Bayesian case influence diagnostics for survival models

We propose Bayesian case influence diagnostics for complex survival models. We develop case deletion influence diagnostics for both the joint and marginal posterior distributions based on the Kullback-Leibler divergence (K-L divergence). We present a simplified expression for computing the K-L divergence between the posterior with the full data and the posterior based on single case deletion, as well as investigate its relationships to the conditional predictive ordinate. All the computations for the proposed diagnostic measures can be easily done using Markov chain Monte Carlo samples from the full data posterior distribution. We consider the Cox model with a gamma process prior on the cumulative baseline hazard. We also present a theoretical relationship between our case-deletion diagnostics and diagnostics based on Cox's partial likelihood. A simulated data example and two real data examples are given to demonstrate the methodology.     

Estimation of breed contributions to present and future genetic diversity of 44 North Eurasian cattle breeds using core set diversity measures

Extinction of breeds threatens genetic diversity of livestock species. The need to conserve genetic diversity is widely accepted but involves in general two questions: (i) is the expected loss of diversity in a set of breeds within a defined future time horizon large enough to establish a conservation plan, and if so (ii) which breeds should be prioritised for such a conservation plan? The present study uses a marker assisted methodology to address these questions. The methodology combines core set diversity measures with a stochastic method for the estimation of expected future diversity and breed marginal diversities. The latter is defined as the change in the total diversity of all breeds caused by a one unit decrease in extinction probability of a particular breed. The stochastic method was validated by means of simulations. A large field data set consisting of 44 North Eurasian cattle breeds was analysed using simplified determined extinction probabilities. The results show that the expected loss of diversity in this set within the next 20 to 50 years is between 1 and 3% of the actual diversity, provided that the extinction probabilities which were used are approximately valid. If this loss is to be reduced, it is sufficient to include those three to five breeds with the highest marginal diversity in a conservation scheme.     

黑河中游干旱绿洲土壤盐渍化对大型土壤动物群落的影响

以内陆干旱区黑河中游绿洲边缘区天然沙质草地及其转变的人工梭梭灌木林（21 a）、人工杨树林（28 a）、人工樟子松林（33 a）和农田（开垦27 a和100 a）为研究对象,对6种样地土壤盐渍化和大型土壤动物群落特征进行调查,采用多变量排序、多元回归和通径分析及一元回归分析等方法,研究了不同土地覆被和管理措施下土壤动物群落组成及对土壤盐碱环境变化的响应.结果表明: 在缺乏管理措施的情况下,单纯改变土地覆被并不会显著影响土壤动物群落结构;而在有管理措施的情况下,土地覆被变化与管理措施耦合可显著改变土壤动物群落结构.土壤动物群落演变受到土壤pH、可溶性盐及Na⁺、Cl^-、HCO₃^-、Mg²⁺浓度的共同影响,其中Na⁺和可溶性盐含量的贡献率最大,是关键影响因子.土壤动物密度和类群丰富度与土壤中的Na⁺和可溶性盐含量呈显著负指数函数关系,与Mg²⁺和HCO₃^-含量呈显著二次曲线关系.研究区土壤动物密度和类群丰富度在Mg²⁺和HCO₃^-含量达到生态阈值点（分别为38.7～39.4 mg·kg^-1和324.9～335.3 mg·kg^-1）时达到峰值（40～43只·m^-2和13～14科·m^-2）.此后,随着Mg²⁺和HCO₃^-含量的增加, 土壤动物密度和类群丰富度下降.     

Selected codon usage bias in members of the class Mollicutes

Mollicutes are parasitic microorganisms mainly characterized by small cell sizes, reduced genomes and great A and T mutational bias. We analyzed the codon usage patterns of the completely sequenced genomes of bacteria that belong to this class. We found that for many organisms not only mutational bias but also selection has a major effect on codon usage. Through a comparative perspective and based on three widely used criteria we were able to classify Mollicutes according to the effect of selection on codon usage. We found conserved optimal codons in many species and study the tRNA gene pool in each genome. Previous results are reinforced by the fact that, when selection is operative, the putative optimal codons found match the respective cognate tRNA. Finally, we trace selection effect backwards to the common ancestor of the class and estimate the phylogenetic inertia associated with this character. We discuss the possible scenarios that explain the observed evolutionary patterns.     

