Genesis of a highly pathogenic and potentially pandemic H5N1 influenza virus in eastern Asia

A highly pathogenic avian influenza virus, H5N1, caused disease outbreaks in poultry in China and seven other east Asian countries between late 2003 and early 2004; the same virus was fatal to humans in Thailand and Vietnam. Here we demonstrate a series of genetic reassortment events traceable to the precursor of the H5N1 viruses that caused the initial human outbreak in Hong Kong in 1997 (refs 2-4) and subsequent avian outbreaks in 2001 and 2002 (refs 5, 6). These events gave rise to a dominant H5N1 genotype (Z) in chickens and ducks that was responsible for the regional outbreak in 2003-04. Our findings indicate that domestic ducks in southern China had a central role in the generation and maintenance of this virus, and that wild birds may have contributed to the increasingly wide spread of the virus in Asia. Our results suggest that H5N1 viruses with pandemic potential have become endemic in the region and are not easily eradicable. These developments pose a threat to public and veterinary health in the region and potentially the world, and suggest that long-term control measures are required.     

A Robust Test for Threshold‐Type Nonlinearity in Multivariate Time Series Analysis

There is growing interest in exploring potential forecast gains from the nonlinear structure of multivariate threshold autoregressive (MTAR) models. A least squares‐based statistical test has been proposed in the literature. However, previous studies on univariate time series analysis show that classical nonlinearity tests are often not robust to additive outliers. The outlier problem is expected to pose similar difficulties for multivariate nonlinearity tests. In this paper, we propose a new and robust MTAR‐type nonlinearity test, and derive the asymptotic null distribution of the test statistic. A Monte Carlo experiment is carried out to compare the power of the proposed test with that of the least squares‐based test under the influence of additive time series outliers. The results indicate that the proposed method is preferable to the classical test when observations are contaminated by outliers. Finally, we provide illustrative examples by applying the statistical tests to two real datasets. Copyright © 2015 John Wiley & Sons, Ltd.     

一种曲面网格优化的通用算法

提出了一种曲面网格优化的通用算法,该算法基于一些预先定义的优化准则,将给定的网格曲面优化成为单位网格曲面,定义了两种指导优化过程的优化标准。在优化过程中采用了三种优化算子（边分裂、边消除、边替换）,是一个简单的曲面网格优化的通用算法。     

Carbon isotope composition of low molecular weight hydrocarbons and monocarboxylic acids from Murchison meteorite

The origin of the organic matter in carbonaceous meteorites remains controversial despite extensive study over the past 20 yr. Motivated by the expectation that the patterns of isotopic variation with molecular structure among the organic compounds would contain important clues to their origin, we have measured the carbon isotopic compositions for individual hydrocarbons and monocarboxylic acids from Murchison meteorite, a C2 carbonaceous chondrite which fell in Australia in 1969. With few exceptions, notably benzene, the volatile products are substantially isotopically heavier than their terrestrial counterparts, signifying their extraterrestrial origin. For both classes of compounds, the ratio of 13C to 12C decreases with increasing carbon number in a roughly parallel manner, and each carboxylic acid exhibits a higher isotopic ratio than the hydrocarbon containing the same number of carbon atoms. These trends are consistent with the kinetically controlled synthesis of higher homologues from lower ones. The results suggest the possibility that the production mechanisms for hydrocarbons and carboxylic acids may be similar; they also impose constraints on the identity of the reactant species.     

Exome sequencing identifies frequent mutation of ARID1A in molecular subtypes of gastric cancer

Gastric cancer is a heterogeneous disease with multiple environmental etiologies and alternative pathways of carcinogenesis. Beyond mutations in TP53, alterations in other genes or pathways account for only small subsets of the disease. We performed exome sequencing of 22 gastric cancer samples and identified previously unreported mutated genes and pathway alterations; in particular, we found genes involved in chromatin modification to be commonly mutated. A downstream validation study confirmed frequent inactivating mutations or protein deficiency of ARID1A, which encodes a member of the SWI-SNF chromatin remodeling family, in 83% of gastric cancers with microsatellite instability (MSI), 73% of those with Epstein-Barr virus (EBV) infection and 11% of those that were not infected with EBV and microsatellite stable (MSS). The mutation spectrum for ARID1A differs between molecular subtypes of gastric cancer, and mutation prevalence is negatively associated with mutations in TP53. Clinically, ARID1A alterations were associated with better prognosis in a stage-independent manner. These results reveal the genomic landscape, and highlight the importance of chromatin remodeling, in the molecular taxonomy of gastric cancer.     

De novo mutations in the actin genes ACTB and ACTG1 cause Baraitser-Winter syndrome

Brain malformations are individually rare but collectively common causes of developmental disabilities. Many forms of malformation occur sporadically and are associated with reduced reproductive fitness, pointing to a causative role for de novo mutations. Here, we report a study of Baraitser-Winter syndrome, a well-defined disorder characterized by distinct craniofacial features, ocular colobomata and neuronal migration defect. Using whole-exome sequencing of three proband-parent trios, we identified de novo missense changes in the cytoplasmic actin-encoding genes ACTB and ACTG1 in one and two probands, respectively. Sequencing of both genes in 15 additional affected individuals identified disease-causing mutations in all probands, including two recurrent de novo alterations (ACTB, encoding p.Arg196His, and ACTG1, encoding p.Ser155Phe). Our results confirm that trio-based exome sequencing is a powerful approach to discover genes causing sporadic developmental disorders, emphasize the overlapping roles of cytoplasmic actin proteins in development and suggest that Baraitser-Winter syndrome is the predominant phenotype associated with mutation of these two genes.