Nonparametric correction for covariate measurement error in a stratified Cox model

Stratified Cox regression models with large number of strata and small stratum size are useful in many settings, including matched case-control family studies. In the presence of measurement error in covariates and a large number of strata, we show that extensions of existing methods fail either to reduce the bias or to correct the bias under nonsymmetric distributions of the true covariate or the error term. We propose a nonparametric correction method for the estimation of regression coefficients, and show that the estimators are asymptotically consistent for the true parameters. Small sample properties are evaluated in a simulation study. The method is illustrated with an analysis of Framingham data.     

The 102-Kilobase Unstable Region of Yersinia pestis Comprises a High-Pathogenicity Island Linked to a Pigmentation Segment Which Undergoes Internal Rearrangement

Several pathogenicity islands have recently been identified in different bacterial species, including a high-pathogenicity island (HPI) in Yersinia enterocolitica 1B. In Y. pestis, a 102-kb chromosomal fragment (pgm locus) that carries genes involved in iron acquisition and colony pigmentation can be deleted en bloc. In this study, characterization and mapping of the 102-kb region of Y. pestis 6/69 were performed to determine if this unstable region is a pathogenicity island. We found that the 102-kb region of Y. pestis is composed of two clearly distinct regions: an ≈35-kb iron acquisition segment, which is an HPI per se, linked to an ≈68-kb pigmentation segment. This linkage was preserved in all of the Y. pestis strains studied. However, several nonpigmented Y. pestis strains harboring an irp2 gene have been previously identified, suggesting that the pigmentation segment is independently mobile. Comparison of the physical map of the 102-kb region of these strains with that of strain 6/69 and complementation experiments were carried out to determine the genetic basis of this phenomenon. We demonstrate that several different mechanisms involving mutations and various-size deletions are responsible for the nonpigmented phenotype in the nine strains studied. However, no deletion corresponded exactly to the pigmentation segment. The 102-kb region of Y. pestis is an evolutionarily stable linkage of an HPI with a pigmentation segment in a region of the chromosome prone to rearrangement in vitro.     

Vegetation responses to past climatic variation

Vegetation responses to climatic change can be studied retrospectively by utilizing the Quaternary fossil record. There has been controversy over the extent to which major changes in vegetation patterns at the continental scale lag behind the climatic changes that drive them, and to what extent vegetation can ever be said to be in equilibrium with climate. The equilibrium question has no single answer. The predominant mode of vegetation response to climatic change depends on the space and time frame and resolution of the data set in which the response is observed.Vegetation (as observed on particular space and time scales) can be in dynamic equilibrium with climate if its response time is sufficiently fast in relation to the rate of climatic change to which it is observed to be responding. Several processes can be involved in the response: successional, migrational, edaphic, and evolutionary. Successional response times can be deduced from forest succession models. The other processes are less well understood and different ideas exist concerning their rates. According to one hypothesis, migrational lags caused delays of thousands of years in the postglacial dynamics of forest composition. The alternative hypothesis explains these changes as dynamic equilibrium responses to changes in climatic seasonality and climatic anomaly patterns. Neither hypothesis need be universally true; gradient analysis and forest succession models are among the techniques that can be used in inferential tests of these hypotheses for particular space-time regions.Dynamic equilibrium may often be a reasonable approximation for the responses of the broadest continental-scale forest patterns to orbitally induced climatic changes. But as spatial and temporal frames of observation are diminished and resolution increased, biotic processes must eventually come to dominate. At sufficiently fine scales the main observable phenomena are successional responses to natural disturbance events. The late-Quaternary record of vegetation change allows a choice of observation scales and thus provides a continuum of possibilities for study, ranging from long-term dynamic bioclimatology to more conventional vegetation dynamics.I thank Margaret Davis, Honor Prentice, Jim Ritchie, Al Solomon, Geoff Spaulding and Tom Webb for their reviews of earlier drafts. Research supported by a US Department of Energy, Carbon Dioxide Research Division, grant to Brown University and a Swedish Natural Science Research Council grant to the project SlsSimulation of Natural Forest Dynamics.I thank Margaret Davis, Honor Prentice, Jim Ritchie, Al Solomon, Geoff Spaulding and Tom Webb for their reviews of earlier drafts. Research supported by a US Department of Energy, Carbon Dioxide Research Division, grant to Brown University and a Swedish Natural Science Research Council grant to the project SlsSimulation of Natural Forest Dynamics.     

