Cross-trait prediction accuracy of summary statistics in genome-wide association studies

In the era of big data, univariate models have widely been used as a workhorse tool for quickly producing marginal estimators; and this is true even when in a high-dimensional dense setting, in which many features are “true,” but weak signals. Genome-wide association studies (GWAS) epitomize this type of setting. Although the GWAS marginal estimator is popular, it has long been criticized for ignoring the correlation structure of genetic variants (i.e., the linkage disequilibrium [LD] pattern). In this paper, we study the effects of LD pattern on the GWAS marginal estimator and investigate whether or not additionally accounting for the LD can improve the prediction accuracy of complex traits. We consider a general high-dimensional dense setting for GWAS and study a class of ridge-type estimators, including the popular marginal estimator and the best linear unbiased prediction (BLUP) estimator as two special cases. We show that the performance of GWAS marginal estimator depends on the LD pattern through the first three moments of its eigenvalue distribution. Furthermore, we uncover that the relative performance of GWAS marginal and BLUP estimators highly depends on the ratio of GWAS sample size over the number of genetic variants. Particularly, our finding reveals that the marginal estimator can easily become near-optimal within this class when the sample size is relatively small, even though it ignores the LD pattern. On the other hand, BLUP estimator has substantially better performance than the marginal estimator as the sample size increases toward the number of genetic variants, which is typically in millions. Therefore, adjusting for the LD (such as in the BLUP) is most needed when GWAS sample size is large. We illustrate the importance of our results by using the simulated data and real GWAS.     

Multikink quantile regression for longitudinal data with application to progesterone data analysis

Motivated by investigating the relationship between progesterone and the days in a menstrual cycle in a longitudinal study, we propose a multikink quantile regression model for longitudinal data analysis. It relaxes the linearity condition and assumes different regression forms in different regions of the domain of the threshold covariate. In this paper, we first propose a multikink quantile regression for longitudinal data. Two estimation procedures are proposed to estimate the regression coefficients and the kink points locations: one is a computationally efficient profile estimator under the working independence framework while the other one considers the within-subject correlations by using the unbiased generalized estimation equation approach. The selection consistency of the number of kink points and the asymptotic normality of two proposed estimators are established. Second, we construct a rank score test based on partial subgradients for the existence of the kink effect in longitudinal studies. Both the null distribution and the local alternative distribution of the test statistic have been derived. Simulation studies show that the proposed methods have excellent finite sample performance. In the application to the longitudinal progesterone data, we identify two kink points in the progesterone curves over different quantiles and observe that the progesterone level remains stable before the day of ovulation, then increases quickly in 5 to 6 days after ovulation and then changes to stable again or drops slightly.     

胀果甘草化学成分的研究（Ⅲ）

继前文工作,本文报道从胀果甘草(Glycyrrhiza inflata Bat)根及根茎用95％乙醇渗滤后的提取部分中获得的另外五个化合物的结构鉴定。经理化性质及波谱分析,分别鉴定为胡萝卜甙(Daucosterol)、甘草查尔酮甲(Licochalcone A)、β-谷甾醇(β-Sitosterol),异芒柄花甙(Isoononin)和4＇,7一二羟基黄酮(4＇,7-Dihydroxy-flavone)。其中胡萝卜甙和异芒柄花甙为首次从该植物中获得。药理实验表明,甘草查尔酮甲对H_2O_2诱异的溶血有极好的抑制作用(97.3％),但甘草甙在三个体外氧化体系中都没有明显的活性。     

鼠兔核质杂交胚胎早期发育的研究

细胞核移植技术已被证明是研究发育中核质相互关系的非常重要的手段之一,电融合技术也是近十年发展起来的新型细胞融合技术。本实验运用这两项技术,进行了鼠、兔目间核质杂交实验,小鼠8-细胞核在激活的兔去核卵母细胞中,发生了染色体超前凝聚及核膨胀,融合卵移植到小鼠输卵管4.5天后,冲洗出,有5.4%的重构卵发育到囊胚期,通过染色体检查,囊胚细胞中均为小鼠染色体,其中一个囊胚为正常小鼠核型(2 n=40,XX)。通过本实验,我们认为:鼠兔远缘核质杂交胚胎的早期发育是可能的。     

