Accurate Reconstruction of Molecular Phylogenies for Proteins Using Codon and Amino Acid Unified Sequence Alignments (CAUSA)

Based on molecular clock hypothesis, and neutral theory of molecular evolution, molecular phylogenies have been widely used for inferring evolutionary history of organisms and individual genes. Traditionally, alignments and phylogeny trees of proteins and their coding DNA sequences are constructed separately, thus often different conclusions were drawn. Here we present a new strategy for sequence alignment and phylogenetic tree reconstruction, codon and amino acid unified sequence alignment (CAUSA), which aligns DNA and protein sequences and draw phylogenetic trees in a unified manner. We demonstrated that CAUSA improves both the accuracy of multiple sequence alignments and phylogenetic trees by solving a variety of molecular evolutionary problems in virus, bacteria and mammals. Our results support the hypothesis that the molecular clock for proteins has two pointers existing separately in DNA and protein sequences. It is more accurate to read the molecular clock by combination (additive) of these two pointers, since the ticking rates of them are sometimes consistent, sometimes different. CAUSA software were released as Open Source under GNU/GPL license, and are downloadable free of charge from the website www.dnapluspro.com

High prevalence of a globally disseminated hypervirulent clone, Staphylococcus aureus CC121, with reduced vancomycin susceptibility in community settings in China

Objectives: Most vancomycin-intermediate Staphylococcus aureus (VISA) and heterogeneous VISA (hVISA) are derived from hospital-associated MRSA due to treatment failure; however, the prevalence of hVISA/VISA in community settings remains unclear. Methods: Four hundred and seventy-six community-associated isolates were collected between 2010 and 2011 during national surveillance for antimicrobial resistance in 31 county hospitals across China. Drug susceptibility evaluation and mecA detection were performed by using broth microdilution and PCR analysis, respectively. hVISA/VISA were identified by using macro-Etest and a modified population analysis profile (PAP)-AUC method. The genetic features of all hVISA/VISA isolates were genotyped. Results: Among 476 isolates, MRSA and MSSA accounted for 19.7% (n = 94) and 80.3% (n = 382), respectively. Two VISA and 36 hVISA isolates were identified by PAP-AUC testing. The VISA isolates and 29 of the hVISA isolates were MRSA. The proportion of hVISA/VISA was significantly higher in MRSA (30.9%) than in MSSA (1.8%). The hVISA/VISA isolates were assigned to 18 STs classified into seven clonal complexes (CCs). CC121 (n = 12) followed by ST239 (n = 11) was the most prevalent hVISA/VISA clone. All ST239-hVISA/VISA were MRSA, while 12 CC121-hVISA isolates included 6 MSSA and 6 MRSA isolates. SCCmec III was predominant among MRSA-hVISA/VISA isolates. agr I and agr IV were detected in ST239 and CC121, respectively. All except two strains were positive for Panton-Valentine leucocidin genes. Conclusions: To the best of our knowledge, this is the first report of CC121 as a prevalent hVISA clone in community settings, highlighting the necessity of surveillance and stricter infection control measures for this globally disseminated lineage

The spatial variability of streambed vertical hydraulic conductivity in an intermittent river, northwestern China

Abstract Streambed vertical hydraulic conductivity (K) plays an important role in river water and groundwater interaction. The K at the ten transects (Ts1-Ts10) at the Donghe River (an intermittent river) in the Ejina Basin, northwestern China, was measured to investigate its spatial variation. Based on the sediment characteristics and vertical hydraulic conductivity of the riverbed, the entire riverbed of the Donghe River could be divided arbitrarily into two parts: an upper part (starting at Ts1 and ending at Ts9, without an obvious and continuous clogging layer) and a lower part (the remaining riverbed, with an obvious and continuous clogging layer). In the upper part, although the K varied with depth within the 0-30 cm layer, the variability with depth could be ignored in practice. The arithmetic mean K of the upper part ranged from 12 to 27.6 m/ day, three orders of magnitude larger than that of the lower part (0.06 m/day). The change of K along the river cross section was significant, and larger values of K often occurred in the parts of the channels with greater water depth. However, there were no consistent patterns of the variability of K at transects across the river, which was influenced by the variation in streambed characteristics. The results could be useful for the estimation of groundwater recharge from river and groundwater resources evaluation in the Ejina Basin

Optimal input potential functions in the interacting particle system method

The assessment of the probability of a rare event with a naive Monte-Carlo method is computationally intensive, so faster estimation methods, such as variance reduction methods, are needed. We focus on one of these methods which is the interacting particle (IPS) system method. The method requires to specify a set of potential functions. The choice of these functions is crucial, because it determines the magnitude of the variance reduction. So far, little information was available on how to choose the potential functions. To remedy this, we provide the expression of the optimal potential functions minimizing the asymptotic variance of the estimator of the IPS method

Defect Study of MgO-CaO Material Doped with CeO 2

MgO-CaO refractories were prepared using analytical reagent chemicals of Ca(OH)2 and Mg(OH)2 as starting materials and CeO2 as dopant, then sintered at 1650°C for 3 h. The effect of CeO2 powders on the defect of MgO-CaO refractories was investigated. The sample characterizations were analyzed by the techniques of XRD and SEM. According to the results, with the addition of CeO2, the lattice constant of CaO increased, and the bulk density of the samples increased while apparent porosity decreased. The densification of MgO-CaO refractories was promoted obviously. In the sintering process, MgO grains grew faster than CaO, pores at the MgO-CaO grain boundaries decreased while pores in the MgO grains increased gradually, and no pores were observed in the CaO grains. The nature of the CeO2 promoting densification lies in the substitution and solution with CaO. Ce4+ approaches into CaO lattices, which enlarges the vacancy concentration of Ca2+ and accelerates the diffusion of Ca2+

Add-On Effect of Chinese Herbal Medicine Bath to Phototherapy for Psoriasis Vulgaris: A Systematic Review

Psoriasis vulgaris is the most common form of psoriasis. Phototherapy has been proven effective for psoriasis, but side effects have become a concern. Chinese herbal medicine (CHM) bath combined with phototherapy has been used in clinical settings, but the additional benefit requires evaluation. This review aims to evaluate the additional benefit and safety of adding CHM bath to phototherapy for psoriasis vulgaris. Cochrane library, PubMed, Embase, CNKI, and CQVIP were searched from their inceptions to 6 August 2012. Randomized controlled trials (RCTs) comparing CHM bath plus phototherapy to phototherapy alone for psoriasis vulgaris were included. Data was analyzed using Review Manager 5.1.0. Thirteen RCTs were included in the review, and eight were included in the meta-analysis. Meta-analysis showed higher efficacy of CHM bath plus phototherapy when compared with phototherapy alone in terms of PASI 60 (RR 1.25; 95% CI: 1.18–1.32). Mild adverse events were reported in ten studies, but these could be alleviated by reducing UV dosage or applying emollient. In conclusion, CHM bath appears to be a beneficial and safe adjunctive therapy to phototherapy for psoriasis vulgaris. However, these results should be interpreted with caution due to the low methodological quality of the included studies