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At least 127 records · Page 7Linked to original sources
PubMed1995

Electrogastrography prior to and following total gastrectomy, subtotal gastrectomy, and gastric tube formation.

On electrogastrography (EGG) spectral analysis, an activity of 3 cycles per minute (cpm) is supposed to be specific for the stomach. After total or subtotal gastrectomy, the original site of the stomach is occupied mainly by the intestine. We attempted to determine if intestinal activity could be recorded in this region with EGG. Epigastric recordings were performed in patients prior and following gastrointestinal or control surgeries. Spectral analysis, using the maximal entropy method and ensemble means was applied to data analysis from these recordings. Preoperatively, the majority of the power peaks were found around 3, 6, and 11 cpm. The postprandial-to-fasting power ratio of all of these power peaks increased significantly postprandially (P < 0.05-0.01). Following total gastrectomy, the power peak around 3 cpm disappeared or was significantly diminished in amplitude (P < 0.05). The postoperative-to-preoperative power ratio ranged from 0.03 to 0.10 (P < 0.001-0.01). However, the power peak around 11 cpm did not significantly change prior to or following total gastrectomy, and the 11 cpm peak appeared relatively dominant. Simultaneous manometric studies in the Roux limb demonstrated a correlation between the power spectral frequency of EGG and manometry at 11 cpm. Therefore, the 11 cpm peak appeared to reflect jejunal or Roux limb electrical activity. The postoperative to preoperative power ratio for the 3 cpm also was significantly reduced following subtotal gastrectomy and gastric tube formation in patients in the postprandial state (P < 0.05-0.001).

Adult↗
PubMed2006

Comparative genomic analysis of human and chimpanzee indicates a key role for indels in primate evolution.

Sequence comparison of humans and chimpanzees is of interest to understand the mechanisms behind primate evolution. Here we present an independent analysis of human chromosome 21 and the high-quality BAC clone sequences of the homologous chimpanzee chromosome 22. In contrast to previous studies, we have used global alignment methods and Ensembl predictions of protein coding genes (n = 224) for the analysis. Divergence due to insertions and deletions (indels) along with substitutions was examined separately for different genomic features (coding, noncoding genic, and intergenic sequence). The major part of the genomic divergence could be attributed to indels (5.07%), while the nucleotide divergence was estimated as 1.52%. Thus the total divergence was estimated as 6.58%. When excluding repeats and low-complexity DNA the total divergence decreased to 2.37%. The chromosomal distribution of nucleotide substitutions and indel events was significantly correlated. To further examine the role of indels in primate evolution we focused on coding sequences. Indels were found within the coding sequence of 13% of the genes and approximately half of the indels have not been reported previously. In 5% of the chimpanzee genes, indels or substitutions caused premature stop codons that rendered the affected transcripts nonfunctional. Taken together, our findings demonstrate that indels comprise the majority of the genomic divergence. Furthermore, indels occur frequently in coding sequences. Our results thereby support the hypothesis that indels may have a key role in primate evolution.

Animals↗
PubMed1984

Pulsatile poststenotic flow studies with laser Doppler anemometry.

The pulsatile flow field distal to axisymmetric constrictions in a straight tube was studied using laser Doppler anemometry. The upstream centerline velocity waveform was sinusoidal at a frequency parameter of 7.5 and mean Reynolds number of 600. Stenosis models of 25, 50 and 75% area reduction were employed and velocity data were derived by ensemble averaging methods. Extensive measurements of the pulsatile velocity profiles are reported, and wall shear rates were computed from the near wall velocity profile gradients. The experiments indicate that a permanent region of poststenotic flow separation does not exist even for the severest constriction, in contrast to results for steady flow. Values of wall shear stress were greatest near the throat of the constriction and were relatively low in the poststenotic region, including the region of most intense flow disturbance. Turbulence was found only for the 75% stenosis model and was created only during a segment of the cycle. Although much emphasis has been placed upon turbulence in the detection of arterial stenoses, particularly as identified by Doppler ultrasound spectral broadening, the present study implies that identification of flow disturbances of an organized nature may be more fundamental in recognizing mild to moderate disease. Additionally, the relationship of these flow field results to the animal aortic coarctation model often employed in atherogenesis studies is discussed.

Arteries↗
PubMed1993

Adaptive segmentation of spontaneous EEG map series into spatially defined microstates.

