Simplified amino acid alphabets based on deviation of conditional probability from random background

The primitive data for deducing the Miyazawa-Jernigan contact energy or BLOSUM score matrix consists of pair frequency counts. Each amino acid corresponds to a conditional probability distribution. Based on the deviation of such conditional probability from random background, a scheme for reduction of amino acid alphabet is proposed. It is observed that evident discrepancy exists between reduced alphabets obtained from raw data of the Miyazawa-Jernigan's and BLOSUM's residue pair counts. Taking homologous sequence database SCOP40 as a test set, we detect homology with the obtained coarse-grained substitution matrices. It is verified that the reduced alphabets obtained well preserve information contained in the original 20-letter alphabet.Comment: 9 pages,3figure

Optical properties of pyrochlore oxide Pb2Ru2O7−δPb_{2}Ru_{2}O_{7-{\delta}}

We present optical conductivity spectra for $Pb_{2}Ru_{2}O_{7-{\delta}}$ single crystal at different temperatures. Among reported pyrochlore ruthenates, this compound exhibits metallic behavior in a wide temperature range and has the least resistivity. At low frequencies, the optical spectra show typical Drude responses, but with a knee feature around 1000 \cm. Above 20000 \cm, a broad absorption feature is observed. Our analysis suggests that the low frequency responses can be understood from two Drude components arising from the partially filled Ru $t_{2g}$ bands with different plasma frequencies and scattering rates. The high frequency broad absorption may be contributed by two interband transitions: from occupied Ru $t_{2g}$ states to empty $e_{g}$ bands and from the fully filled O 2p bands to unoccupied Ru $t_{2g}$ states.Comment: 4 pages, 6 figure

Non-Markovian dynamics for an open two-level system without rotating wave approximation: Indivisibility versus backflow of information

By use of the two measures presented recently, the indivisibility and the backflow of information, we study the non-Markovianity of the dynamics for a two-level system interacting with a zero-temperature structured environment without using rotating wave approximation (RWA). In the limit of weak coupling between the system and the reservoir, and by expanding the time-convolutionless (TCL) generator to the forth order with respect to the coupling strength, the time-local non-Markovian master equation for the reduced state of the system is derived. Under the secular approximation, the exact analytic solution is obtained and the sufficient and necessary conditions for the indivisibility and the backflow of information for the system dynamics are presented. In the more general case, we investigate numerically the properties of the two measures for the case of Lorentzian reservoir. Our results show the importance of the counter-rotating terms to the short-time-scale non-Markovian behavior of the system dynamics, further expose the relations between the two measures and their rationality as non-Markovian measures. Finally, the complete positivity of the dynamics of the considered system is discussed

Analysis of community structure of a microbial consortium capable of degrading benzo(a)pyrene by DGGE

A microbial consortium was obtained by enrichment culture of sea water samples collected from Botan oil port in Xiamen, China, using the persistent high concentration of a mixture of polycyclic aromatic hydrocarbons enrichment strategy. Denaturing gradient gel electrophoresis (DGGE) was used to investigate the bacterial composition and community dynamic changes based on PCR amplification of 16S rRNA genes during batch culture enrichment. Using the spray-plate method, three bacteria, designated as BL01, BL02 and BL03, which corresponded to the dominant bands in the DGGE profiles, were isolated from the consortium. Sequence analysis showed that BL01, BL02 and BL03 were phylogenetically close to Ochrobactrum sp., Stenotrophomonas maltophilia and Pseudomonas fluorescens, respectively. The degradation of benzo(a)pyrene (BaP), a model high-molecular-weight polycyclic aromatic hydrocarbon (HMW PAH) compound was investigated using individual isolates, a mixture of the three isolates, and the microbial consortium (BL) originally isolated from the oil port sea water. Results showed that the order of degradative ability was BL > the mixture of the three isolates > individual isolates. BL degraded 44.07% of the 10 ppm BaP after 14 days incubation, which showed the highest capability for HMW PAH compound degradation. Our results revealed that this high selective pressure strategy was feasible and effective in enriching the HMW PAH-degraders from the original sea water samples. (C) 2009 Elsevier Ltd. All rights reserved

Microbial modulation in the biomass and toxin production of a red-tide causing alga

The effect of S10, a strain of marine bacteria isolated from sediment in the Western Xiamen Sea, on the growth and paralytic shellfish poison (PSP) production in the alga Alexandrium tamarense (A. tamarense) was studied under controlled experimental conditions.The results of these experiments have shown that the growth of A. tamarense is obviously inhibited by S10 at high concentrations,however no evident effect on its growth was observed at low concentrations. Its PSP production was also inhibited by S10 at different concentrations, especially at low concentrations. The toxicity of this strain of A. tamarense is about (0.95– 12.14) • 10－6 MU/cell, a peak toxicity value of 12.14 • 10－6 MU/cell appeared on the 14th day, after which levels decreased gradually.The alga grew well in conditions of pH 6–8 and salinities of 20–34‰. The toxicity of the alga varied markedly at different pH and salinity levels. Toxicity decreased as pH increased, while it increased with salinity and reached a peak value at a salinity of 30‰,after which it declined gradually. S10 at a concentration of 1.02 • 109 cells/ml inhibited growth and the PSP production of A. tamarense at different pH and salinity levels. S10 had the strongest inhibitory function on the growth of A. tamarense under conditions of pH 7 and a salinity of 34‰. The best inhibitory effect on PSP production by A. tamarense was at pH 7, this inhibitory effect on PSP production did not relate to salinity. Interactions between marine bacteria and A. tamarense were also investigated using the flow cytometer technique (FCM) as well as direct microscope counting. S10 was identified as being a member of the genus Bacillus, the difference in 16S rDNA between S10 and Bacillus halmapalus was only 2%. The mechanism involved in the inhibition of growth and PSP production of A. tamarense by this strain of marine bacteria, and the prospect of using it and other marine bacteria in the biocontrol of red-tides was discussed