The legacy effect of biochar application on soil nitrous oxide emissions

Existing studies suggest that biochar application can reduce soil nitrous oxide (N₂O) emissions, mainly based on short-term results. However, it remains unclear what the effects (i.e., legacy effects) and underlying mechanisms are on N₂O emissions after many years of a single application of biochar. Here, we collected intact soil columns from plots without and with biochar application in a subtropical tea plantation 7 years ago for an incubation experiment. We used the N₂O isotopocule analysis combined with ammonia oxidizer-specific inhibitors and molecular biology approaches to investigate how the legacy effect of biochar affected soil N₂O emissions. Results showed that the soil in the presence of biochar had lower N₂O emissions than the control albeit statistically insignificant. The legacy effect of biochar in decreasing N₂O emissions may be attributed to the reduced effectiveness of the soil substrate, nitrification and denitrification activities, and the promotion of the further reduction of N₂O. The legacy effect of biochar reduced the relative contribution of nitrifier denitrification/bacterial denitrification, nitrification-related N₂O production, and the relative abundance of several microorganisms involved in the nitrogen cycle. Our global meta-analysis also showed that the reduction of N₂O by biochar increased with increasing application rate but diminished and possibly even reversed with increasing experimental time. In conclusion, our findings suggest that the abatement capacity of biochar on soil N₂O emissions may weaken over time after biochar application, but this remains under further investigation.     

The effects of feeding by the rice water weevil, Lissorhoptrus oryzophilus Kuschel, on the growth and yield components of rice, Oryza sativa

Abstract 1 The effects of feeding by larvae of the rice water weevil, Lissorhoptrus oryzophilus Kuschel, on the growth and yield components of rice, Oryza sativa, were evaluated using four varieties of rice, ‘Cocodrie’, ‘Cypress’, ‘Bengal’ and ‘XP1003’, over 2 years. 2 Both adults and larvae of L. oryzophilus feed on rice plants, but it is feeding by the larval stage that causes economic losses. Feeding by L. oryzophilus larvae resulted in extensive damage to root systems. Pruning of root systems resulted in a decrease in tiller number and shoot biomass of rice plants in the vegetative stage of growth. 3 Yield losses were due to a combination of decreases in panicle densities, numbers of grains per panicle, and grain weights. Decreases in panicle densities were a direct result of the reductions in tiller numbers. Reductions in numbers of grains per panicle and grain weights probably resulted from decreases in shoot biomass. 4 Injury by rice water weevil larvae is chronic. The tillering stage of rice suffered the majority of weevil damage, but the growth effects were not manifested until later.     

异色瓢虫若虫对麦三叉蚜的捕食作用

研究表明,异色瓢虫高龄若虫捕食麦二叉蚜的功能反应为ＨｏｌｌｉｎｇⅡ型反应,喜好捕食低龄若蚜;在４０℃下捕食率最低,１０℃次之,２５℃最高．在１０～２５℃内捕食率ｙ与温度ｘ的关系为ｙ＝２８．１３０３＋２．６６６５ｘ,在２５～４０℃内为ｙ＝１９９．９２７５－３．６４２ｘ;在种内干扰条件下,其捕食作用率Ｅ与开敌密度Ｐ的关系为Ｅ＝０．６８９７Ｐ－０．７９３０,搜索常数Ｑ为０．６８９７,干扰系数ｍ为０．７９３０;其分摊竞争强度Ｉ与异色瓢虫密度Ｐ的关系为Ｉ＝０．０４００＋１．０３８３ｌｏｇＰ．     

准分子激光治疗近视眼

本文对准分子激光PRK治疗近视眼息者503例的早期临床结果进行分析,近视范围为－2．0至－15．0D,根据术前屈光度不同分为三组,术后随访三个月．结果证实准分子激光是一种安全、有效、预测性较好的治疗近视眼方法．全部病人提高了裸眼视力,绝大部分保持了最佳矫正视力,且没有产生危及视力的并发症．