Abstract:
Since organism development and many critical cell biology processes are organized in modular patterns, many algorithms have been proposed to detect modules. In this study, a new method, MOfinder, was developed to detect overlapping modules in a protein-protein interaction (PPI) network. We demonstrate that our method is more accurate than other 5 methods. Then, we applied MOfinder to yeast and human PPI network and explored the overlapping information. Using the overlapping modules of human PPI network, we constructed the module-module communication network. Functional annotation showed that the immune-related and cancer-related proteins were always together and present in the same modules, which offer some clues for immune therapy for cancer. Our study around overlapping modules suggests a new perspective on the analysis of PPI network and improves our understanding of disease.

Abstract:
The evaluation of CMASA shows that the CMASA is highly accurate (0.96), sensitive (0.86), and fast enough to be used in the large-scale functional annotation. Comparing to both sequence-based and global structure-based methods, not only the CMASA can find remote homologous proteins, but also can find the active site convergence. Comparing to other local structure comparison-based methods, the CMASA can obtain the better performance than both FFF (a method using geometry to predict protein function) and SPASM (a local structure alignment method); and the CMASA is more sensitive than PINTS and is more accurate than JESS (both are local structure alignment methods). The CMASA was applied to annotate the enzyme catalytic sites of the non-redundant PDB, and at least 166 putative catalytic sites have been suggested, these sites can not be observed by the Catalytic Site Atlas (CSA).The CMASA is an accurate algorithm for detecting local protein structural similarity, and it holds several advantages in predicting enzyme active sites. The CMASA can be used in large-scale enzyme active site annotation. The CMASA can be available by the mail-based server (http://159.226.149.45/other1/CMASA/CMASA.htm webcite).With the development of both the genome project and the structural genomics, large of unknown functional protein structures were deposited in PDB, these protein functions need to be annotated. In addition, because of the fast development of bioinformatics, some known structure and function proteins may also need to be re-annotated. Thus, several methods of protein structural and functional prediction were developed, which can be classified as the sequence-based and the structure-based methods.Sequence-based methods, such as, BLAST/PSI-BLAST[1,2] or PROSITE[3], are based on the concept of "similar protein sequences with similar function". The performance of these methods critically depends on the sequence similarity between the query structure and annotated structure. Howeve

Abstract:
The primate α-/θ-defensin multigene family encodes versatile endogenous cationic and amphipathic peptides that have broad-spectrum antibacterial, antifungal and antiviral activity. Although previous studies have reported that α-/θ-defensin (DEFA/DEFT) genes are under birth-and-death evolution with frequent duplication and rapid evolution, the phylogenetic relationships of the primate DEFA/DEFT genes; the genetic bases for the existence of similar antimicrobial spectra among closely related species; and the evolutionary processes involved in the emergence of cyclic θ-defensins in Old World monkeys and their subsequent loss of function in humans, chimpanzees and gorillas require further investigation. In this study, the DEFA/DEFT gene repertoires from primate and treeshrew were collected, followed by detailed phylogenetic, sequence and structure, selection pressure and comparative genomics analyses. All treeshrew, prosimian and simian DEFA/DEFT genes are grouped into two major clades, which are tissue-specific for enteric and myeloid defensins in simians. The simian enteric and myeloid α-defensins are classified into six functional gene clusters with diverged sequences, variable structures, altered functional constraints and different selection pressures, which likely reflect the antimicrobial spectra among closely related species. Species-specific duplication or pseudogenization within each simian cluster implies that the antimicrobial spectrum is ever-shifting, most likely challenged by the ever-changing pathogen environment. The DEFT evolved from the myeloid DEFA8. The prosegment of θ-defensin is detected with adaptive changes coevolving with the new protein fold of mature peptide, coincident with the importance of the prosegment for the correct folding of the mature peptide. Lastly, a less-is-hitchhiking hypothesis was proposed as a possible explanation for the expansion of pseudogene DEFTP and the loss of functional DEFT, where the gain or loss of the hitchhiker is determined by its adjacent driver gene during the birth-and-death evolutionary process.

