缺失数据均值推断的经验似然方法

研究了缺失数据的均值推断问题.在随机缺失及半参数模型的假设下,设计了基于影响函数理论的经验似然推断方法,证明了所构造的对数经验似然比检验统计量具有非参数Wilks性质.此外,该经验似然方法可以利用辅助协变量中提供的附加信息来提高检验的功效.在近邻备择假设下,计算了检验统计量的功效,并且通过一些模拟考察了该方法在有限样本下的表现.     

因变量缺失下部分线性变系数变量含误差模型的估计

该文主要考虑部分线性变系数模型在自变量含有测量误差以及因变量存在缺失情形下的估计问题.基于Profile最小二乘技术,针对参数分量和非参数分量提出了多种估计方法.第一种估计方法只利用了完整观测数据,而第二种和第三种估计方法分别利用了插补技术和替代技术.参数分量的所有估计被证明是渐近正态的,非参数分量的所有估计被证明和一般非参数回归函数的估计具有相同的收敛速度.对于因变量的均值,构造了两类估计并证明了它们的渐近正态性.最后,通过数值模拟验证了所提方法.     

Principles for the organization of gene-sets

A gene-set, an important concept in microarray expression analysis and systems biology, is a collection of genes and/or their products (i.e. proteins) that have some features in common. There are many different ways to construct gene-sets, but a systematic organization of these ways is lacking. Gene-sets are mainly organized ad hoc in current public-domain databases, with group header names often determined by practical reasons (such as the types of technology in obtaining the gene-sets or a balanced number of gene-sets under a header). Here we aim at providing a gene-set organization principle according to the level at which genes are connected: homology, physical map proximity, chemical interaction, biological, and phenotypic-medical levels. We also distinguish two types of connections between genes: actual connection versus sharing of a label. Actual connections denote direct biological interactions, whereas shared label connection denotes shared membership in a group. Some extensions of the framework are also addressed such as overlapping of gene-sets, modules, and the incorporation of other non-protein-coding entities such as microRNAs.     

K2Sb(P2O7)F: Cairo Pentagonal Layer with Bifunctional Genes Reveal Optical Performance

Discovering new functional genes, designing perfect crystal structures, and developing high-performance materials are the goals being pursued by scientists. Herein, the first antimony pyrophosphate, K₂Sb(P₂O₇)F, possessing an optimal layered structure, is reported, where the perfect structural arrangement induces excellent optical properties. K₂Sb(P₂O₇)F not only displays a sharply enhanced birefringence (0.157@546 nm) compared to the existing phosphate optical materials, but also exhibits a strong second-harmonic generation response (4.0×KDP). Remarkably, a new bifunctional gene, the square-pyramidal SbO₄F group, was discovered, and a unique two-dimensional arrangement of Cairo pentagonal tiling units was observed in inorganic compounds for the first time.     

Interferon induced Mx protein from Indian snow trout Schizothorax richardsonii (Gray) lacks critical functional features unlike its mammalian homologues

Viral attack within host cells triggers the production of type I interferons and leads to the induction of interferon stimulated genes (ISGs). One of the ISG Mx, encodes type I interferon inducible GTPase that is responsible for the establishment of an anti-viral state within cells. Intriguingly, several isoforms of Mx have been reported in fish, but the structural analysis of fish Mx proteins remains unexplored. For the first time, we have identified and unraveled the molecular structure of Mx protein from Indian snow trout, Schizothorax richardsonii (Gray) a Coldwater fish that inhabits the water bodies in the sub-Himalayan region. The snow trout Mx coding region consists of 2518 nucleotides with an open reading frame (ORF) of 1854 nucleotides. It codes for a polypeptide of 617 amino acids with a predicted molecular weight of 70 kDa. In silico analysis of snow trout Mx protein revealed signature of dynamin family (LPRGTGIVTR) along with a tripartite GTP-binding domain (GDQSSGKS, DLPG, and TKPD). Homology modelling established that the Mx protein is an elongated structure with a G domain, bundle signaling element (BSE) and a GTPase effector domain (GED). Moreover, the GED of Mx contains two highly conserved leucine zippers at the COOH-terminal of the protein suggesting its structural similarity with human homologues. However, snow trout Mx lacks the essential features of its mammalian homologues questioning its functional characteristics. Further, a ligand binding site in the said protein has also been predicted adjacent to the GTPase switch within the G domain.     

