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PubMed2006

Carrier-envelope phase shift caused by variation of grating separation.

The effects of variation of the grating separation in a stretcher on the carrier-envelope (CE) phase of amplified pulses are investigated. By translating one of the telescope mirrors in the stretcher with a piezoelectric transducer, it is found that a 1 mum change of the distance causes a 3.7+/-1.2 rad shift of the CE phase, which is consistent with theoretical estimations. The results indicate that optical mounts used for gratings and telescope mirrors must be interferometrically stable; otherwise their vibration and thermal drift will cause significant phase error. The CE phase drift was corrected by feedback controlling the grating separation.

Journal Article↗
PubMed2006

Speckle activity images based on the spatial variance of the phase.

We propose the display of the local spatial variance of the temporal variations of the phase as an activity descriptor in dynamic speckle images. The spatial autocorrelation of the speckle intensity is calculated in sliding windows, and an estimation of the variance of the phase variations in each region of the sample is determined. The activity images obtained in this way depict some interesting features and in some cases they could be related to physical magnitudes in the samples. A simulation is presented, and examples corresponding to usual study cases are also shown, namely, fruit bruising and paint drying.

Journal Article↗
PubMed1997

Individual variation in reentrainment after phase shifts of light-dark cycle in a diurnal rodent Octodon degus.

The rate and pattern of activity and temperature reentrainment was determined after 3-, 6-, and 9-h phase advances and phase delays in two groups of Octodon degus for whom phase response curves (PRCs) to light and dark pulses and free-running periods (tau) in constant darkness and constant light had previously been determined [T.M. Lee and S. E. Labyak. Am. J. Physiol. 273 (Regulatory Integrative Comp. Physiol. 42): R278-R286, 1997.]. We predicted that individuals with light-pulse PRCs containing both significant phase delay and phase advance regions would phase delay more rapidly than individuals lacking significant phase delays after light pulses. We also expected that animals without a phase delay region in the light-pulse PRC would demonstrate more temporary circadian abnormalities during the period of reentrainment (periods of masking, bimodal patterns of activity, and abnormal phase relationships between activity and temperature). Degus with light-pulse PRCs containing both a significant phase-delay and -advance region reentrained significantly faster and with fewer disrupted patterns of entrainment after 6- and 9-h phase delays than degus without phase-delay regions in the PRC. The rate of reentrainment after phase advances did not differ between animals with the two types of PRC except for temperature after a 6-h phase shift. Because animals with and without phase-delay regions in the light-pulse PRC had equivalent tau s, the interindividual variation in reentrainment is best explained by the fundamental differences in the light-pulse PRCs. The variation of rate and pattern of reentrainment for both groups of animals were reasonably predicted or explained by knowledge of the light-pulse and dark-pulse PRCs.

Activity Cycles↗
PubMed2000

Electronic structures of M21S8 (M = Nb, Zr) and (M,M')21S8 (M, M' = Hf, Ti; Nb, Ta) phases and reasons for variations in the metal site occupations.

The electronic structures of binary M21S8 (M = Nb, Zr) and isostructural ternary (M,M')21S8 (M, M' = Hf, Ti; Nb, Ta) phases have been studied by means of extended Hückel tight-binding band structure calculations. For the valence electron concentration in the binary group 5 metal phase Nb21S8, metal-metal bonding is optimized whereas, in the isostructural group 4 metal phase Zr21S8, metal-metal bonding levels exist above the Fermi level. However, the electronic structure analysis suggests a stable structure for M21S8 phases with group 4 metals and that (M,M')21S8 phases with mixed group 4 and group 5 metals, even if not yet reported, could well exist. In the ternary phase Nb6.9Ta14.1S8, a linear relationship exists between the magnitude of the metal-metal bonding capacity (as expressed by the total metal-metal Mulliken overlap population) of each crystallographically independent metal site and the occupation of the site with the heavier metal (i.e., the element with the greater bonding capability). The situation is quite more complex in Hf7.5Ti13.5S8, where the metal-metal bonding capacity of each site, differences in electronegativity between Ti and Hf, and site volume arguments must be taken into account to understand the metal site occupation.

Journal Article↗
PubMed1981

Pulse wave propagation.