Space-oriented segmentation can decompose multi-channel EEG map series into time segments characterized by quasi-stationary field map configurations. This assesses the dynamics of the underlying processes as activities of different neural generator ensembles. Our method of space-oriented segmentation describes the scalp field at times of maximal field strength (Global Field Power) by the locations of the centroids of positive and negative map areas. A quantitative measure of the simultaneous distance of the centroid locations evaluates the similarity between consecutive maps. A segment is defined as a sequence of maps that do not differ from each other by more than a present value. Finally, the average centroid locations for each segment are entered into an agglomerative clustering procedure to obtain a set of distinct classes of field configurations. Four records of 16 s of 42-channel resting EEG (band-pass filtered 2-16 Hz) from six subjects were analyzed. Average segment duration was 157.9 ms. Most segments belonged to a small number of classes (from 2 to 6, mean 3.7 classes for 90% of analysis time). The most frequent class showed an anterior-posterior field orientation and covered from 45 to 74% (mean 55% across subjects) of total time, with an average duration of 265 ms. The procedure was also tested using temporally and spatially unstructured data (white noise and randomly shuffled EEG) to ascertain that the methods reflect the spatio-temporal structure of the EEG processes.

Adult↗
PubMed2006

Quantification of the size-dependent energy gap of individual CdSe quantum dots by valence electron energy-loss spectroscopy.

Valence electron energy-loss spectroscopy (VEELS) performed in a monochromated scanning transmission electron microscope was used to measure the energy gaps of individual quantum dots (QDs). The gap energies of a series of CdSe QDs measured by VEELS reveal the expected quantum confinement effect; the gap energy increases with decreasing particle size. However, the values derived from these first VEELS measurements of single QDs are larger than the values commonly measured by optical spectroscopy. As standard optical methods lack the spatial resolution to probe individual nanoparticles, the particle-size distribution influences the optical response. It is suggested that the impact of the particle-size distribution accounts for the discrepancy between the energy-gap values derived from VEELS of single QDs and from optical methods of ensembles of QDs.

Journal Article↗
PubMed2002

Application of simulated annealing for estimating BAEPs in endocochlear pathologies.

In this paper, we propose a new approach aimed at handling the temporal Brainstem Auditory Evoked Potentials (BAEPs) non-stationarity. It is pointed out that for some endocochlear pathologies, BAEPs could be randomly delayed from one response to another. This non-stationarity leads to smoothed BAEPs when applying ensemble averaging or any other technique based on BAEPs stationarity. In that case, waves identification is very difficult, sometimes impossible. The problem consists in estimating time delays. Knowing the distribution of delays allows subsequent study of the dynamic of the cochlea and, perhaps, identification of the nature of its pathology. The approach suggested in this paper is based on Simulated Annealing, used to minimize a non-linear criterion involving delays. This technique is advantageously compared to the non-corrected ensemble averaging method, using a set of simulated data based on a realistic model. As an illustration, results based on real signals recorded from two patients are presented and discussed at the end of the paper.

Aged↗
PubMed2002

Selectivity enhancement for high-speed GC analysis of volatile organic compounds with portable instruments designed for vacuum-outlet and atmospheric-pressure inlet operation using air as the carrier gas.

A tandem ensemble of two 4.5-m-long x 0.25-mm-i.d. capillary columns with the first using a 0.50-microm film of nonpolar dimethyl polysiloxane and the second using a 0.25-microm film of polar trifluoropropylmethyl polysiloxane is operated with atmospheric pressure air as the carrier gas and an outlet pressure of 50.5 kPa established using a small vacuum pump. A thicker stationary-phase film is used in the first column to increase retention for very volatile compounds. This significantly increases the resolution of these compounds. The thicker film in the first (nonpolar) column decreases the polarity of the tandem column ensemble and, thus, changes its selectivity. A low-dead-volume valve, connected between the column junction point and a source of atmospheric pressure air, is used to obtain pulsed modulation of the carrier gas flow through the column ensemble. When the valve is open, the ensemble inlet pressure and the junction-point pressure are nearly the same, and carrier gas flow nearly stops in the first column, and flow in the second column increases. Enhanced resolution of a component pair that is separated by the first column but coelutes from the column ensemble can be obtained if the valve is opened for a few seconds after one of the components has crossed the junction and is in the second column, but the other component is still in the first column. A sequence of appropriately timed pulses is used to obtain enhanced resolution of several pairs of components that coelute from the column ensemble. These methods enabled the complete separation of an 18-component vapor mixture of common solvents in air in 3.5 min.

