A two-phase approach for detecting recombination in nucleotide sequences

Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer picture of the phylogenetic relationships among different gene sequences or genomes. Nevertheless, detecting recombination events can be a daunting task, as the performance of different recombination-detecting approaches can vary, depending on evolutionary events that take place after recombination. We recently evaluated the effects of post-recombination events on the prediction accuracy of recombination-detecting approaches using simulated nucleotide sequence data. The main conclusion, supported by other studies, is that one should not depend on a single method when searching for recombination events. In this paper, we introduce a two-phase strategy, applying three statistical measures to detect the occurrence of recombination events, and a Bayesian phylogenetic approach in delineating breakpoints of such events in nucleotide sequences. We evaluate the performance of these approaches using simulated data, and demonstrate the applicability of this strategy to empirical data. The two-phase strategy proves to be time-efficient when applied to large datasets, and yields high-confidence results.

Entanglement in a simple quantum phase transition

What entanglement is present in naturally occurring physical systems at thermal equilibrium? Most such systems are intractable and it is desirable to study simple but realistic systems that can be solved. An example of such a system is the one-dimensional infinite-lattice anisotropic XY model. This model is exactly solvable using the Jordan-Wigner transform, and it is possible to calculate the two-site reduced density matrix for all pairs of sites. Using the two-site density matrix, the entanglement of formation between any two sites is calculated for all parameter values and temperatures. We also study the entanglement in the transverse Ising model, a special case of the XY model, which exhibits a quantum phase transition. It is found that the next-nearest-neighbor entanglement (though not the nearest-neighbor entanglement) is a maximum at the critical point. Furthermore, we show that the critical point in the transverse Ising model corresponds to a transition in the behavior of the entanglement between a single site and the remainder of the lattice.

Achromatic optical phase shifter/modulator

We propose and demonstrate, theoretically and experimentally, a novel achromatic optical phase shifter modulator based on a frequency-domain optical delay line configured to maintain zero group delay as variable phase delay is generated by means of tilting a mirror. Compared with previously reported phase shifter modulators, e.g., based on the Pancharatnam (geometric) phase, our device is high speed and polarization insensitive and produces a large, bounded phase delay that, uniquely, is one-to-one mapped to a measurable parameter, the tilt angle.

Hamiltonian mappings and circle packing phase spaces.

We introduce three area preserving maps with phase space structures which resemble circle packings. Each mapping is derived from a kicked Hamiltonian system with one of the three different phase space geometries (planar, hyperbolic or spherical) and exhibits an infinite number of coexisting stable periodic orbits which appear to ‘pack’ the phase space with circular resonances.

A two-phase strategy for detecting recombination in nucleotide sequences

Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer picture of the phylogenetic relationships among different gene sequences or genomes. Nevertheless, detecting recombination events can be a daunting task, as the performance of different recombination-detecting approaches can vary, depending on evolutionary events that take place after recombination. We previously evaluated the effects of post-recombination events on the prediction accuracy of recombination-detecting approaches using simulated nucleotide sequence data. The main conclusion, supported by other studies, is that one should not depend on a single method when searching for recombination events. In this paper, we introduce a two-phase strategy, applying three statistical measures to detect the occurrence of recombination events, and a Bayesian phylogenetic approach to delineate breakpoints of such events in nucleotide sequences. We evaluate the performance of these approaches using simulated data, and demonstrate the applicability of this strategy to empirical data. The two-phase strategy proves to be time-efficient when applied to large datasets, and yields high-confidence results.

Surface Waves and Roughness in Self-Aerated Supercritical Flow

In high-velocity open channel flows, free-surface aeration is commonly observed. The effects of surface waves on the air-water flow properties are tested herein. The study simulates the air-water flow past a fixed-location phase-detection probe by introducing random fluctuations of the flow depth. The present model yields results that are close to experimental observations in terms of void fraction, bubble count rate and bubble/droplet chord size distributions. The results show that the surface waves have relatively little impact on the void fraction profiles, but that the bubble count rate profiles and the distributions of bubble and chord sizes are affected by the presence of surface waves.