This report evaluates pulse wave propagation with respect to contributions by vascular wall elastic and geometric properties, vessel wall and blood viscosity, and nonlinearities in system parameters and in the equations of motion. Discrepancies in results obtained with different experimental methods and theory are discussed and resolved. A three-point pressure technique was used to obtain measurements from the abdominal aorta, carotid, iliac, and femoral arteries of dogs. Computations involved linear, as well as nonlinear methods. Results are presented along a continuous path of transmission (abdominal aorta, iliac, femoral), and it is shown that variations in phase velocity can be explained entirely by the geometric variation of these vessels. Phase velocities are shown to be frequency independent at approximately greater than 4 Hz whereas attenuation increases progressively for higher frequencies. Determination of propagation coefficients using maximal, compounded values of reported viscoelastic and geometric properties just manages to span the range of phase velocities, determined in different laboratories, but does not do so for attenuation. Also, differences in experimental techniques cannot explain these discrepancies. Consideration of geometric taper, nonlinear compliance, all the terms in the equation of motion, and the effect of wall and blood viscosity resolves discrepancies between theoretical and experimentally derived phenomena.

Animals↗
PubMed2005

A Markov model approach shows a large variation in the length of S phase in MCF-7 breast cancer cells.

BACKGROUND: The potential doubling time of a tumor has been suggested to be a measurement of tumor aggressiveness; therefore, it is of interest to find reliable methods to estimate this time. Because of variability in length of the various cell cycle phases, stochastic modeling of the cell cycle might be a suitable approach. METHODS: The relative movement curve and the DNA synthesis time were estimated by using local polynomial regression methods. Further, the rate of nucleotide incorporation was estimated by using a Markov pure birth process with one absorbing state to model the progression of the DNA distribution through S phase. RESULTS: An estimate of the DNA synthesis time, with confidence intervals, was obtained from the relative movement curve. The Markov approach provided an estimate of the distribution of the time to complete S phase given the initial distribution. Using the Markov approach we also made an estimate of the mean number of active replicons during S phase. CONCLUSIONS: A Markov pure birth process has shown to be useful to model the progression of cells through S phase and to increase knowledge about the variability in the length of S phase and a large variation is shown.

Analysis of Variance↗
PubMed2002

Complexities in ETS-domain transcription factor function and regulation: lessons from the TCF (ternary complex factor) subfamily. The Colworth Medal Lecture.

The ETS-domain transcription factor family can be divided into a series of subfamilies. Elk-1 represents the founding member of the ternary complex factor (TCF) subfamily. By focusing on the TCF subfamily, we can demonstrate the complexities that exist in the function and regulation of ETS-domain transcription factors. This article focuses on Elk-1 in detail and summarizes the functions of other TCFs. The key themes covered include the domain structure of the TCFs, the mechanisms of complex formation with serum response factor, regulation of TCFs by mitogen-activated protein kinase cascades, and transcriptional regulatory properties of the TCFs. Finally, the emerging role of the TCFs in vivo is discussed. A picture is developing indicating that, while these proteins exhibit significant sequence and functional conservation, key differences in their structure and regulation are being identified which may relate to unique functions of these proteins in vivo.

Amino Acid Sequence↗
PubMed1997

Phase relations of rhythmic neuronal firing in the supramammillary nucleus and mammillary body to the hippocampal theta activity in urethane anesthetized rats.

Structures in the caudal diencephalon including the posterior hypothalamic nucleus, the supramammillary nucleus (SUM) and the nuclei of the mammillary body (MB) occupy a strategic position in the crossroads of ascending and descending traffic between the brainstem and the limbic forebrain (septum/hippocampus). In this study we analyzed the phase relations of rhythmically discharging SUM/MB cells to hippocampal theta rhythm in urethane anesthetized rats with a dual aim of separating different functional types of SUM and MB neurons and characterizing their coupling to septohippocampal theta oscillators. We found that rhythmically firing neurons in the SUM/MB represent a functionally heterogenous population of cells that are coupled with forebrain theta oscillators at different preferred phases. Based on their phase relations to hippocampal theta four groups of rhythmic SUM/MB cells were identified. Neurons of the first and second groups fired out-of-phase relative to each other and synchronously with the positive (8 degrees +/- 7) or negative peaks (-177 degrees +/- 7) of theta field activity in the hippocampus, recorded above the CA1 pyramidal layer. Cells of the other two groups, also forming out-of-phase counter-parts, fired on the rising (97 degrees +/- 9) or falling segments (-97 degrees +/- 6) of CA1 theta waves. The peaks in the phase distribution histogram were well separated, and the empty zones between them were wider (40-70 degrees) than those comprising the phase data for different groups. The variations of phase values for individual neurons, when tested during several theta epochs, did not exceed the range of a single group. Theta field potentials were also recorded in the SUM/MB and were advanced by one quarter of the cycle (79 degrees +/- 9, range 56-99 degrees) relative to CA1 theta oscillations. The present results indicate that, similar to other theta-generating structures, rhythmically firing neurons can be classified on the basis of their phase relations in the SUM/MB as well. Different classes of SUM/MB neurons might play different roles in generating and/or transmitting theta rhythmic activity of the limbic system.

