Empirical Bayes estimation of random effects parameters in mixed effects logistic regression models

We extend an approach for estimating random effects parameters under a random intercept and slope logistic regression model to include standard errors, thereby including confidence intervals. The procedure entails numerical integration to yield posterior empirical Bayes (EB) estimates of random effects parameters and their corresponding posterior standard errors. We incorporate an adjustment of the standard error due to Kass and Steffey (KS; 1989, Journal of the American Statistical Association 84, 717-726) to account for the variability in estimating the variance component of the random effects distribution. In assessing health care providers with respect to adult pneumonia mortality, comparisons are made with the penalized quasi-likelihood (PQL) approximation approach of Breslow and Clayton (1993, Journal of the American Statistical Association 88, 9-25) and a Bayesian approach. To make comparisons with an EB method previously reported in the literature, we apply these approaches to crossover trials data previously analyzed with the estimating equations EB approach of Waclawiw and Liang (1994, Statistics in Medicine 13, 541-551). We also perform simulations to compare the proposed KS and PQL approaches. These two approaches lead to EB estimates of random effects parameters with similar asymptotic bias. However, for many clusters with small cluster size, the proposed KS approach does better than the PQL procedures in terms of coverage of nominal 95% confidence intervals for random effects estimates. For large cluster sizes and a few clusters, the PQL approach performs better than the KS adjustment. These simulation results agree somewhat with those of the data analyses.     

Ski slope vegetation at Snoqualmie Pass, Washington State, USA, and a comparison with ski slope vegetation in temperate coniferous forest zones

Ski slope vegetation at Snoqualmie Pass in Washington State, USA, was surveyed in order to identify community types and to compare it with vegetation development patterns in Japan. Ski slopes in Japan, most of which were constructed after 1960, underwent heavy land recontouring, while those at Snoqualmie Pass were constructed before 1950 with less modification. Three points apply to Japanese ski slope vegetation and differentiate these slopes from those at Snoqualmie Pass: (i) grasslands of introduced species are widespread and persistent; (ii) unvegetated patches are uncommon; and (iii) wetland vegetation has developed. These differences are mainly derived from the intensity of human impact, history of the slope and its scale: namely, ski slopes in Washington are older and larger than those in Japan. Ski slope vegetation in Washington was primarily differentiated by a soil moisture gradient. The large size of Washington ski slopes permitted the inclusion and development of wetland habitats, whereas most ski slopes in Japan are constructed on ridges and do not contain wetlands. Most introduced species in Japan are eliminated soon after seeding. In contrast, the long-term management of ski slopes decreased soil erosion and/or unvegetated patches in Washington and created relatively permanent grasslands composed of introduced species. Tsuga heterophylla and Abies amabilis were found established on the ski slopes in Washington, whereas in Japan the pioneer tree species are shade-intolerant broadleaved species. These differences may be a result of the different disturbance histories of ski slopes in the two countries. In addition, along with the conifers, early successional forbs such as Anaphalis margaritacea and Epilobium angustifolium are well established on Washington ski slopes. Results show that disturbances created by ski slope development greatly affect the vegetation, even on older, less heavily impacted ski slopes.     

城市污泥应用于边坡植被恢复对地表水环境的影响

将城市污泥应用于生态恢复因能避开粮食作物食物链而具有良好前景,但其对地表水环境影响仍不十分清楚.本文将城市污泥与建筑垃圾按1∶1体积比混合为生长基质,覆盖在模拟的煤矸石边坡上,播种8种乡土木本植物,对生长季植物生长情况以及坡面地表水和下渗水的电导率、p H、氮磷钾、重金属、多环芳烃等含量进行分析.结果表明:坡面植物生长良好,平均覆盖度达60%;地表水和下渗水的p H值近中性,变化不大,而电导率、氮磷钾、重金属和多环芳烃含量均较高,其中,氮、磷含量在整个生长季超过国家地表水环境质量Ⅴ类水质标准;7月重金属含量最高,其中,As含量只达地表水环境质量Ⅳ~Ⅴ类标准,其余重金属含量多达Ⅱ~Ⅳ标准;随着夏季雨水淋洗增加以及植物-土壤系统对化学物质的吸收、降解和固着作用,地表水和下渗水的电导率、氮磷钾、重金属和多环芳烃含量均显著下降,生长季后期重金属含量达到地表水环境质量Ⅱ~Ⅲ类标准,多环芳烃含量减少约一半.将城市污泥直接应用在煤矸石边坡生态恢复中有利于植物生长,植物-土壤系统使得生长基质中的有害物含量逐渐降低,对地表水环境的负影响主要表现为氮、磷的富营养化,但总体上其环境安全性可控.     

