Improving the Excited Nucleon Spectrum in Hard-Wall AdS/QCD

We show that the nucleon spectrum in a hard-wall AdS/QCD model can be improved by use of a relatively large IR cutoff. All of the spin-1/2 nucleon masses listed in PDG can be fit quite well within 11%. The average error is remarkably only 4.66%.Comment: 11 pages, 2 figures. v2: references added. v3: add a section about the pion-nucleon coupling, published versio

A γ\gamma-ray Quasi-Periodic modulation in the Blazar PKS 0301−-243?

We report a nominally high-confidence $\gamma$-ray quasi-periodic modulation in the blazar PKS 0301$-$243. For this target, we analyze its \emph{Fermi}-LAT Pass 8 data covering from 2008 August to 2017 May. Two techniques, i.e., the maximum likelihood optimization and the exposure-weighted aperture photometry, are used to build the $\gamma$-ray light curves. Then both the Lomb-Scargle Periodogram and the Weighted Wavelet Z-transform are applied to the light curves to search for period signals. A quasi-periodicity with a period of $2.1\pm0.3$ yr appears at the significance level of $\sim5\sigma$, although it should be noted that this putative quasi-period variability is seen in a data set barely four times longer. We speculate that this $\gamma$-ray quasi-periodic modulation might be evidence of a binary supermassive black hole.Comment: 9 pages, 8 figures; Accepted for publication in Ap

γ-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates

<p>Abstract</p> <p>Background</p> <p>Over the past two decades, there have been several approximate methods that adopt different mutation models and used for estimating nonsynonymous and synonymous substitution rates (Ka and Ks) based on protein-coding sequences across species or even different evolutionary lineages. Among them, MYN method (a Modified version of Yang-Nielsen method) considers three major dynamic features of evolving DNA sequences–bias in transition/transversion rate, nucleotide frequency, and unequal transitional substitution but leaves out another important feature: unequal substitution rates among different sites or nucleotide positions.</p> <p>Results</p> <p>We incorporated a new feature for analyzing evolving DNA sequences–unequal substitution rates among different sites–into MYN method, and proposed a modified version, namely <it>γ </it>(gamma)-MYN, based on an assumption that the evolutionary rate at each site follows a mode of <it>γ</it>-distribution. We applied <it>γ</it>-MYN to analyze the key estimator of selective pressure ω (Ka/Ks) and other relevant parameters in comparison to two other related methods, YN and MYN, and found that neglecting the variation of substitution rates among different sites may lead to biased estimations of ω. Our new method appears to have minimal deviations when relevant parameters vary within normal ranges defined by empirical data.</p> <p>Conclusion</p> <p>Our results indicate that unequal substitution rates among different sites have variable influences on ω under different evolutionary rates while both transition/transversion rate ratio and unequal nucleotide frequencies affect Ka and Ks thus selective pressure ω.</p> <p>Reviewers</p> <p>This paper was reviewed by Kateryna Makova, David A. Liberles (nominated by David H Ardell), Zhaolei Zhang (nominated by Mark Gerstein), and Shamil Sunyaev.</p

Expression of VP60 gene from rabbit haemorrhagic disease virus (RHDV) YL strain under control of the ats1A promoter in tobacco

The VP60 gene from rabbit haemorrhagic disease virus (RHDV) YL strain in Northeast of China, under control of the ats1A promoter from Rubisco small subunit genes of Arabidopsis thaliana, was introduced into the transfer deoxyribonucleic acid (T-DNA) region of plant transfer vector pCAMBIA1300 and transferred to tobacco (Nicotiana tabacum cv. Petit Havanna SR1) with Agrobacterium tumefaciens-mediated method. Polymerase chain reaction (PCR) reverse transcription(RT) and -PCR analysis of the transformed tobacco plants confirmed the integration of the VP60 gene copy into the plant DNA and VP60 gene transcription produced. Western blot analysis revealed that the VP60 protein was expressed in tobacco under control of ats1A promoter.Key words: Agrobacterium tumefaciens, rabbit haemorrhagic disease virus (RHDV), VP60 protein, ats1A promoter, plant-derived vaccine