Impact of nonignorable coarsening on Bayesian inference

The coarse data model of Heitjan and Rubin (1991) generalizes the missing data model of Rubin (1976) to cover other forms of incompleteness such as censoring and grouping. The model has 2 components: an ideal data model describing the distribution of the quantity of interest and a coarsening mechanism that describes a distribution over degrees of coarsening given the ideal data. The coarsening mechanism is said to be nonignorable when the degree of coarsening depends on an incompletely observed ideal outcome, in which case failure to properly account for it can spoil inferences. A theme in recent research is to measure sensitivity to nonignorability by evaluating the effect of a small departure from ignorability on the maximum likelihood estimate (MLE) of a parameter of the ideal data model. One such construct is the "index of local sensitivity to nonignorability" (ISNI) (Troxel and others, 2004), which is the derivative of the MLE with respect to a nonignorability parameter evaluated at the ignorable model. In this paper, we adapt ISNI to Bayesian modeling by instead defining it as the derivative of the posterior expectation. We propose the application of ISNI as a first step in judging the robustness of a Bayesian analysis to nonignorable coarsening. We derive formulas for a range of models and apply the method to evaluate sensitivity to nonignorable coarsening in 2 real data examples, one involving missing CD4 counts in an HIV trial and the other involving potentially informatively censored relapse times in a leukemia trial.     

Smoothing spline ANOVA frailty model for recurrent event data

Gap time hazard estimation is of particular interest in recurrent event data. This article proposes a fully nonparametric approach for estimating the gap time hazard. Smoothing spline analysis of variance (ANOVA) decompositions are used to model the log gap time hazard as a joint function of gap time and covariates, and general frailty is introduced to account for between-subject heterogeneity and within-subject correlation. We estimate the nonparametric gap time hazard function and parameters in the frailty distribution using a combination of the Newton-Raphson procedure, the stochastic approximation algorithm (SAA), and the Markov chain Monte Carlo (MCMC) method. The convergence of the algorithm is guaranteed by decreasing the step size of parameter update and/or increasing the MCMC sample size along iterations. Model selection procedure is also developed to identify negligible components in a functional ANOVA decomposition of the log gap time hazard. We evaluate the proposed methods with simulation studies and illustrate its use through the analysis of bladder tumor data.     

Statistical considerations for in vitro research: II — Data to presentation

Summary The paper is the second of two papers about statistical considerations that researchers should make while doing in vitro plant biology research. The first paper focused on aspects from developing a plan to do research through the collection of data. This paper continues with information about editing data, handling outliers, analyzing quantitative and qualitative data, comparing treatment means, preparing graphs and tables, and presenting results.     

生态环境移动数据采集系统研究与实现

针对快速、实时、有效采集并录入生态环境野外调查大样本量、多源数据的需求,充分应用移动GIS技术、移动智能终端、3G等现代信息技术优势,提出了基于ArcGIS for Mobile的移动数据采集方案,研究解决了包括系统运行机制、数据访问模式、移动数据库技术等面向全国生态环境野外调查的移动GIS关键技术,设计并研发野外调查移动数据采集系统。该系统采用C#和Java语言,以SQL Server 2008 为服务器端的数据库环境,在Microsoft Visual Studio 2008集成开发环境上实现设计开发,并在全国生态环境10年变化遥感调查与评估项目土地覆盖类型地面核查、生态系统参数野外观测等工作中予以应用。实践检验表明：该系统实现了野外调查数据的数字采集、智能校验、实时上传与有效管理,简化了填报程序,规范了填报内容,提高了工作效率,能够为生态环境相关的调查数据采集提供信息化支持。     

长白山站的研究数据库管理系统

长白山站的研究数据库管理系统翟永华,赵士洞（中国科学院沈阳应用生态研究所１１００１５）Ｄａｔｅ－ＢａｓｅＭａｎａｇｅｍｅｎｔＳｙｓｔｅｍｉｎＣｈａｎｇｂａｉｓｈａｎＦｏｒｅｓｔＥｃｏｓｙｓｔｅｍＲｅｓｅａｒｃｈＳｔａｔｉｏｎ．￥ＺｈａｉＹｏｎｇｈｕａ...     