元谋干热河谷冲沟坡度与植物优势种关系

在元谋干热河谷冲沟发育典型的三个样区(沙地村、金雷村、苴林村)采集48条冲沟的植物样方数据和冲沟沟底的坡度数据,运用重要值方法对植被优势种进行判别和筛选,以灌木优势种和草本优势种为主要研究对象,探讨植被优势种与冲沟沟底坡度的关系。结果表明：(1)灌木优势种为车桑子Dodonaea viscosa和山合欢Albizia kalkora,重要值分别为0.486和0.342,占灌木总体的83%;草本优势种为扭黄茅Heteropogon contortus、孔颖草Bothriochloa pertusa和茅草Imperata cylindrica,重要值分别为0.386、0.140及0.196,占草本总体的72%。(2)除草本优势种中的茅草盖度与坡度相关性显著(P<0.05)外,样区冲沟沟底坡度与灌木优势种和草本优势种相关性均不显著(P>0.05),表明在元谋干热河谷地区,冲沟沟底坡度对植被优势种生长状况影响较小。     

Chloroplast position and photosynthetic characteristics in two monostromatic species,Monostroma angicava and Protomonostroma undulatum (Ulvophyceae), having a shared ecological niche

Monostroma angicava and Protomonostroma undulatum are monostromatic green benthic algae (Ulvophyceae), which grow together in the same intertidal habitat of Muroran, Hokkaido, Japan, during the spring season. Commonly, both species have a single chloroplast with one pyrenoid per cell. The parietal chloroplast is located on the periphery of the thallus in both species, although the location of the chloroplast differs in the two. In M. angicava , the chloroplast was observed to be arranged on one‐side of the thallus surface, whereas, in P. undulatum , it was dispersed and randomly located on either side of the thallus or on the lateral face. The density of chlorophylls (Chls) assessed from the absorption spectra of the thallus and its solvent extract was higher in M. angicava , which appeared dark‐green in color, than in the light‐green colored P. undulatum . The maximum photosynthetic rate per thallus area (μmol O₂ m^?2 s^?1) was higher in M. angicava , whereas, per total chlorophyll content (μmol O₂ g Chl a + Chl b ^?1 s^?1) was higher in P. undulatum . Both species showed similar efficiency of photosynthesis at light‐limiting conditions. The efficiency of light absorption by photosystem II (PSII ) in P. undulatum was higher than M. angicava , whereas the photoprotective response was higher in M. angicava . This indicates that more energy is utilized in M. angicava to protect its PSII due to the chloroplast position, which has more direct exposure to light and, therefore, lowers the efficiency of light absorption by PSII . The higher density of chlorophylls in M. angicava could explain higher photosynthesis per thallus area, whereas, higher efficiency of light absorption by PSII in P. undulatum could explain higher photosynthesis per total chlorophyll content. The differences in light absorption efficiency and quantum efficiency of PSII might be an important ecological strategy in these two species for their coexistence in the intertidal area.     

Hidden biodiversity in the Arctic – a study of soil seed banks at Disko Island,Qeqertarsuaq, West Greenland

Seed dispersal is a key process in plant community dynamics, and soil seed banks represent seed dispersal in time rather than in space. Despite their potential importance, seed bank dynamics in the Arctic are poorly understood. We investigated soil seed banks and corresponding plant community composition in three contrasting vegetation types in West Greenland, viz. dwarf shrub heaths, herb slopes and fell‐fields. Through germination testing, 31 species were documented in soil seed banks. All of these were herbaceous, while no dwarf‐shrub species, which represents the dominating growth form in the above‐ground vegetation, were emerging from the seed bank. Consequently, across vegetation types, the lowest similarity between seed bank and above‐ground vegetation was found in dwarf shrub heath. Nine plant species were exclusively found in seed bank, all of which were non‐clonal forbs. Seed bank size (total number of seeds) and species richness seemed to increase with the level of natural disturbance. Additionally, we examined the effect of different experimental light and temperature conditions on the quantity and diversity of germinating seeds. The difference in diversity in vegetation and seed bank at the species level will impact population dynamics, regeneration of vegetation after disturbances and its potential to respond to climate change.     