Abstract:
In this work, we constrain the spectral index $n_t$ of the primordial gravitational wave power spectrum in a universe with sterile neutrinos by using the Planck temperature data, the WMAP 9-year polarization data, the baryon acoustic oscillation data, and the BICEP2 data. We call this model the $\Lambda$CDM+$r$+$\nu_s$+$n_t$ model. The additional massive sterile neutrino species can significantly relieve the tension between the Planck and BICEP2 data, and thus can reduce the possible effects of this tension on the fit results of $n_t$. To constrain the parameters of sterile neutrino, we also utilize the Hubble constant direct measurement data, the Planck Sunyaev-Zeldovich cluster counts data, the Planck CMB lensing data, and the cosmic shear data. We find that due to the fact that the BICEP2 data are most sensitive to the multipole $\ell\sim150$ corresponding to $k\sim0.01$ Mpc$^{-1}$, there exists a strong anticorrelation between $n_t$ and $r_{0.002}$ in the BICEP2 data, and this further results in a strongly blue-tilt spectrum. However, a slightly red-tilt tensor power spectrum is also allowed by the BICEP2 data in the region with larger value of $r_{0.002}$. By using the full data sets, we obtain $m_{\nu,{\rm{sterile}}}^{\rm{eff}}=0.48^{+0.11}_{-0.13}$ eV, $N_{\rm{eff}}=3.73^{+0.34}_{-0.37}$, and $n_t=0.96^{+0.48}_{-0.63}$ for the $\Lambda$CDM+$r$+$\nu_s$+$n_t$ model.

Abstract:
We show that involving a sterile neutrino species in the $\Lambda$CDM+$r$ model can help relieve the tension about the tensor-to-scalar ratio $r$ between the Planck temperature data and the BICEP2 B-mode polarization data. Such a model is called the $\Lambda$CDM+$r$+$\nu_s$ model in this paper. Compared to the $\Lambda$CDM+$r$ model, there are two extra parameters, $N_{\rm eff}$ and $m_{\nu,{\rm sterile}}^{\rm eff}$, in the $\Lambda$CDM+$r$+$\nu_s$ model. We show that in this model the tension between Planck and BICEP2 can be greatly relieved at the cost of the increase of $n_s$. However, comparing with the $\Lambda$CDM+$r$+$dn_s/d\ln k$ model that can significantly reduce the tension between Planck and BICEP2 but also makes trouble to inflation due to the large running of the spectral index of order $10^{-2}$ produced, the $\Lambda$CDM+$r$+$\nu_s$ model is much better for inflation. By including a sterile neutrino species in the standard cosmology, besides the tension with BICEP2, the other tensions of Planck with other astrophysical data, such as the $H_0$ direct measurement, the Sunyaev-Zeldovich cluster counts, and the galaxy shear data, can all be significantly relieved. So, this model seems to be an economical choice. Combining the Planck temperature data, the WMAP-9 polarization data, and the baryon acoustic oscillation data with all these astrophysical data (including BICEP2), we find that in the $\Lambda$CDM+$r$+$\nu_s$ model $n_s=0.999\pm 0.011$, $r=0.21^{+0.04}_{-0.05}$, $N_{\rm eff}=3.95\pm 0.33$ and $m_{\nu,{\rm sterile}}^{\rm eff}=0.51^{+0.12}_{-0.13}$ eV. Thus, our results prefer $\Delta N_{\rm eff}>0$ at the 2.7$\sigma$ level and a nonzero mass of sterile neutrino at the 3.9$\sigma$ level.

Abstract:
We perform a global fit study on the new agegraphic dark energy (NADE) model in a non-flat universe by using the MCMC method with the full CMB power spectra data from the WMAP 7-yr observations, the SNIa data from Union2.1 sample, BAO data from SDSS DR7 and WiggleZ Dark Energy Survey, and the latest measurements of $H_0$ from HST. We find that the value of $\Omega_{k0}$ is greater than 0 at least at the 3$\sigma$ confidence levels (CLs), which implies that the NADE model distinctly favors an open universe. Besides, our results show that the value of the key parameter of NADE model, $n=2.673^{+0.053+0.127+0.199}_{-0.077-0.151-0.222}$, at the 1--3$\sigma$ CLs, where its best-fit value is significantly smaller than those obtained in previous works. We find that the reason leading to such a change comes from the different SNIa samples used. Our further test indicates that there is a distinct tension between the Union2 sample of SNIa and other observations, and the tension will be relieved once the Union2 sample is replaced by the Union2.1 sample. So, the new constraint result of the NADE model obtained in this work is more reasonable than before.