The role of fish-poultry integration on fish growth performance,yields and economic benefits among smallholder farmers in sub-Saharan Africa,Tanzania

Aquaculture practices from sub-Saharan Africa are characterised by low production, owing to improper technology. Production can be increased through integrating fish farming with other existing on-farm activities, particularly livestock husbandry. We assessed the role of fish-poultry integration on all male Nile tilapia, Oreochromis niloticus growth performance, yields and economic benefits among smallholder farmers in sub-Saharan Africa, Tanzania. The study also compared phytoplankton species composition, abundance and biomass between the fish-poultry integration and non-integrated system. After 180 days of the experiment, all male O. niloticus cultured under fish-poultry integration exhibited significantly higher growth rates than those in the non-integrated system (p < 0.05). Gross fish yield (GFY), net fish yield (NFY) and net annual yields (NAY) obtained from fish-poultry integration were significantly higher than those from non-integrated system (p < 0.05). Partial enterprise budget analysis revealed that fish-poultry integration was more profitable than the non-integrated system. Moreover, fish-poultry integrated system produced significantly higher phytoplankton abundance and biomass than those from the non-integrated system. Results demonstrate that rural smallholder farmers can achieve higher growth rate, farm net yields and income by integrating all male O. niloticus with other on-farm activities than practising a stand-alone fish culture system.     

毛乌素沙地南缘沙丘生物结皮对凝结水形成和蒸发的影响

在水分极度匮乏的荒漠生态系统,凝结水是除降雨之外最重要的水分来源之一,它对荒漠生态系统结构、功能和过程的维持产生重要的影响。为探明半干旱沙区生物结皮表面的凝结水形成和蒸发特征,采用自制的微型蒸渗计(直径7 cm、高5 cm的PVC管)实验观测了不同类型地表(裸沙、浅灰色藻类结皮、黑褐色藻类结皮和苔藓结皮)对凝结水形成和蒸发的影响。结果表明:(1)观测期间共有20次凝结水形成记录,除降雨天气外,几乎每天都能观测到水分凝结现象;(2)不同类型地表凝结水总量依次为(1.998±0.075),(2.326±0.083),(2.790±0.058)和(3.416±0.068) mm,生物结皮表面的凝结水总量显著大于裸沙(P < 0.05);随生物结皮的发育,不同类型生物结皮表面的凝结水总量呈增加的趋势,凝结水总量之间差异显著(P < 0.05);观测期间不同类型地表日平均凝结水量依次为(0.100±0.003),(0.116±0.004),(0.140±0.002)和(0.171± 0.003) mm,不同类型地表日平均凝结水量之间差异极显著(P < 0.01);(3)凝结水形成过程的观测结果显示,凝结水19:00开始形成,23:00-凌晨1:00形成不明显,1:00-7:00继续形成,除浅灰色藻类结皮外,太阳升出后在黑褐色藻类结皮和苔藓结皮表面继续形成少量的凝结水;凝结水7:30开始蒸发,10:30到11:00之间结束蒸发,凝结水在裸沙和浅灰色藻类结皮中的保持时间显著大于黑褐色藻类结皮和苔藓结皮中的保持时间(P < 0.05);(4)凝结水的形成受大气温度、地表温度、空气相对湿度和大气地表温度差等气象因素的影响,但其形成过程不与某一个气象因素呈简单的线性关系。