Improved alignment of nucleosome DNA sequences using a mixture model

DNA sequences that are present in nucleosomes have a preferential ∼10 bp periodicity of certain dinucleotide signals (1,2), but the overall sequence similarity of the nucleosomal DNA is weak, and traditional multiple sequence alignment tools fail to yield meaningful alignments. We develop a mixture model that characterizes the known dinucleotide periodicity probabilistically to improve the alignment of nucleosomal DNAs. We assume that a periodic dinucleotide signal of any type emits according to a probability distribution around a series of ‘hot spots’ that are equally spaced along nucleosomal DNA with 10 bp period, but with a 1 bp phase shift across the middle of the nucleosome. We model the three statistically most significant dinucleotide signals, AA/TT, GC and TA, simultaneously, while allowing phase shifts between the signals. The alignment is obtained by maximizing the likelihood of both Watson and Crick strands simultaneously. The resulting alignment of 177 chicken nucleosomal DNA sequences revealed that all 10 distinct dinucleotides are periodic, however, with only two distinct phases and varying intensity. By Fourier analysis, we show that our new alignment has enhanced periodicity and sequence identity compared with center alignment. The significance of the nucleosomal DNA sequence alignment is evaluated by comparing it with that obtained using the same model on non-nucleosomal sequences

Low compressible noble metal carbides with rock-salt structure: ab initio total energy calculations of the elastic stability

We have systematically studied the mechanical stability of all noble metal carbides with the rock-salt structure by calculating their elastic constants within the density function theory scheme. It was found that only four carbides (RuC, PdC, AgC and PtC) are mechanically stable. In particular, we have shown that RuC, PdC, and PtC have very high bulk modulus, which has been remarkably observed by the most recent experiment for the case of PtC. From the calculated density of states, we can conclude that these compounds are metallic, like the conventional group IV and group V transition metal carbides.Comment: Appl. Phys. Lett. 89, 071913 (2006

Gene capture prediction and overlap estimation in EST sequencing from one or multiple libraries

BACKGROUND: In expressed sequence tag (EST) sequencing, we are often interested in how many genes we can capture in an EST sample of a targeted size. This information provides insights to sequencing efficiency in experimental design, as well as clues to the diversity of expressed genes in the tissue from which the library was constructed. RESULTS: We propose a compound Poisson process model that can accurately predict the gene capture in a future EST sample based on an initial EST sample. It also allows estimation of the number of expressed genes in one cDNA library or co-expressed in two cDNA libraries. The superior performance of the new prediction method over an existing approach is established by a simulation study. Our analysis of four Arabidopsis thaliana EST sets suggests that the number of expressed genes present in four different cDNA libraries of Arabidopsis thaliana varies from 9155 (root) to 12005 (silique). An observed fraction of co-expressed genes in two different EST sets as low as 25% can correspond to an actual overlap fraction greater than 65%. CONCLUSION: The proposed method provides a convenient tool for gene capture prediction and cDNA library property diagnosis in EST sequencing

Phase Separation and Magnetic Order in K-doped Iron Selenide Superconductor

Alkali-doped iron selenide is the latest member of high Tc superconductor family, and its peculiar characters have immediately attracted extensive attention. We prepared high-quality potassium-doped iron selenide (KxFe2-ySe2) thin films by molecular beam epitaxy and unambiguously demonstrated the existence of phase separation, which is currently under debate, in this material using scanning tunneling microscopy and spectroscopy. The stoichiometric superconducting phase KFe2Se2 contains no iron vacancies, while the insulating phase has a \surd5\times\surd5 vacancy order. The iron vacancies are shown always destructive to superconductivity in KFe2Se2. Our study on the subgap bound states induced by the iron vacancies further reveals a magnetically-related bipartite order in the superconducting phase. These findings not only solve the existing controversies in the atomic and electronic structures in KxFe2-ySe2, but also provide valuable information on understanding the superconductivity and its interplay with magnetism in iron-based superconductors

Measurement of \psip Radiative Decays

Using 14 million psi(2S) events accumulated at the BESII detector, we report first measurements of branching fractions or upper limits for psi(2S) decays into gamma ppbar, gamma 2(pi^+pi^-), gamma K_s K^-pi^++c.c., gamma K^+ K^- pi^+pi^-, gamma K^{*0} K^- pi^+ +c.c., gamma K^{*0}\bar K^{*0}, gamma pi^+pi^- p pbar, gamma 2(K^+K^-), gamma 3(pi^+pi^-), and gamma 2(pi^+pi^-)K^+K^- with the invariant mass of hadrons below 2.9GeV/c^2. We also report branching fractions of psi(2S) decays into 2(pi^+pi^-) pi^0, omega pi^+pi^-, omega f_2(1270), b_1^\pm pi^\mp, and pi^0 2(pi^+pi^-) K^+K^-.Comment: 5 pages, 4 figure

Experimental study of ψ(2S)\psi(2S) decays to \K^+ K^- \pi^+ \pi^- \pi^0 final states

$K^+K^-\pi^+\pi^-\pi^0$ final states are studied using a sample of $14\times10^6$ $\psi(2S)$ decays collected with the Beijing Spectrometer (BESII) at the Beijing Electron-Position Collider. The branching fractions of $\psi(2S)$ decays to $K^+K^-\pi^+\pi^-\pi^0$, $\omega K^+ K^-$, $\omega f_0(1710)$, $K^{\ast}(892)^0 K^- \pi^+\pi^0+c.c.$, $K^{\ast}(892)^{+} K^- \pi^+\pi^- +c.c.$, $K^{\ast}(892)^{+} K^- \rho^0+c.c.$ and $K^{\ast}(892)^0 K^-\rho^+ + c.c.$ are determined. The first two agree with previous measurements, and the last five are first measurements.Comment: 19 pages, 9 figure

First observation of ψ(2S)→pnˉπ−+c.c.\psi(2S) \to p \bar{n} \pi^- +c.c.