Anesthetics, Intravenous↗
PubMed1997

Molecular biology of Mycoplasma.

Mycoplasmas are the smallest free living microorganisms with the smallest genome. The G+C content is in general low (25-33%) and the coding capacity is about 600 proteins. Mycoplasma species are phylogenetically related, they use the genetic codon UGA for tryptophan, and show rapid evolution, with a high rate of divergence. The genomes of Mycoplasma genitalium and Mycoplasma pneumoniae have been fully sequenced. Striking features of the M. genitalium sequencing project are the presence of a high number of membrane proteins with no resemblance to previously sequenced genes and the presence of repeated fragments of the gene encoding the tip-localized 140 kDa adhesin (MgPa). Many Mycoplasma species display a high frequency of antigenic variation, both as phase and size variation of individual antigens. Mycoplasma hominis isolates are known to be antigenic heterogeneous, as reflected in the reactivity with monoclonal antibodies (MAbs). The genetics of the antigenic variation has been studied for three different surface exposed antigens: P120, Lmp, and P50/Vaa. The gene encoding P120 had a hyper-variable region in the N-terminal region. In addition, a second gene with homology to p120 was identified. The gene encoding Lmp, a 135 kDa protein is repeated and both genes are translated and both contain internal repeated sequences. Deletion mutants in the lmp gene were obtained by cultivation of M. hominis PG21 with MAb 552 specific for the repeated part of Lmp. One of the lmp genes had deletions of from four to eight repeats. The other gene was left unaltered. The genes encoding P50/Vaa show a different form of variability where domains of the genes seem to be exchangeable. The genomic maps of five M. hominis strains showed that even though the size of the genomes varied the position of the different genes were in general conserved.

Animals↗
PubMed1998

Pressure-induced retention variations in reversed-phase alternate-pumping recycle chromatography.

The progressions of peak width and peak separation in reversed-phase alternate-pumping (AP) recycle chromatography are found to be inconsistent with conventional chromatographic theory. These discrepancies are explained by subtle pressure-induced variations of solute retention that become amplified by AP recycling. The presence of these retention variations is demonstrated by multiply injecting a single solute into an AP system at offset times. As the serially injected peaks are recycled, the separation time between the peaks is shown to vary significantly, indicating that the retention of the solute is dependent upon the position of the peak. A new model of chromatographic retention that appropriately accounts for this variable retention is presented. When this retention model is applied to an AP system for the binary separation of phenylalanine and a pentadeuterated phenylalanine, the model accurately describes the experimentally observed progressions of peak width and peak separation. Furthermore, the retention model predicts that the improvement of resolution in AP recycling closely matches the expectations of conventional theory, so the effectiveness of AP recycling is not significantly compromised by the variations in retention.

Chromatography, High Pressure Liquid↗
PubMed1974

Dynamic local distensibility of living arteries and its relation to wave transmission.