Air↗
PubMed2004

Semiclassical Liouville method for the simulation of electronic transitions: single ensemble formulation.

In this paper, we describe a single ensemble implementation of the semiclassical Liouville method for simulating quantum processes using classical trajectories. In this approach, one ensemble of trajectories supports the evolution of all semiclassical density matrix elements, rather than employing a distinct ensemble for each. The ensemble evolves classically under a single reference Hamiltonian, which is chosen based on physical grounds; for electronic relaxation of an initially excited state, the initially populated upper surface Hamiltonian is the natural choice. Classical trajectories evolving on the reference potential then represent the time-dependent upper state population density and also the electronic coherence and the ground state density created by electronic transition. The error made in the classical motion of the trajectories for these latter distributions is compensated for by incorporating the difference between the correct and reference Liouville propagators into the calculation of the coefficients of the individual trajectories. This approach gives very accurate results for a number of model problems and cases describing ultrafast electronic relaxation dynamics.

Journal Article↗
PubMed1997

A model of the lutropin/choriogonadotropin receptor: insights into the structural and functional effects of constitutively activating mutations.

A model of the seven transmembrane helical domain (7-TM) of the human lutropin receptor was constructed from the 2D electron density map of bovine rhodopsin and a set of geometric parameters derived from a published analysis of 204 G-protein coupled receptor sequences. The Self-Consistent Ensemble Optimization method was applied to predict overall side chain packing. The model is consistent with the general helical packing properties expected of transmembrane proteins and suggests possible structural and functional effects of constitutively activating mutations. A tightly packed hydrophobic cluster formed between the intracellular halves of TM5 and TM6, as well as a specific H-bonding network formed between the central regions of TM6 and TM7, is proposed to be critical for stabilizing the inactive form of the receptor. The model suggests that single activating mutations perturb the specific interactions of TM6 with TM5 and TM7, either by disrupting the hydrophobic packing between TM5 and TM6, or by weakening the H-bonds between TM6 and TM7.

Amino Acid Sequence↗
PubMed2003

Use of arterial transfer functions for the derivation of aortic waveform characteristics.

OBJECTIVE: To investigate the utility and accuracy of radial-aortic arterial transfer functions for the derivation of central blood pressure waveforms. DESIGN Prospective measurement of central and peripheral waveforms in patients undergoing coronary angiography or percutaneous coronary intervention. METHODS: Simultaneous invasive central aortic and non-invasive radial pressure waveforms were recorded in 78 subjects (61 male : 17 female). Data were applied to a single-input/single-output model for the calculation of a transfer function (TF). Individual TFs were derived by two methods and ensemble averaged TFs obtained for the group. Reverse transformation was performed using each averaged TF applied to the radial data of each subject. RESULTS: There was close linear correlation between measured aortic parameters and both radial and TF-derived aortic systolic and diastolic pressures (P < 0.001) and most other waveform parameters. However, despite small mean differences between measured and most TF-derived aortic parameters (systolic pressure 0.8-2.9 mmHg, augmentation index 4.3-5.6%), individual scatter was marked, with 95% limits of agreement of +/- 14.6 mmHg (systolic pressure) and +/- 24.4% [augmentation index (AI)]. Indeed, scatter for AI was so marked that measured and derived values were not statistically significantly correlated. CONCLUSIONS: Transfer functions may be valid for the derivation of some central aortic waveform characteristics. However, in providing neither improved reproducibility nor data on parameters not obtainable from the radial waveform, transfer function techniques may offer no additional clinical benefit. The absence of correlation between measured and TF-derived aortic AI and wide limits of agreement of other parameters should be considered if this technique is utilized in clinical practice.

Aged↗
PubMed2006

Loop updates for quantum Monte Carlo simulations in the canonical ensemble.

We present a new nonlocal updating scheme for quantum Monte Carlo simulations, which conserves particle number and other symmetries. It allows exact symmetry projection and direct evaluation of the equal-time Green's function and other observables in the canonical ensemble. The method is applicable to a wide variety of systems. We show results for bosonic atoms in optical lattices, neutron pairs in atomic nuclei, and electron pairs in ultrasmall superconducting grains.

Journal Article↗
PubMed2004

Variational learning and bits-back coding: an information-theoretic view to Bayesian learning.