人巨细胞病毒UL131A,UL130,UL128基因在先天感染患儿临床株中的变异

对18株临床低传代分离株和5株未传代的人巨细胞病毒（HCMV）临床标本分别进行HCMV UL131A，UL130，UL128基因全序列PCR扩增，并进行序列测定及分析．对23株HCMV临床株的UL131A，UL130，UL128基因编码区域进行比较，结果显示此3个基因核苷酸及其编码蛋白是高度保守的，3个基因的核苷酸同源性为96．2％，95．8％，96.0％，编码蛋白的同源性为97．2％，96．6％，96．9％．不同临床症状患儿的HCMV UL131A，UL130，UL128基因及其编码蛋白具有相似的结构．临床株HCMV UL130和UL128基因编码蛋白具有趋化因子的相似结构．所有结果表明临床株中的UL131A，UL130，UL128序列的保守性可能与HCMV在上皮细胞的增殖有关，也与HCMV转移到白细胞和树突状细胞相关．HCMV UL130和UL128基因编码蛋白具有趋化因子的相似结构可能与HCMV的感染相关．     

Dissolving capability difference based sequential extraction: A versatile tool for in-depth membrane proteome analysis

Profiling membrane proteins would facilitate revealing disease mechanism and discovering new drug targets as they play essential roles in cellular signaling, substrate transport, and cell adhesion. However, the analysis of membrane proteins still remains a challenge due to their high hydrophobicity, as well as the suppression effect of high abundant soluble proteins. In this work, to achieve a membrane proteome profiling, a sample preparation strategy based on sequential extraction at the protein level assisted by a range of extraction reagents with different dissolving capabilities, followed by nano-RPLC-ESI-MS/MS analysis was developed and applied for HeLa cell line analysis. It was found that with progressively harsher extraction reagents (i.e., 2 M NaCl, 4 M urea, 0.1 M Na₂CO₃, and 10% 1-dodecyl-3- methyl-imidazolium chloride (C12ImCl) performed, much more high hydrophobic proteins and low abundant proteins were identified. With our developed strategy, 5553 of the identified proteins (4419 gene products) were annotated to be membrane proteins and 2573 proteins (2183 gene products) have at least one transmembrane domain, to our best knowledge, which is the most comprehensive membrane proteome dataset for HeLa cell line. Notably, 110 of the identified membrane proteins were discovered in the “missing proteins” list referred to those in the neXtProt database. All above results indicated that our strategy has great potential to tackle the difficult but relevant task of identifying and profiling membrane proteins.     

Missing in total OH reactivity of VOCs from gasoline evaporation

Gasoline evaporation is an important anthropogenic source of atmospheric volatile organic compounds (VOCs). Total OH reactivity for gasoline vapor was measured from 4 kinds of gasoline for the first time by comparative reactivity method (CRM) using proton transfer reaction mass spectrometer (PTR-MS). Compositions of 56 PAMS (photochemical assessment monitoring station) nonmethane hydrocarbons (NMHCs) were measured for both liquid and headspace of gasoline. We found high abundance of alkenes and aromatics in gasoline. The calculated OH reactivity derived from quantified NMHCs speciation accounted for only 57±4% of total reactivity obtained from CRM method. N-Alkenes, only 6 wt% in liquid gasoline, contributed to 70% of calculated reactivity. We assume that the undetected branched alkenes are the possible reason for the missing reactivity. Wesuggest that the priority of gasoline quality improvement is to reduce alkenes content in gasoline in term of reactivity-based control.