The dynamic local distensibility of the abdominal aorta was measured in 11 anesthetized dogs by recording simultaneously phasic pressure and instantaneous intravascular cross-sectional area, utilizing a special transducer. Axial motion of the vessel wall was recorded using a modification of the same transducer. A nonlinear relationship was found to exist between area and pressure in most cases studied. Fourier analysis was performed on data from eight experiments in order to obtain frequency characteristics of distensibility. In roughly half of the cases, Fourier analysis revealed that pressure variations displayed a phase lead over area variations for frequencies up to 10 Hz. This phenomenon was ascribed to viscoelastic properties of the vessel wall and the magnitude of the phase leads roughly matched those found in vitro by others. The behavior of the vessel wall in these instances was correctly predicted by the dynamic formula for distensibility, derived by others from wave transmission theory in which absence of axial wall motion is assumed. In these experiments, axial motion of the wall was found to be virtually absent. In the other half of the cases, the reverse situation was obtained: a phase lead of area variations over pressure variations for frequencies up to 15 Hz. In those cases a craniocaudal axial displacement of the vessel wall was observed with each systole, amounting to around 1 mm. The finding of the phase leads was partially explained by a dynamic formula for distensibility, developed by us from the theory of wave transmission in which free axial motion of the wall is a chosen boundary condition. The sign and order of magnitude of the phase leads were correctly predicted by the theoretical formula, but there was a disagreement on the frequency range in which they occurred. We concluded that additional forces, not yet considered in theoretical treatments, are operative on the aortic wall, which account for this lack of agreement. The frequency dependent properties of distensibility in vivo cannot be compared to those obtained in vitro in those cases in which there is axial displacement of the vessel wall of the same order of magnitude as the radial extensions.

Animals↗
PubMed2001

Epigenetic randomness, complexity and singularity of human iris patterns.

We investigated the randomness and uniqueness of human iris patterns by mathematically comparing 2.3 million different pairs of eye images. The phase structure of each iris pattern was extracted by demodulation with quadrature wavelets spanning several scales of analysis. The resulting distribution of phase sequence variation among different eyes was precisely binomial, revealing 244 independent degrees of freedom. This amount of statistical variability corresponds to an entropy (information density) of about 3.2 bits mm(-2) over the iris. It implies that the probability of two different irides agreeing by chance in more than 70% of their phase sequence is about one in 7 billion. We also compared images of genetically identical irides, from the left and right eyes of 324 persons, and from monozygotic twins. Their relative phase sequence variation generated the same statistical distribution as did unrelated eyes. This indicates that apart from overall form and colour, iris patterns are determined epigenetically by random events in the morphogenesis of this tissue. The resulting diversity, and the combinatorial complexity created by so many dimensions of random variation, mean that the failure of a simple test of statistical independence performed on iris patterns can serve as a reliable rapid basis for automatic personal identification.

Functional Laterality↗
PubMed2002

A novel paralogous gene family involved in phase-variable flagella-mediated motility in Campylobacter jejuni.

Flagella-mediated motility is recognized to be one of the major factors contributing to virulence in Campylobacter jejuni. Motility of this bacterium is known to be phase variable, although the mechanism of such variation remains unknown. C. jejuni genome sequencing revealed a number of genes prone to phase variation via a slipped-strand mispairing mechanism. Many of these genes are hypothetical and are clustered in the regions involved in formation of three major cell surface structures: capsular polysaccharide, lipooligosaccharide and flagella. Among the genes of unknown function, the flagellar biosynthesis and modification region contains seven hypothetical paralogous genes designated as the motility accessory factor (maf) family. Remarkably, two of these genes (maf1 and maf4) were found to be identical and both contain homopolymeric G tracts. Using insertional mutagenesis it was demonstrated that one of the genes, maf5, is involved in formation of flagella. Phase variation of the maf1 gene via slipped-strand mispairing partially restored motility of the maf5 mutant. The maf family represents a new class of bacterial genes related to flagellar biosynthesis and phase variation. Reversible expression of flagella may be advantageous for the adaptation of C. jejunito the varied in vivo and ex vivo environments encountered during its life cycle, as well in evasion of the host immune response.

Amino Acid Sequence↗
PubMed2003

Contribution of synaptic depression to phase maintenance in a model rhythmic network.

In many rhythmic neuronal networks that operate in a wide range of frequencies, the time of neuronal firing relative to the cycle period (the phase) is invariant. This invariance suggests that when frequency changes, firing time is precisely adjusted either by intrinsic or synaptic mechanisms. We study the maintenance of phase in a computational model in which an oscillator neuron (O) inhibits a follower neuron (F) by comparing the dependency of phase on cycle period in two cases: when the inhibitory synapse is depressing and when it is nondepressing. Of the numerous ways of changing the cycle period, we focus on three cases where either the duration of the active state, the inactive state, or the duty cycle of neuron O remains constant. In each case, we measure the phase at which neuron F fires with respect to the onset of firing in neuron O. With a nondepressing synapse, this phase is generally a monotonic function of cycle period except in a small parameter range in the case of the constant inactive duration. In contrast, with a depressing synapse, there is always a parameter regime in which phase is a cubic function of cycle period: it decreases at short cycle periods, increases in an intermediate range, and decreases at long cycle periods. This complex shape for the phase-period relationship arises because of the interaction between synaptic dynamics and intrinsic properties of the postsynaptic neuron. By choosing appropriate parameters, the cubic shape of the phase-period curve results in a small variation in phase for a large interval of periods. Consequently, we find that although a depressing synapse does not produce perfect phase maintenance, in most cases it is superior to a nondepressing synapse in promoting a constant phase difference.