Abstract:
In this paper, a new version of the interacting model of new agegraphic dark energy (INADE) is proposed and analyzed in detail. The interaction between dark energy and dark matter is reconsidered. The interaction term $Q=bH_0\rho_{\rm de}^\alpha\rho_{\rm dm}^{1-\alpha}$ is adopted, which abandons the Hubble expansion rate $H$ and involves both $\rho_{\rm de}$ and $\rho_{\rm dm}$. Moreover, the new initial condition for the agegraphic dark energy is used, which solves the problem of accommodating baryon matter and radiation in the model. The solution of the model can be given using an iterative algorithm. A concrete example for the calculation of the model is given. Furthermore, the model is constrained by using the combined Planck data (Planck+BAO+SNIa+$H_0$) and the combined WMAP-9 data (WMAP+BAO+SNIa+$H_0$). Three typical cases are considered: (A) $Q=bH_0\rho_{\rm de}$, (B) $Q=bH_0\sqrt{\rho_{\rm de}\rho_{\rm dm}}$, and (C) $Q=bH_0\rho_{\rm dm}$, which correspond to $\alpha=1$, 1/2, and 0, respectively. The departures of the models from the $\Lambda$CDM model are measured by the $\Delta$BIC and $\Delta$AIC values. It is shown that the INADE model is better than the NADE model in the fit, and the INADE(A) model is the best in fitting data among the three cases.

Abstract:
The initial condition $\Omega_{\rm de}(z_{\rm ini})=n^2(1+z_{\rm ini})^{-2}/4$ at $z_{\rm ini}=2000$ widely used to solve the differential equation of the density of the new agegraphic dark energy (NADE) $\Omega_{\rm de}$, makes the NADE model be a single-parameter dark-energy cosmological model. However, we find that this initial condition is only applicable in a flat universe with only dark energy and pressureless matter. In fact, in order to obtain more information from current observational data, such as cosmic microwave background (CMB) and baryon acoustic oscillations (BAO), we need to consider the contribution of radiation. For this situation, the initial condition mentioned above becomes invalid. To overcome this shortage, we investigate the evolution of dark energy in the matter-dominated and radiation-dominated epochs, and obtain a new initial condition $\Omega_{\rm de}(z_{\rm ini})=\frac{n^2(1+z_{\rm ini})^{-2}}{4}(1+\sqrt{F(z_{\rm ini})})^2$ at $z_{\rm ini}=2000$, where $F(z)\equiv\frac{\Omega_{r0}(1+z)}{\Omega_{m0}+\Omega_{r0}(1+z)}$ with $\Omega_{r0}$ and $\Omega_{m0}$ being the current density parameters of radiation and pressureless matter, respectively. This revised initial condition is applicable for the differential equation of $\Omega_{\rm de}$ obtained in the standard Friedmann-Robertson-Walker (FRW) universe with dark energy, pressureless matter, radiation, and even spatial curvature, and can still keep the NADE model being a single-parameter model. With the revised initial condition and the observational data of type Ia supernova (SNIa), CMB and BAO, we finally constrain the NADE model. The results show that the single free parameter $n$ of the NADE model can be constrained tightly.

Abstract:
Consistency tests for the general relativity (GR) can be performed by constraining the growth index $\gamma$ using the measurements of redshift-space distortions (RSD) in conjunction with other observations. In previous studies, deviations from the GR expected value of $\gamma\approx 0.55$ at the 2--3$\sigma$ level were found. In this work, we reconsider the measurement of $\gamma$ in a universe with sterile neutrinos. We constrain the sterile neutrino cosmological model using the RSD measurements combined with the cosmic microwave background data (Planck temperature data plus WMAP 9-yr polarization data), the baryon acoustic oscillation data, the Hubble constant direct measurement, the Planck Sunyaev-Zeldovich cluster counts data, and the galaxy shear data. We obtain the constraint result of the growth index, $\gamma=0.584^{+0.047}_{-0.048}$, well consistent with the GR expected value (the consistency is at the 0.6$\sigma$ level). For the parameters of sterile neutrino, we obtain $N_{\rm{eff}}=3.62^{+0.26}_{-0.42}$ and $m_{\nu,{\rm{sterile}}}^{\rm{eff}}=0.48^{+0.11}_{-0.14}$ eV. We also consider the BICEP2 data and perform an analysis on the model with tensor modes. Similar fit results are obtained, showing that once light sterile neutrino is considered in the universe, GR will become well consistent with the current observations.

Abstract:
Dark energy might directly interact with cold dark matter. However, in such a scenario, an early-time large-scale instability occurs occasionally, which may be due to the incorrect treatment for the pressure perturbation of dark energy as a nonadiabatic fluid. To avoid this nonphysical instability, we establish a new framework to correctly calculate the cosmological perturbations in the interacting dark energy models. Inspired by the well-known parametrized post-Friedmann approach, the condition of the dark energy pressure perturbation is replaced with the relationship between the momentum density of dark energy and that of other components on large scales. By reconciling the perturbation evolutions on the large and small scales, one can complete the perturbation equations system. The large-scale instability can be successfully avoided and the well-behaved density and metric perturbations are obtained within this framework. Our test results show that this new framework works very well and is applicable to all the interacting dark energy models.