用笛卡儿座标对菲氏叶猴和黑叶猴颅骨的比较形态研究

本文利用三维笛卡儿空间座标对菲氏叶猴(Presbytis phayrei)和黑叶猴(P.francoisi)颅骨的形态结构作了比较研究,描绘了它们的侧视和俯视投影图形。结果表明,两种投影图形均显示黑叶猴的颅骨大于菲氏叶猴,且显著性增大的区域出现在眉点、囟门、枕骨大孔附近和下颌骨体的高度。但菲氏叶猴较黑叶猴具有更凸的面颅。据枕骨隆突至眉点的侧视投影弧长,两种叶猴的数学模式均为:Y=a+bX-cX~2(R=0.92)。从侧视投影看,两种叶猴自枕骨隆突至眉点主要表出大小的不同。若据俯视投影图,两种颅骨的差异主要出现在外耳道以前的部分。黑叶猴较菲氏叶猴具有十分显著性增高的下颌骨体以及相对应更发达的咬肌和咀嚼器官,这很可能与它取食更多的果类食物有关。     

中国生物多样性在线数据处理平台的构建

高质量的生物多样性数据能够为生物多样性的研究与保护提供数据支撑。目前研究人员开发了大量的生物多样性数据处理软件或工具, 包括工作流系统、R语言包、Python语言包和Excel工具等, 但是使用这些软件或工具需要用户安装相应的软件客户端, 并掌握一定的编程语言、软件开发和复杂的Excel公式等知识和技能。为降低用户的学习成本和使用门槛, 本文采用了Browser/Server模式设计技术、Web技术、可视化技术、响应式开发技术、网络爬虫技术、数据处理技术和Solr智能检索技术等, 针对不同维度的生物多样性数据设计和开发了相应的数据处理模块, 构建了中国生物多样性在线数据处理平台(http://dp.iflora.cn/)。该平台能够有效地帮助科研人员对物种名称、地理位置、时间日期和经纬度等数据进行处理, 并提供数据格式转换、数据质量评测和资源统计分析等辅助功能, 帮助科研人员实现零代码和低门槛地处理生物多样性数据, 提供便捷、高效和简单的数据清洗、校正、转换和整合等数据处理渠道, 为生物多样性研究和保护提供信息化技术支持与服务。     

Electrotonic and action potentials in the Venus flytrap

The electrical phenomena and morphing structures in the Venus flytrap have attracted researchers since the nineteenth century. We have observed that mechanical stimulation of trigger hairs on the lobes of the Venus flytrap induces electrotonic potentials in the lower leaf. Electrostimulation of electrical circuits in the Venus flytrap can induce electrotonic potentials propagating along the upper and lower leaves. The instantaneous increase or decrease in voltage of stimulating potential generates a nonlinear electrical response in plant tissues. Any electrostimulation that is not instantaneous, such as sinusoidal or triangular functions, results in linear responses in the form of small electrotonic potentials. The amplitude and sign of electrotonic potentials depend on the polarity and the amplitude of the applied voltage. Electrical stimulation of the lower leaf induces electrical signals, which resemble action potentials, in the trap between the lobes and the midrib. The trap closes if the stimulating voltage is above the threshold level of 4.4 V. Electrical responses in the Venus flytrap were analyzed and reproduced in the discrete electrical circuit. The information gained from this study can be used to elucidate the coupling of intracellular and intercellular communications in the form of electrical signals within plants.     

Phylogenetics and comparative analysis of the mitochondrial genomes of three violet‐ringed octopuses

Similar morphological characters and little molecular data of Amphioctopus rex, A. neglectus and A. cf. ovulum resulted in their unknown phylogenetic statuses and equivocal relationships. In this study, the complete mitochondrial genomes of these three species collected in Chinese waters were sequenced and compared with each other to clarify the relationships among them. The lengths of the mitochondrial genomes varied from 15,646 bp to 15,814 bp, and the A + T content and GC skew for protein‐coding genes showed little variation. In contrast, both a dendrogram based on codon usage and the gene arrangements of the three octopuses showed that A. rex was more closely related to A. neglectus than to A. cf. ovulum. Five data sets and two methods (maximum likelihood and Bayesian inference) were utilized for the first time to explore the phylogenetic relationships among these three species in Octopodidae. The results indicated that a data set combining protein‐coding genes and RNA genes (PR) was optimal for analysing the relationships among 43 cephalopods. All of the phylogenetic trees divided the cephalopods into 10 taxa and supported the monophyly of Oegopsida, Myopsida, Sepiidae and Octopodidae. In this study, Idiosepiidae was classified as sister to Sepiolidae. Trees constructed using all data sets robustly supported the monophyly of the genus Amphioctopus. Notably, A. rex was more closely related to A. neglectus than to A. cf. ovulum, although these three species share the characteristic of violet rings on dark ocelli.