier transform infrared (FT-IR) spectroscopic imaging employing focal plane array detectors. To recover time-averaging advantages in these cases, we present a general coaddition method that uses two statistical measures, the mean and median of the ensemble of measurements of a signal, to obtain a better estimate of the true signal than that estimated by time averaging alone. This method, termed median filtered time averaging, is shown to be an effective noise removal procedure for FT-IR imaging data. The effects of noise removal on time averaging and multiplexing are examined theoretically and are demonstrated for hyperspectral infrared microspectroscopic imaging data obtained from human skin biopsies by using a rapid data acquisition procedure.

Spectroscopy, Fourier Transform Infrared↗
PubMed2005

Poisson's ratio of the fcc hard sphere crystal at high densities.

Elastic constants and the Poisson ratio of the fcc hard-sphere crystalline phases, free of defects and with vacancies, are determined by two Monte Carlo methods: (i) the analysis of the box fluctuations in the constant pressure ensemble with variable box shape (N-P-T) and (ii) by the free-energy differentiation with respect to deformation in the fixed box ensemble (N-V-T). Very good agreement is observed for the extrapolated to the infinitely large system limit results of both the methods. The coefficients of the leading singularities of the elastic constants near close packing are estimated; they are well described by the free volume approximation. Two mechanisms influencing the Poisson ratio are studied. (i) It is shown that at high densities particle motions decrease the Poisson ratio with respect to the static case which corresponds to zero temperature. Simulations performed for systems of soft spheres, interacting through n-inverse-power potentials, r-n, show that the elastic constants of the hard spheres can be obtained in the limit n-->infinity. When T-->0 the elastic constants of the soft spheres tend to those of the static model. (ii) It is also shown that vacancies decrease C11 and C44 and increase C12 and, hence, increase the Poisson ratio with respect to the defect-free state of the system.

Journal Article↗
PubMed1975

A pattern analysis study of weanling diarrhoeal disease of infants.

Methods of pattern analysis based on statistical signal procedures have been applied to (512-day) records of daily defaecation rate obtained in an ensemble of weanling infants. Careful analysis of the records using several different methods has established the potential significance of the signal. A technique of coherent averaging has produced a stable consistent age-dependent baseline of average behaviour, referred to as an average profile. Extensions have been proposed for the application of statistical methods for the acquisition of standard patterns of diarrhoeal behaviour. Numerical low pass filtering the signal allows a dichotomization of cases, the significance of which is confirmed by differences of class average profiles. Removing the class average profile from the records shows that the majority of cases exhibit consistent individual signal patterns; standardized patterns of behaviour can also be discussed. It is tentatively concluded that objective specification of normal and abnormal defaecation behaviour could be based on spontaneous patterns identified in the records. Several methods have been suggested. Methods similar to those applied here would appear, on the evidence of this study, to be applicable to a variety of other longitudinal epidemiological studies.

Defecation↗
PubMed2005

Sampling rare switching events in biochemical networks.

Bistable biochemical switches are widely found in gene regulatory networks and signal transduction pathways. Their switching dynamics are difficult to study, however, because switching events are rare, and the systems are out of equilibrium. We present a simulation method for predicting the rate and mechanism of the flipping of these switches. We apply it to a genetic switch and find that it is highly efficient. The path ensembles for the forward and reverse processes do not coincide. The method is widely applicable to rare events and nonequilibrium processes.

Bacteriophage lambda↗
PubMed2003

Chemistry. The motions of an enzyme soloist.

Dynamics of proteins are crucial to their function. In his Perspective, Orrit stresses the advantages of studying these dynamics with single-molecule methods--which require no synchronization--rather than with conventional ensemble measurements. He highlights the report by Yang et al., who follow the fluorescence of a single enzyme molecule. Electron transfer from the fluorophore to a quencher induces fluctuations of the fluorescence lifetime along with the fluorophore-quencher distance. The wide range of characteristic times of those fluctuations reveals the complexity of the protein's potential energy landscape. As a new molecular ruler, electron transfer complements other single-molecule methods such as energy transfer (FRET) for distances shorter than a few nanometers.

Catalysis↗
PubMed1995

Intravascular ultrasound image subtraction: a contrast enhancing technique to facilitate automatic three-dimensional visualization of the arterial lumen.