ZFX Mediates Non-canonical Oncogenic Functions of the Androgen Receptor Splice Variant 7 in Castrate-Resistant Prostate Cancer

Androgen receptor splice variant 7 (AR-V7) is crucial for prostate cancer progression and therapeutic resistance. We show that, independent of ligand, AR-V7 binds both androgen-responsive elements (AREs) and non-canonical sites distinct from full-length AR (AR-FL) targets. Consequently, AR-V7 not only recapitulates AR-FL's partial functions but also regulates an additional gene expression program uniquely via binding to gene promoters rather than ARE enhancers. AR-V7 binding and AR-V7-mediated activation at these unique targets do not require FOXA1 but rely on ZFX and BRD4. Knockdown of ZFX or select unique targets of AR-V7/ZFX, or BRD4 inhibition, suppresses growth of castration-resistant prostate cancer cells. We also define an AR-V7 direct target gene signature that correlates with AR-V7 expression in primary tumors, differentiates metastatic prostate cancer from normal, and predicts poor prognosis. Thus, AR-V7 has both ARE/FOXA1 canonical and ZFX-directed non-canonical regulatory functions in the evolution of anti-androgen therapeutic resistance, providing information to guide effective therapeutic strategies. By cistrome profiling of endogenous androgen receptor (AR) versus an AR splice variant, AR-V7, Cai et al. uncovered non-canonical pathways uniquely targeted by AR-V7 and ZFX, a previously unknown AR-V7 partner. Targeting cofactors (ZFX or BRD4) or non-canonical downstream pathways of AR-V7 provides potential therapeutic ways for treating prostate cancer

A study of charged kappa in J/ψ→K±Ksπ∓π0J/\psi \to K^{\pm} K_s \pi^{\mp} \pi^0

Based on $58 \times 10^6$ $J/\psi$ events collected by BESII, the decay $J/\psi \to K^{\pm} K_s \pi^{\mp} \pi^0$ is studied. In the invariant mass spectrum recoiling against the charged $K^*(892)^{\pm}$, the charged $\kappa$ particle is found as a low mass enhancement. If a Breit-Wigner function of constant width is used to parameterize the kappa, its pole locates at $(849 \pm 77 ^{+18}_{-14}) -i (256 \pm 40 ^{+46}_{-22})$ MeV/$c^2$. Also in this channel, the decay $J/\psi \to K^*(892)^+ K^*(892)^-$ is observed for the first time. Its branching ratio is $(1.00 \pm 0.19 ^{+0.11}_{-0.32}) \times 10^{-3}$.Comment: 14 pages, 4 figure

Multipartite entangled states in coupled quantum dots and cavity-QED

We investigate the generation of multipartite entangled state in a system of N quantum dots embedded in a microcavity and examine the emergence of genuine multipartite entanglement by three different characterizations of entanglement. At certain times of dynamical evolution one can generate multipartite entangled coherent exciton states or multiqubit $W$ states by initially preparing the cavity field in a superposition of coherent states or the Fock state with one photon, respectively. Finally we study environmental effects on multipartite entanglement generation and find that the decay rate for the entanglement is proportional to the number of excitons.Comment: 9 pages, 4 figures, to appear in Phys. Rev.

Measurements of the observed cross sections for e+e−→e^+e^-\to exclusive light hadrons containing π0π0\pi^0\pi^0 at s=3.773\sqrt s= 3.773, 3.650 and 3.6648 GeV

By analyzing the data sets of 17.3, 6.5 and 1.0 pb$^{-1}$ taken, respectively, at $\sqrt s= 3.773$, 3.650 and 3.6648 GeV with the BES-II detector at the BEPC collider, we measure the observed cross sections for $e^+e^-\to \pi^+\pi^-\pi^0\pi^0$, $K^+K^-\pi^0\pi^0$, $2(\pi^+\pi^-\pi^0)$, $K^+K^-\pi^+\pi^-\pi^0\pi^0$ and $3(\pi^+\pi^-)\pi^0\pi^0$ at the three energy points. Based on these cross sections we set the upper limits on the observed cross sections and the branching fractions for $\psi(3770)$ decay into these final states at 90% C.L..Comment: 7 pages, 2 figure

Measurements of the observed cross sections for exclusive light hadron production in e^+e^- annihilation at \sqrt{s}= 3.773 and 3.650 GeV

By analyzing the data sets of 17.3 pb$^{-1}$ taken at $\sqrt{s}=3.773$ GeV and 6.5 pb$^{-1}$ taken at $\sqrt{s}=3.650$ GeV with the BESII detector at the BEPC collider, we have measured the observed cross sections for 12 exclusive light hadron final states produced in $e^+e^-$ annihilation at the two energy points. We have also set the upper limits on the observed cross sections and the branching fractions for $\psi(3770)$ decay to these final states at 90% C.L.Comment: 8 pages, 5 figur