Sedimentary nitrogen uptake and assimilation in the temperate zooxanthellate sea anemone Anthopleura aureoradiata

The sea anemone Anthopleura aureoradiata (Carlgren), which harbours symbiotic dinoflagellates (zooxanthellae), is abundant on mudflats and rocky shores around New Zealand. We measured the potential for particulate nitrogen uptake from sediment by A. aureoradiata and the subsequent consequences of this uptake on the nitrogen status of its zooxanthellae. Sediment was rinsed, labelled with (¹⁵NH₄)₂SO₄, and provided to anemones at low (0.23 g ml^− 1) and high (1.33 g ml^− 1) sediment loads for 6 h. Both anemone tissues and zooxanthellae became enriched with ¹⁵N. Enrichment of anemone tissues was similar at both high and low sediment loads, but the zooxanthellae became more enriched at the lower load. This was presumably because the uptake of ammonium, arising from host catabolism, by zooxanthellae is light driven and because the anemones at the lower load were able to extend their tentacles into the light while those at the higher load were not. The influence of sediment uptake on the nitrogen status of the zooxanthellae was determined by measuring the extent to which 20 μM NH₄⁺ enhanced the rate of zooxanthellar dark carbon fixation above that seen in filtered seawater (FSW) alone; the ammonium enhancement ratio (AER) was expressed as [dark NH₄⁺ rate/dark FSW rate], where ‘rate’ refers to C fixation and a ratio of 1.0 or less indicates nitrogen sufficiency. When anemones were starved with and without rinsed sediment in nitrogen-free artificial seawater for 8 weeks, zooxanthellar nitrogen deficiency became apparent at 2-4 weeks and reached similar levels in both treatments (AER = ~ 2). In contrast, anemones fed 5 times per week for 8 weeks with Artemia nauplii were nitrogen sufficient (AER = 1.03). In the field, zooxanthellae from mudflat anemones were largely nitrogen sufficient (AER = 1.26), while nitrogen deficient zooxanthellae were present in anemones from a rocky intertidal site (AER = 2.93). These results suggest that, while there was evidence for particulate nitrogen uptake, dissolved inorganic nitrogen (especially ammonium) in interstitial pore water may be a more important source of nitrogen for the zooxanthellae in mudflat anemones, and may explain the marked difference in nitrogen status between the mudflat and rocky shore populations.     

SNMDA: A novel method for predicting microRNA‐disease associations based on sparse neighbourhood

miRNAs are a class of small noncoding RNAs that are associated with a variety of complex biological processes. Increasing studies have shown that miRNAs have close relationships with many human diseases. The prediction of the associations between miRNAs and diseases has thus become a hot topic. Although traditional experimental methods are reliable, they could only identify a limited number of associations as they are time‐consuming and expensive. Consequently, great efforts have been made to effectively predict reliable disease‐related miRNAs based on computational methods. In this study, we present a novel approach to predict the potential microRNA‐disease associations based on sparse neighbourhood. Specifically, our method takes advantage of the sparsity of the miRNA‐disease association network and integrates the sparse information into the current similarity matrices for both miRNAs and diseases. To demonstrate the utility of our method, we applied global LOOCV, local LOOCV and five‐fold cross‐validation to evaluate our method, respectively. The corresponding AUCs are 0.936, 0.882 and 0.934. Three types of case studies on five common diseases further confirm the performance of our method in predicting unknown miRNA‐disease associations. Overall, results show that SNMDA can predict the potential associations between miRNAs and diseases effectively.     

警惕杰克贝尔氏粉蚧Pseudococcus jackbeardsleyi Gimpel & Miller在中国大陆扩散

杰克贝尔氏粉蚧原产于新热带区,是新近传入中国大陆的一种外来生物,主要危害水果、蔬菜、园林植物和粮食作物。该虫于2012年首次在我国海南乐东被发现,寄主植物为丝瓜;之后又在新疆乌鲁木齐的花卉市场被发现,寄主植物为来自广东或福建的盆景人参榕。杰克贝尔氏粉蚧寄主范围广泛,涉及50科200多种,且极易随农产品的贸易活动进行远距离传播扩散,对我国农林产业的安全生产构成了潜在巨大威胁。概述了杰克贝尔氏粉蚧的地理分布和生物学特征,浅析了其在我国的传播扩散趋势,并从物种鉴定、生物防治和检验检疫处理等方面提出了防控建议,以期为有效预防和控制该种粉蚧在我国的进一步传播扩散提供参考。