At 30 MHz, the intravascular ultrasound backscatter of blood confounds the discrimination of the lumen from the arterial wall. This study validates a subtraction method which creates a still-frame image with a sharp demarcation of the lumen. The method involves subtraction of consecutive images and 2D ensemble averaging of the absolute pixel values. Subtraction exploits the dynamic properties of flowing red blood cells. Three phantom arteries were used, with erythrocytes in their lumens and wall. For this reason, it was not possible, in one single original image, to discriminate the blood in the lumen from the phantom wall. Based on 26 consecutive original images, in the mean subtraction image contrast between lumen and phantom wall grey values increased eightfold from 10.9 (5.3-19.2) (mean and range) in the original image to 87.7 (73.6-107.0) (P < 0.001). A sufficiently large contrast increase to allow automatic segmentation was obtained by using five original images (0.3-s acquisition time) for any single mean subtraction image. Low blood flow velocities (down to 0.5 cm/s) did not alter this result. Automatic segmentation of the lumen allowed fast 3D reconstruction of the lumen in all three phantom arteries. In phantom arteries, the intravascular ultrasound image subtraction technique improved contrast between lumen and wall which enabled automated lumen segmentation and fast 3D visualization of both the lumen and defects in the wall.

Arteries↗
PubMed2002

NMR evidence for different conformations of the bioactive region of rat CCK-8 and CCK-58.

Sulfated CCK-58 and CCK-8 have identical bioactive C-terminal primary sequences but distinct C-terminal solution structures and different bioactivities. To examine structural differences in greater detail, rat CCK-58 and -8 were synthesized with isotopic enrichment of C-terminal residues with (15)N at alpha-amino nitrogens. Proton and nitrogen chemical shift assignments of peptide solutions were obtained by homo- and heteronuclear NMR methods. These data show that the tertiary structure ensembles of C-terminal CCK-8 and CCK-58 differ significantly. Thus, distinct solution conformations may explain differences in CCK(A) and CCK(B) receptor interactions of large and small molecular forms of CCK.

Amino Acid Sequence↗
PubMed1999

Solution structure and dynamics of the CX3C chemokine domain of fractalkine and its interaction with an N-terminal fragment of CX3CR1.

Fractalkine, a novel CX3C chemokine, is unusual because of both its membrane-associated structure and its direct role in cell adhesion. We have solved the solution structure of the chemokine domain of fractalkine (residues 1-76) by heteronuclear NMR methods. The 20 lowest energy structures in the ensemble have an average backbone rmsd of 0.43 A, excluding the termini. In contrast to many other chemokines which form homodimers, fractalkine's chemokine module is monomeric. Comparison of the structure to CC and CXC chemokines reveals interesting differences which are likely to be relevant to receptor binding. These include a bulge formed by the CX3C motif, the relative orientation of the N-terminus and 30's loop (residues 30-38), and the conformation of the N-loop (residues 9-19). 15N backbone relaxation experiments indicate that these same regions of the protein are dynamic. We also titrated 15N-labeled protein with a peptide from the N-terminus of the receptor CX3CR1 and confirmed that this region of the receptor contacts the fractalkine chemokine domain. Interestingly, the binding site maps roughly to the regions of greatest flexibility and structural variability. Together, these data provide a first glimpse of how fractalkine interacts with its receptor and should help guide mutagenesis studies to further elucidate the molecular details of binding and signaling through CX3CR1.

Amino Acid Sequence↗
PubMed2006

Self-assembly of 1,4-benzenedithiolate/tetrahydrofuran on a gold surface: a Monte Carlo simulation study.

We report a Monte Carlo simulation study of the self-assembly of 1,4-benzenedithiolate (BDT), tetrahydrofuran (THF), and their mixtures on a Au (111) surface. We use the grand canonical Monte Carlo method to obtain the equilibrium adsorption coverage. Canonical ensemble (NVT) simulation is then used to explore further the structural information of the equilibrated systems. Our results indicate that BDT molecules adsorb onto the Au (111) surface with one of the sulfur atoms bonded to Au atoms. THF molecules form clusters on the surface. For BDT-THF mixtures, BDT can selectively adsorb on Au (111) to form a monolayer, whereas the solvent THF molecules either float above BDT monolayer or occupy vacancies on the surface that are not covered by BDT molecules. BDT molecules adsorb on a Au (111) surface with an average tilt angle of about 18-35 degrees to the surface normal. The tilting angle decreases as the coverage increases. In addition, the BDT monolayer constitutes an ordered herringbone structure on the Au (111) surface, and the ordering pattern is insensitive to the BDT coverage. In comparison, the THF molecules exhibit amorphous structure on the Au surface. Interestingly, simulations indicate that the bonding behavior of BDT molecules on Au (111) is coverage-dependent. BDT bonds preferably on the Au top site when the surface coverage is low. As coverage increases, most BDT molecules bond on the bridge and fcc hollow sites.