The bits-back coding first introduced by Wallace in 1990 and later by Hinton and van Camp in 1993 provides an interesting link between Bayesian learning and information-theoretic minimum-description-length (MDL) learning approaches. The bits-back coding allows interpreting the cost function used in the variational Bayesian method called ensemble learning as a code length in addition to the Bayesian view of misfit of the posterior approximation and a lower bound of model evidence. Combining these two viewpoints provides interesting insights to the learning process and the functions of different parts of the model. In this paper, the problem of variational Bayesian learning of hierarchical latent variable models is used to demonstrate the benefits of the two views. The code-length interpretation provides new views to many parts of the problem such as model comparison and pruning and helps explain many phenomena occurring in learning.

Algorithms↗
PubMed1991

Visual evoked potential measurement by maximum length sequence technique.

The maximum length sequence (MLS) technique is applied to improve data collection of a clinically important long latency visual potential. Given a limited time for measuring the response and with low number of stimulus presentation, the MLS technique exceeded the conventional method of ensemble averaging in attaining a higher signal-to-noise ratio (SNR). The theoretical consideration of such improvement is developed along with the system implementation. Typical examples of the results obtained in a human subject are presented.

Algorithms↗
PubMed2004

Application of the ensemble nonequilibrium response spectroscopy to shaker potassium channel gating.

Standard electrophysiology techniques study relaxation transients in voltage-gated ion channels generated by discrete voltage steps. The nonequilibrium response spectroscopy involves analyzing responses to fluctuating potentials. We apply the ensemble NRS method to gating kinetics of Shaker potassium ion channels. We evaluate various proposed Markov models of channel gating from the nonequilibrium response viewpoint. These new NRS protocols can be used to test otherwise indistinguishable models or improve estimates for parameters of channel kinetics models.

Animals↗
PubMed1994

Visual evoked potential measurement by adaptive filtering.

The method of ensemble averaging (EA), commonly used to improve signal-to-noise ratio (SNR) in evoked potential measurements, loses potentially useful information regarding response variability across trials. Due to the usually low SNR, it is difficult to extract the response from individual trials. The present paper describes an adaptive signal enhancer (ASE) that is capable of tracking the variation of visual evoked potential (VEP) from trial to trial as well as improving SNR. This ASE requires two inputs: a primary input, which is the raw noise-corrupted response, and a reference input, which is designed for an optional performance of ASE. We used moving ensemble averaging (MEA) to form the dynamic reference input. Experimental results in humans show a satisfactory performance of the ASE in determining VEP to single stimulus and in tracking the temporal changes of the signal.

Algorithms↗
PubMed1997

Identification of synaptic connections in neural ensembles by graphical models.

A method for the identification of direct synaptic connections in a larger neural net is presented. It is based on a conditional correlation graph for multivariate point processes. The connections are identified via the partial spectral coherence of two neurons, given all others. It is shown how these coherences can be calculated by inversion of the spectral density matrix. In simulations with GENESIS, we discuss the relevance of the method for identifying different neural ensembles including an excitatory feedback loop and networks with lateral inhibitions.

Computer Graphics↗
PubMed2005

A unified methodological framework for the simulation of nonisothermal ensembles.

A general framework is developed for the simulation of nonisothermal statistical-mechanical ensembles. This framework is intended to synthesize the formulation of advanced Monte Carlo simulation methods such as multihistogram reweighting, replica-exchange methods, and expanded ensemble techniques so that they can be applied to different nonisothermal ensembles. Using Lennard-Jones systems as test cases, novel implementations of these methods are demonstrated with different ensembles including the microcanonical, isobaric-isoenthalpic, and isobaric-semigrand ensembles. In particular, it is shown that the use of multiensemble methods allows the efficient simulation of microcanonical density of states, entropies, vapor-liquid and solid-liquid equilibrium for pure component systems, and fluid-phase coexistence for binary mixtures. In these applications, comparisons are also presented that highlight the advantages of the proposed multiensemble implementations over alternative methods used before.

Journal Article↗
PubMed1985

A kinetic approach to the prediction of RNA secondary structures.

A new approach to the prediction of secondary RNA structures based on the analysis of the kinetics of molecular self-organisation is proposed herein. The Markov process is used to describe structural reconstructions during secondary structure formation. This process is modelled by a Monte-Carlo method. Examples of the calculation by this method of the secondary structures kinetic ensemble are given. Distribution of time-dependent probabilities within the ensembles is obtained. An effective method for search for the equilibrium ensemble is also suggested. This method is based on the construction of a tree of all possible secondary structures of RNA. By ascribing a probability for each structure (according to its free energy) the Boltzmann equilibrium ensemble can be obtained.

Computers↗