Using 14 million $\psi(2S)$ events collected with the Beijing Spectrometer (BESII) at the Beijing Electron-Positron Collider, the branching fractions of $\psi(2S)$ decays to $p \bar{n} \pi^-$ and $\bar{p} n \pi^+$ and the branching fractions of the main background channels $\psi(2S) \to p \bar{n} \pi^-\pi^0$, $\psi(2S) \to \gamma\chi_{c0} \to \gamma p \bar{n} \pi^-$, $\psi(2S) \to \gamma\chi_{c2} \to \gamma p \bar{n} \pi^-$, and $\psi(2S) \to \gamma \chi_{cJ} \to \gamma p \bar{n} \pi^- \pi^0$ are determined. The contributions of the $N^{\ast}$ resonances in $\psi(2S) \to p \bar{n} \pi^- +c.c.$ are also discussed.Comment: 19 pages, 8 figures, add vertex requirement systematic erro

Measurements of J/ψJ/\psi and ψ(2S)\psi(2S) decays into ΛΛˉπ0\Lambda \bar{\Lambda}\pi^0 and ΛΛˉη\Lambda \bar{\Lambda}\eta

Using 58 million $J/\psi$ and 14 million $\psi(2S)$ events collected by the BESII detector at the BEPC, branching fractions or upper limits for the decays $J/\psi$ and $\psi(2S) \to \Lambda \bar{\Lambda}\pi^0$ and $\Lambda \bar{\Lambda}\eta$ are measured. For the isospin violating decays, the upper limits are determined to be ${\cal B}(J/\psi \to \Lambda \bar{\Lambda}\pi^0)<6.4\times 10^{-5}$ and ${\cal B}(\psi(2S) \to \Lambda \bar{\Lambda}\pi^0)<4.9\times 10^{-5}$ at the 90% confidence level. The isospin conserving process $J/\psi \to \Lambda \bar{\Lambda}\eta$ is observed for the first time, and its branching fraction is measured to be ${\cal B}(J/\psi \to \Lambda \bar{\Lambda}\eta)=(2.62\pm 0.60\pm 0.44)\times 10^{-4}$, where the first error is statistical and the second one is systematic. No $\Lambda \bar{\Lambda}\eta$ signal is observed in $\psi(2S)$ decays, and ${\cal B}(\psi(2S) \to \Lambda \bar{\Lambda}\eta)<1.2\times 10^{-4}$ is set at the 90% confidence level. Branching fractions of $J/\psi$ decays into $\Sigma^+ \pi^- bar{\Lambda}$ and $\bar{\Sigma}^- \pi^+ \Lambda$ are also reported, and the sum of these branching fractions is determined to be ${\cal B}(J/\psi \to \Sigma^+\pi^- \bar{\Lambda} + c.c.)=(1.52\pm 0.08\pm 0.16)\times 10^{-3}$.Comment: 7 pages, 10 figures. Phys.Rev.D comments considere

Study of χcJ\chi_{cJ} radiative decays into a vector meson

The decays $\chi_{cJ}\to\gamma V$ ($V=\phi, \rho^0, \omega$) are studied with a sample of radiative \psip\to\gamma\chi_{cJ} events in a sample of (1.06\pm0.04)\times 10^{8} \psip events collected with the BESIII detector. The branching fractions are determined to be: ${\cal B}(\chi_{c1}\to \gamma\phi)=(25.8\pm 5.2\pm 2.3)\times 10^{-6}$, ${\cal B}(\chi_{c1}\to \gamma\rho^0)=(228\pm 13\pm 22)\times 10^{-6}$, and ${\cal B}(\chi_{c1}\to \gamma\omega)=(69.7\pm 7.2\pm 6.6)\times 10^{-6}$. The decay $\chi_{c1}\to \gamma\phi$ is observed for the first time. Upper limits at the 90% confidence level on the branching fractions for $\chi_{c0}$ and \chict decays into these final states are determined. In addition, the fractions of the transverse polarization component of the vector meson in $\chi_{c1}\to \gamma V$ decays are measured to be $0.29_{-0.12-0.09}^{+0.13+0.10}$ for $\chi_{c1}\to \gamma\phi$, $0.158\pm 0.034^{+0.015}_{-0.014}$ for $\chi_{c1}\to \gamma\rho^0$, and $0.247_{-0.087-0.026}^{+0.090+0.044}$ for $\chi_{c1}\to \gamma\omega$, respectively. The first errors are statistical and the second ones are systematic.Comment: 8 pages, 3 figure