Journal Article↗
PubMed2001

Tunable quantum tunnelling of magnetic domain walls.

Perhaps the most anticipated, yet experimentally elusive, macroscopic quantum phenomenon is spin tunnelling in a ferromagnet, which may be formulated in terms of domain wall tunnelling. One approach to identifying such a process is to focus on mesoscopic systems where the number of domain walls is finite and the motion of a single wall has measurable consequences. Research of this type includes magnetotransport measurements on thin ferromagnetic wires, and magnetization experiments on single particles, nanomagnet ensembles and rare-earth multilayers. A second method is to investigate macroscopic disordered ferromagnets, whose dynamics are dominated by domain wall motion, and search the associated relaxation-time distribution functions for the signature of quantum effects. But whereas the classical, thermal processes that operate in these experiments are easily regulated via temperature, the quantum processes have so far not been tunable, making difficult a definitive interpretation of the results in terms of tunnelling. Here we describe a disordered magnetic system for which it is possible to adjust the quantum tunnelling probabilities. For this material, we can model both the classical, thermally activated response at high temperatures and the athermal, tunnelling behaviour at low temperatures within a unified framework, where the domain wall is described as a particle with a fixed mass. We show that it is possible to tune the quantum tunnelling processes by adjusting the 'mass' of this particle with an external magnetic field.

Journal Article↗
PubMed2004

Molecular simulation of the reversible mechanical unfolding of proteins.

In this work we have combined a Wang-Landau sampling scheme [F. Wang and D. Landau, Phys. Rev. Lett. 86, 2050 (2001)] with an expanded ensemble formalism to yield a simple and powerful method for computing potentials of mean force. The new method is implemented to investigate the mechanical deformation of proteins. Comparisons are made with analytical results for simple model systems such as harmonic springs and Rouse chains. The method is then illustrated on a model 15-residue alanine molecule in an implicit solvent. Results for mechanical unfolding of this oligopeptide are compared to those of steered molecular dynamics calculations.

Alanine↗
PubMed2004

Thermodynamics and partitioning of homopolymers into a slit-A grand canonical Monte Carlo simulation study.

Grand canonical ensemble Monte Carlo simulation (GCMC) combined with the histogram reweighting technique was used to study the thermodynamic equilibrium of a homopolymer solution between a bulk and a slit pore. GCMC gives the partition coefficients that agree with those from canonical ensemble Monte Carlo simulations in a twin box, and it also gives results that are not accessible through the regular canonical ensemble simulation such as the osmotic pressure of the solution. In a bulk polymer solution, the calculated osmotic pressure agrees very well with the scaling theory predictions both for the athermal polymer solution and the theta solution. However, one cannot obtain the osmotic pressure of the confined solution in the same way since the osmotic pressure of the confined solution is anisotropic. The chemical potentials in GCMC simulations were found to differ by a translational term from the chemical potentials obtained from canonical ensemble Monte Carlo simulations with the chain insertion method. This confirms the equilibrium condition of a polymer solution partition between the bulk and a slit pore: the chemical potentials of the polymer chain including the translational term are equal at equilibrium. The histogram reweighting method enables us to obtain the partition coefficients in the whole range of concentrations based on a limited set of simulations. Those predicted bulk-pore partition coefficient data enable us to perform further theoretical analysis. Scaling predictions of the partition coefficient at different regimes were given and were confirmed by the simulation data.

Journal Article↗
PubMed2005

Identification of network-level coding units for real-time representation of episodic experiences in the hippocampus.

To examine the network-level organizing principles by which the brain achieves its real-time encoding of episodic information, we have developed a 96-channel array to simultaneously record the activity patterns of as many as 260 individual neurons in the mouse hippocampus during various startling episodes. We find that the mnemonic startling episodes triggered firing changes in a set of CA1 neurons in both startle-type and environment-dependent manners. Pattern classification methods reveal that these firing changes form distinct ensemble representations in a low-dimensional encoding subspace. Application of a sliding window technique further enabled us to reliably capture not only the temporal dynamics of real-time network encoding but also postevent processing of newly formed ensemble traces. Our analyses revealed that the network-encoding power is derived from a set of functional coding units, termed neural cliques, in the CA1 network. The individual neurons within neural cliques exhibit "collective cospiking" dynamics that allow the neural clique to overcome the response variability of its members and to achieve real-time encoding robustness. Conversion of activation patterns of these coding unit assemblies into a set of real-time digital codes permits concise and universal representation and categorization of discrete behavioral episodes across different individual brains.

Animals↗
PubMed1999

Voronoi-Delaunay analysis of voids in systems of nonspherical particles.