ESEM observations of SCC initiation for 4340 high strength steel in distilled water

The stress corrosion cracking (SCC) initiation process for 4340 high strength steel in distilled water at room temperature was studied using a new kind of instrument: an environmental scanning electron microscope (ESEM). It was found that the applied stress accelerated oxide film formation which has an important influence on the subsequent SCC initiation. SCC was observed to initiate in the following circumstances: (1) cracking of a thick oxide film leading to SCC initiation along metal grain boundaries, (2) the initiation of pits initiating SCC in the metal and (3) SCC initiating from the edge of the specimen. All these three SCC initiation circumstances are consistent with the following model which couples SCC initiation with cracking of a surface protective oxide. There is a dynamic interaction between oxide formation, the applied stress, oxide cracking, pitting and the initiation of SCC. An aspect of the dynamic interaction is cracks forming in a protective surface oxide because of the applied stress, exposing to the water bare metal at the oxide crack tip, and oxidation of the bare metal causing crack healing. Oxide crack healing would be competing with the initiation of intergranular SCC if an oxide crack meets the metal surface at a grain boundary. If the intergranular SCC penetration is sufficiently fast along the metal grain boundary, then the crack yaws open preventing healing of the oxide crack. If intergranular SCC penetration is not sufficiently fast, then the oxidation process could produce sufficient oxide to fill both the stress corrosion crack and the oxide crack; in this case there would be initiation of SCC but only limited propagation of SCC. Stress-induced cracks in very thin oxide can induce pits which initiate SCC, and under some conditions such stress induced cracks in a thin oxide can directly initiate SCC.

p-cresol as a reversible acylium ion scavenger in solid-phase peptide synthesis

In this work we have defined the nature of the p-cresol and p-thiocresol adducts generated from acylium ions during HF cleavage, following contemporary Boc/benzyl solid-phase peptide synthesis. Contrary to the results in previous reports, we found that both p-cresol and p-thiocresol predominantly form. aryl esters under typical cleavage conditions. Initially we investigated a number of small peptides containing either a single glutamate residue or a C-terminal long-chain amino acid which allowed us to unambiguously characterize the scavenged side products. Whereas, the p-cresol esters are stable at 0 degrees C they rearrange irreversibly at higher temperatures (5-20 degrees C) to form aryl ketones. By contrast, p-thiocresol esters do not undergo a Fries rearrangement but readily undergo further additions of p-thiocresol to form ketenebisthioacetals and trithio ortho esters, even at low temperatures. Importantly, we found by LC/MS and FT-ICR MS analysis that peptides containing p-cresol esters at glutamyl side chains are susceptible to amidation and fragmentation reactions at these sites during standard mild base workup procedures. The significance of these side reactions was further demonstrated in the synthesis of neutrophil immobilization factor, a 26-residue peptide, containing four glutamic acid residues. The side reactions were largely avoided by mild hydrogen peroxide-catalyzed hydrolysis which converted the p-cresol adducts to the free carboxylic acids in near quantitative yield. The choice of p-cresol as a reversible acylium ion scavenger when coupled with the simple workup conditions described is broadly applicable to Boc/benzyl peptide synthesis and will significantly enhance the quality of peptides produced.

Improved one-step solid-phase extraction method for morphine, morphine-3-glucuronide, and morphine-6-glucuronide from plasma and quantitation using high-performance liquid chromatography with electrochemical detection

This communication describes an improved one-step solid-phase extraction method for the recovery of morphine (M), morphine-3-glucuronide (M3G), and morphine-6-glucuronide (M6G) from human plasma with reduced coextraction of endogenous plasma constituents, compared to that of the authors' previously reported method. The magnitude of the peak caused by endogenous plasma components in the chromatogram that eluted immediately before the retention time of M3G has been reduced (similar to 80%) significantly (p < 0.01) while achieving high extraction efficiencies for the compounds of interest, viz morphine, M6G, and M3G (93.8 +/- 2.5, 91.7 +/- 1.7, and 93.1 +/- 2.2%, respectively). Furthermore, when the improved solid-phase extraction method was used, the extraction cartridge-derived late-eluting peak (retention time 90 to 100 minutes) reported in our previous method, was no longer present in the plasma extracts. Therefore the combined effect of reducing the recovery of the endogenous components of plasma that chromatographed just before the retention time of M3G and the removal of the late-eluting, extraction cartridge-derived peak has resulted in a decrease in the chromatographic run-time to 20 minutes, thereby increasing the sample throughput by up to 100%.

Contradiction of quantum mechanics with local hidden variables for quadrature phase amplitude measurements

We demonstrate a contradiction of quantum mechanics with local hidden variable theories for continuous quadrature phase amplitude (position and momentum) measurements. For any quantum state, this contradiction is lost for situations where the quadrature phase amplitude results are always macroscopically distinct. We show that for optical realizations of this experiment, where one uses homodyne detection techniques to perform the quadrature phase amplitude measurement, one has an amplification prior to detection, so that macroscopic fields are incident on photodiode detectors. The high efficiencies of such detectors may open a way for a loophole-free test of local hidden variable theories.

