Comprehensive Characterization of the Transmitted/Founder env Genes From a Single MSM Cohort in China

Background: The men having sex with men (MSM) population has become one of the major risk groups for HIV-1 infection in China. However, the epidemiological patterns, function of the env genes, and autologous and heterologous neutralization activity in the same MSM population have not been systematically characterized. Methods: The env gene sequences were obtained by the single genome amplification. The time to the most recent common ancestor was estimated for each genotype using the Bayesian Markov Chain Monte Carlo approach. Coreceptor usage was determined in NP-2 cells. Neutralization was analyzed using Env pseudoviruses in TZM-bl cells. Results: We have obtained 547 full-length env gene sequences by single genome amplification from 30 acute/early HIV-1–infected individuals in the Beijing MSM cohort. Three genotypes (subtype B, CRF01_AE, and CRF07_BC) were identified and 20% of the individuals were infected with multiple transmitted/founder (T/F) viruses. The tight clusters of the MSM sequences regardless of geographic origins indicated nearly exclusive transmission within the MSM population and limited number of introductions. The time to the most recent common ancestor for each genotype was 10–15 years after each was first introduced in China. Disparate preferences for coreceptor usages among 3 genotypes might lead to the changes in percentage of different genotypes in the MSM population over time. The genotype-matched and genotype-mismatched neutralization activity varied among the 3 genotypes. Conclusions: The identification of unique characteristics for transmission, coreceptor usage, neutralization profile, and epidemic patterns of HIV-1 is critical for the better understanding of transmission mechanisms, development of preventive strategies, and evaluation of vaccine efficacy in the MSM population in China

A novel configuration model for random graphs with given degree sequence

Recently, random graphs in which vertices are characterized by hidden variables controlling the establishment of edges between pairs of vertices have attracted much attention. Here, we present a specific realization of a class of random network models in which the connection probability between two vertices (i,j) is a specific function of degrees ki and kj. In the framework of the configuration model of random graphs, we find analytical expressions for the degree correlation and clustering as a function of the variance of the desired degree distribution. The expressions obtained are checked by means of numerical simulations. Possible applications of our model are discussed.Comment: 7 pages, 3 figure

Elucidating the Limit of Li Insertion into the Spinel Li4Ti5O12

In this work, we show that the well-known lithium-ion anode material, Li4Ti5O12, exhibits exceptionally high initial capacity of 310 mAh g-1 when it is discharged to 0.01 V. It maintains a reversible capacity of 230 mAh g-1, far exceeding the "theoretical" capacity of 175 mAh g-1 when this anode is lithiated to the composition Li7Ti5O12. Neutron diffraction analyses identify that additional Li reversibly enters into the Li7Ti5O12 to form Li8Ti5O12. density functional theory (DFT) calculations reveal the average potentials of the Li4Ti5O12 to Li7Ti5O12 step and the Li7Ti5O12 to Li8Ti5O12 step are 1.57 and 0.19 V, respectively, which are in excellent agreement with experimental results. Transmission electron microscopy (TEM) studies confirm that the irreversible capacity of Li4Ti5O12 during its first cycle originates from the formation of a solid electrolyte interface (SEI) layer. This work clarifies the fundamental lithiation mechanism of the Li4Ti5O12, when lithiated to 0.01 V vs Li

Statefinder diagnosis in a non-flat universe and the holographic model of dark energy

In this paper, we study the holographic dark energy model in non-flat universe from the statefinder viewpoint. We plot the evolutionary trajectories of the holographic dark energy model for different values of the parameter $c$ as well as for different contributions of spatial curvature, in the statefinder parameter-planes. The statefinder diagrams characterize the properties of the holographic dark energy and show the discrimination between this scenario and other dark energy models. As we show, the contributions of the spatial curvature in the model can be diagnosed out explicitly by the statefinder diagrams. Furthermore, we also investigate the holographic dark energy model in the $w-w'$ plane, which can provide us with a useful dynamical diagnosis complement to the statefinder geometrical diagnosis.Comment: 16 pages, 4 figures; final versio

On Gauge Theory and Topological String in Nekrasov-Shatashvili Limit

We study the Nekrasov-Shatashvili limit of the N=2 supersymmetric gauge theory and topological string theory on certain local toric Calabi-Yau manifolds. In this limit one of the two deformation parameters \epsilon_{1,2} of the Omega background is set to zero and we study the perturbative expansion of the topological amplitudes around the remaining parameter. We derive differential equations from Seiberg-Witten curves and mirror geometries, which determine the higher genus topological amplitudes up to a constant. We show that the higher genus formulae previously obtained from holomorphic anomaly equations and boundary conditions satisfy these differential equations. We also provide a derivation of the holomorphic anomaly equations in the Nekrasov-Shatashvili limit from these differential equations.Comment: 41 pages, no figure. v2: references adde

Jet Quenching in the Opposite Direction of a Tagged Photon in High-Energy Heavy-Ion Collisions

We point out that events associated with large $E_T$ direct photons in high-energy heavy-ion collisions can be used to study jet energy loss in dense matter. In such events, the $p_T$ spectrum of charged hadrons from jet fragmentation in the opposite direction of the tagged photon is estimated to be well above the background which can be reliably subtracted at moderately large $p_T$. We demonstrate that comparison between the extracted fragmentation function in $AA$ and $pp$ collisions can be used to determine the jet energy loss and the interaction mean-free-path in the dense matter produced in high-energy heavy-ion collisions.Comment: 4 pages in RevTex twocolumn with embedded psfigure

Statefinder diagnostic for holographic dark energy model

In this paper we study the holographic dark energy model proposed by Li from the statefinder viewpoint. We plot the evolutionary trajectories of the model with $c=1$ in the statefinder parameter-planes. The statefinder diagrams characterize the properties of the holographic dark energy and show the discrimination between this scenario and other dark energy models. We also perform a statefinder diagnostic to the holographic dark energy model in cases of different $c$ which given by three fits to observational data. The result indicates that from the statefinder viewpoint $c$ plays a significant role in this model and should thus be determined seriously by future high precision experiments.Comment: 13 pages, 3 figure

Inflationary universe in loop quantum cosmology

Loop quantum cosmology provides a nice solution of avoiding the big bang singularity through a big bounce mechanism in the high energy region. In loop quantum cosmology an inflationary universe is emergent after the big bounce, no matter what matter component is filled in the universe. A super-inflation phase without phantom matter will appear in a certain way in the initial stage after the bounce; then the universe will undergo a normal inflation stage. We discuss the condition of inflation in detail in this framework. Also, for slow-roll inflation, we expect the imprint from the effects of the loop quantum cosmology should be left in the primordial perturbation power spectrum. However, we show that this imprint is too weak to be observed.Comment: 21 pages, 4 figures; accepted for publication in JCA