Models, Neurological↗
PubMed1987

Variation in physical and biological properties of solid gold sodium thiomalate on dissolution: an electron microscopic and energy dispersive spectroscopic study.

The dissolution of solid gold sodium thiomalate (GSTM) in water results in loss of yellow color. We studied the initial reaction on dissolution. It was associated with the disappearance of 2 absorption peaks on ultraviolet spectrum, one a well defined peak at 335 nm and the other a shoulder at 370 nm. This solution caused platelet aggregation and on transmission electron microscopy, dense gold containing particles measuring 125 nm are seen. Within 10 min of onset of dissolution, no gold containing particulate matter was detectable on electron microscopy. By 20 min, fibrillar particles measuring 40-150 nm appear. These resembled in general morphology and element composition the particles seen within aurosomes in platelets treated with Myochrysine (GSTM) and in synovium and other tissues by other workers. Our data elaborate on previous physical and chemical studies and correlate with morphological variations of gold containing particles at different phases. These variations in GSTM may be due to polymer size and/or structural change within the polymer. The biochemical significance of our data should provide better understanding of the biological effects of these gold thiol compounds in vivo.

Blood Platelets↗
PubMed1999

Phase correction for collision model analysis and enhanced resolving power of fourier transform ion cyclotron resonance mass spectra.

Phase correction of FT-ICR data yields an absorption spectrum that offers a gain by up to a factor of 2 in mass resolving power (at half-maximum peak height), compared to conventional magnitude-mode display. That improvement is equivalent to doubling the applied magnetic field strength, without loss in signal-to-noise (S/N) ratio, provided that the time-domain data are padded with an equal number of zeroes before FFT. Our simple, visual, user-interactive algorithm quickly corrects for zero-order and first-order variation of phase with frequency. We find that the theoretical mass resolving power enhancement for pressure-limited absorption-mode over magnitude-mode line shape depends on the collision mechanism: factor of 1.40 for hard sphere vs 3(1/2) for Langevin (ion: induced dipole). Thus, the experimental enhancement in mass resolving power (factor of 1.43 +/- 0.09) for isotopically resolved peaks in the FT-ICR mass spectra of electrosprayed bovine carbonic anhydrase (approximately 29 kDa) directly supports the hard-sphere collision model. Optimal implementation of phasing requires the following: (a) a delay between excitation and detection of less than half of one sampling interval to avoid baseline "roll" and Gibb's oscillations; (b) accurate analog-to-digital conversion; (c) a sufficiently long acquisition period to yield several data points per absorption-mode peak width at half-maximum peak height; and (d) avoidance of FT-ICR apodization functions (e.g., Hamming and Hanning) that suppress the initial time-domain data. Pulsed single-frequency excitation (duration much less than the reciprocal of the Nyquist bandwidth) can eliminate higher than first-order variation of phase with frequency. Phased FT-ICR spectra should prove especially desirable for analysis of complex mixtures, for resolving isotopic distributions in electrosprayed multiply charged macromolecules and for characterizing ion collisions (and thus ion size and shape).

Animals↗
PubMed2002

Menstrual cycle effects on performance of mental arithmetic task.

The purpose of this research was to identify the relationship between task performance and menstrual cycle. The difference of performance on menstrual cycle phase was investigated. The task was the mental arithmetic task which involved the non-sequential and higher order cognitive processes. The duration of the experiment was twenty minutes. Two-way analysis of variance by repeated-measures design was used to examine the differences in task performance between phases and temporal variations. Results showed that there was a significant difference in correct input time during temporal variations though there was no significant difference between phases. Moreover, the relationships between phases and intra-individual variations in task performance were examined using coefficient of variance (CV). CVs were plotted in three dimensions to examine the relationships between intra-individual variations and phases. Based on CVs, the subjects who showed differences were classified into two groups: those with a small difference in three phases and those with a difference every phase. The phase which indicated large CV changed with individuals.

Adult↗