CO2 reforming of methane on Ni catalysts: Effects of the support phase and preparation technique

The effects of the support phase and catalyst preparation methods on catalytic activity and carbon deposition were systematically investigated over nickel catalysts supported on Al2O3, SiO2 and MgO for the reforming reaction of methane with carbon dioxide. It is found that the pore structure of the support and metal-support interaction significantly affected the catalytic activity and coking resistance. Catalyst with well-developed porosity exhibited higher catalytic activity. Strong interaction between metal and the support made the catalyst more resistant to sintering and coking, thus resulting in a longer time of catalyst stability. (C) 1998 Elsevier Science B.V.

Bimanual co-ordination in Parkinson's disease

The basal ganglia may be involved in bimanual co-ordination. Parkinson's disease (which impairs basal ganglia output) is clinically reported to cause difficulties in the performance of co-ordinated bimanual movements. Nevertheless, any bimanual co-ordination difficulties may be task specific, as experimental observations are equivocal. To infer the role of the basal ganglia in co-ordinating the two arms, this study investigated the bimanual co-ordination of patients with Parkinson's disease. Sixteen Parkinson's disease patients and matched control subjects performed a bimanual cranking task, at different speeds (1 and 2 Hz) and phase relationships. All subjects performed the required bimanual in-phase movement on a pair of cranks, at fast (2 Hz) and slow (1 Hz) speeds. However the Parkinson's disease patients were unable to perform the asymmetrical anti-phase movement, in which rotation of the cranks differed by 180 degrees, at either speed; but instead reverted to the in-phase symmetrical movement. For Parkinson's disease patients, performance of the in-phase movement was more accurate and stable when an external timing cue was used; however for anti-phase movement, the external cue accentuated the tendency for patients to revert to more symmetrical, in-phase movements.

Decoherence in ion traps due to laser intensity and phase fluctuations

We consider one source of decoherence for a single trapped ion due to intensity and phase fluctuations in the exciting laser pulses. For simplicity we assume that the stochastic processes involved are white noise processes, which enables us to give a simple master equation description of this source of decoherence. This master equation is averaged over the noise, and is sufficient to describe the results of experiments that probe the oscillations in the electronic populations as energy is exchanged between the internal and electronic motion. Our results are in good qualitative agreement with recent experiments and predict that the decoherence rate will depend on vibrational quantum number in different ways depending on which vibrational excitation sideband is used.

Observations of QSO J2233-606 in the Southern Hubble Deep Field

The Hubble Deep Field South (HDF-S) Hubble Space Telescope (HST) observations are expected to begin in 1998 October. We present a composite spectrum of the QSO in the HDF-S held covering UV/optical/near-IR wavelengths, obtained by combining data from the Australian National University 2.3 m telescope with STIS on the HST.(1) This intermediate-resolution spectrum covers the range 1600-10000 Angstrom and allows us to derive some basic information on the intervening absorption systems which will be important in planning future higher resolution studies of this QSO. The QSO J2233 - 606 coordinates are alpha = 22(h)33(m)37(s).6, delta = -60 degrees 33'29 (J2000), the magnitude is B = 17.5, and its redshift is z(em) = 2.238, derived by simultaneously fitting several emission lines. The spectral index is alpha = -0.7 +/- 0.1, measured between the Ly alpha and Mg II emission lines. Many absorption systems are present, including systems with metal lines redward of the Ly alpha emission line at z(abs) 2.204, 1.942, 1.870, 1.787 and a few very strong Ly alpha features at z(abs) = 2.077, 1.928, without similarly strong metal lines. There is a conspicuous Lyman limit (LL) absorption system that is most likely associated with the z(abs) = 1.942 system with a neutral hydrogen column density of N-HI = (3.1 +/- 1.0) x 10(17) cm(-2). There is some evidence for the presence of a second LL absorber just to the blue of the conspicuous system at z = 1.870. We have employed a new technique, based on an analysis of the shape of the observed spectrum in the region of the LL absorption, to explore the properties of the gas. We tentatively conclude that this system might have suitable characteristics for measuring the deuterium-to-hydrogen (D/H) ratio.

Phase diagram of the one-dimensional Holstein model of spinless fermions

The one-dimensional Holstein model of spinless fermions interacting with dispersionless phonons is studied using a new variant of the density matrix renormalization group. By examining various low-energy excitations of finite chains, the metal-insulator phase boundary is determined precisely and agrees with the predictions of strong coupling theory in the antiadiabatic regime and is consistent with renormalization group arguments in the adiabatic regime. The Luttinger liquid parameters, determined by finite-size scaling, are consistent with a Kosterlitz-Thouless transition.