摩天岭北坡森林木本植物叶性状在物种和群落水平沿海拔梯度的变化

该研究采用样线和样地相结合的方法,对甘肃省白水江国家级自然保护区摩天岭北坡大垭子梁森林不同海拔(1 600~2 100m)的植物群落进行野外调查、采样分析,并运用线性回归分析、Pearson相关性分析及曲线拟合分析方法,研究木本植物的比叶面积(SLA)、叶干物质含量(LDMC)、叶碳氮磷含量(LCC、LNC、LPC)及其计量比(C/N、C/P、N/P)等叶性状变化特征,以及在物种和群落水平随海拔梯度的变化趋势和相关性。结果表明:(1)摩天岭北坡大垭子梁山地森林为落叶阔叶林带,共有木本植物13科23种,其中乔木6种,灌木17种,且整体上灌木种类较为丰富。此外,有些物种在不同海拔间都有分布,如华北落叶松(Larix principis-rupprechtii)、胡枝子(Lespedeza bicolor)等,反映出不同植物对于异质环境的适应。(2)8个叶功能性状中变异系数最小的是LCC(4.6%),属于弱变异,最大的是SLA(42.1%),其他叶性状都属于中等变异,表明在其他叶性状的协同作用下,使得木本植物的碳获取保持在一定的水平以确保群落的稳定性。(3)叶片功能性状间的关联性普遍存在,是植物适应环境的一种对策.该研究表明SLA-LNC以及LNC-LPC在物种和群落水平上的相关性及其相关程度均一致,而其他叶性状间相关关系则有所不同,这为以后进行大尺度研究时对叶性状的选择提供了一定的依据。(4)叶性状随海拔的变化趋势,除C/N和N/P在物种和群落水平上变化趋势不一致外,其他各个性状随海拔的总体变化趋势基本一致,但显著程度只有LNC一致外其他均不同,反映了木本植物的不同叶片功能性状对海拔造成的不同环境的适应。     

川西高原不同坡向云、冷杉树轮对快速升温的响应差异

在川西高原松潘县二道海林区的东南坡、西北坡和扎日寺林区的东坡用零信号法建立4条云、冷杉树轮年表,通过年轮 气候响应分析、多因素方差分析等方法研究不同坡向树木生长对快速升温的响应差异.结果表明： 快速升温(1980年)后,东坡紫果云杉生长显著加速(0.011 a^-1),而西北坡紫果云杉生长则显著降低(-0.006 a^-1),东南坡紫果云杉和西北坡岷江冷杉生长降低,但不显著.随着快速升温,不同坡向云、冷杉径向生长与气候因子的关系均出现显著变化.快速升温后,生长季温度对东坡紫果云杉径向生长的促进作用显著增加,对东南坡和西北坡紫果云杉径向生长的抑制作用也显著增加,但生长季温度对西北坡岷江冷杉径向生长的影响在升温前后变化不明显.5月降水量对东坡紫果云杉径向生长由升温前的抑制作用变为升温后的显著促进作用,而对东南坡和西北坡紫果云杉径向生长的抑制作用显著增加,5月降水量对西北坡岷江冷杉径向生长的影响在升温前后变化不明显.树轮与帕尔默干旱指数响应分析表明,快速升温后,不同坡向的土壤湿度变化是造成树轮响应差异的重要原因.多因素方差分析表明,坡向与温度、降水的综合作用是影响紫果云杉径向生长的重要因素.因此,在模拟预测树木生长对气候变暖的响应动态时,应考虑不同坡向与温度、降水的综合作用.     

基于耦合模型的干旱区植被净初级生产力估算

净初级生产力是陆地生态系统物质与能量运转研究的基础, 在干旱区生态环境演变及其与气候相互作用和影响方面极为敏感,是揭示干旱区生态环境特征的重要指标.本研究基于RS和GIS技术,利用地面气象数据、涡度相关数据、Landsat 8数据和MODIS数据,通过SEBAL模型和光能利用率模型的耦合,估算了新疆玛纳斯河流域植被净初级生产力(NPP),分析了其空间格局及与高程和坡度的关系.结果表明: SEBAL模型与光能利用率模型的耦合对玛纳斯河流域山地-绿洲-荒漠生态系统植被NPP的模拟效果较合理,能较好地反映植被净初级生产力的实际情况;2013年,玛纳斯河流域植被NPP总量为7066.72 Tg C·a^-1,平均值为278.06 g C·m^-2·a^-1,总体分布趋势是自南向北先增加后减少再增加最后减少,随着地貌和土地利用类型的变化呈现明显的分布规律,且其月变化比较明显,7—8月达到最大值,占总量NPP的52.2%;植被净初级生产力随海拔和坡度的增加整体呈下降趋势,但随海拔增加植被NPP出现3次波动.这些波动主要由地表植被覆盖类型和环境因素所引起.