The Voronoi network is known to be a useful tool for the structural description of voids in the packings of spheres produced by computer simulations. In this article we extend the Voronoi-Delaunay analysis to packings of nonspherical convex objects. Main properties of the Voronoi network, which are known for systems of spheres, are valid for systems of any convex objects. A general numerical algorithm for calculation of the Voronoi network in three dimensions is proposed. It is based on the calculation of the trajectory of the imaginary empty sphere of variable size, moving inside a system (the Delaunay empty sphere method). Analysis of voids is presented for an ensemble of random straight lines and for a molecular dynamics model of liquid crystal. The spatial distribution of voids and a simple percolation analysis are obtained. The distributions of the bottleneck radii and the radii of spheres inscribed in the voids are calculated.

Journal Article↗
PubMed2000

Using x-ray reflectivity to determine the structure of surfactant monolayers

Interactions among the multiple degrees of freedom of surfactant molecules cause fascinating richness in the structure of their monolayers. Beyond this scientific motivation for studying surfactant monolayers, the technological use of monolayers for interfacial control and molecular assembly demands a clear understanding of monolayer structure. X-ray and neutron reflectivity have become prime techniques for determining this structure. We present x-ray reflectivity data for a representative surfactant monolayer system and outline an objective procedure for obtaining the maximum amount of structural information possible. Our approach combines tight control of instrumental parameters, dynamically optimized Monte Carlo and simulated annealing to probe the chi(2) hypersurface, and a set of statistical criteria for accepting and rejecting fits. We justify our procedure through tests using simulated data. Results indicate that an ensemble of fits must be performed for each set of reflectivity data in order to survey the chi(2) hypersurface adequately. A single good fit may yield structural parameters which are quite misleading, yet physically plausible. Thus, one must never be satisfied with performing just a single fit. In cases for which multiple, statistically equivalent fits are obtained, the apparent ambiguity is substantially mitigated by averaging the parameters over the ensemble of good fits. We also introduce a method of dealing with cases for which a good fit may be extremely difficult to find. Our analysis procedures can be generalized to other monolayer or multilayer systems and are also applicable to neutron reflectivity.

Journal Article↗
PubMed2003

Drift-wave turbulence and zonal flow generation.

Drift-wave turbulence in a plasma is analyzed on the basis of the wave Liouville equation, describing the evolution of the distribution function of wave packets (quasiparticles) characterized by position x and wave vector k. A closed kinetic equation is derived for the ensemble-averaged part of this function by the methods of nonequilibrium statistical mechanics. It has the form of a non-Markovian advection-diffusion equation describing coupled diffusion processes in x and k spaces. General forms of the diffusion coefficients are obtained in terms of Lagrangian velocity correlations. The latter are calculated in the decorrelation trajectory approximation, a method recently developed for an accurate measure of the important trapping phenomena of particles in the rugged electrostatic potential. The analysis of individual decorrelation trajectories provides an illustration of the fragmentation of drift-wave structures in the radial direction and the generation of long-wavelength structures in the poloidal direction that are identified as zonal flows.

Journal Article↗
PubMed2004

Model-based neural decoding of reaching movements: a maximum likelihood approach.

A new paradigm for decoding reaching movements from the signals of an ensemble of individual neurons is presented. This new method not only provides a novel theoretical basis for the task, but also results in a significant decrease in the error of reconstructed hand trajectories. By using a model of movement as a foundation for the decoding system, we show that the number of neurons required for reconstruction of the trajectories of point-to-point reaching movements in two dimensions can be halved. Additionally, using the presented framework, other forms of neural information, specifically neural "plan" activity, can be integrated into the trajectory decoding process. The decoding paradigm presented is tested in simulation using a database of experimentally gathered center-out reaches and corresponding neural data generated from synthetic models.

Action Potentials↗
PubMed1985

Quantitative analysis of ginsenosides in fresh Panax ginseng.

TLC, DCC and HPLC were used to study the ginsenoside composition of the main root, lateral root, rhizome, leaves and seeds of Panax ginseng cultivated in Jilin, China. Each of these methods has advantages of its own and the ensemble reveal the special features of Jilin ginseng. Total saponin content of various plant parts in Jilin ginseng showed a mid-range value as compared to those in ginsengs reported in literature. Fresh as well as sun-dried specimens from the same batch possessed a high percentage of Rg1 in the main root and this might account for the traditional preference of this plant part despite its lowest percentage of saponin in the whole plant. Large amounts of polar saponins were also observed in roots and rhizome of fresh Jilin ginseng, the nature and significance of which remained to be investigated.

China↗