GEE with Gaussian estimation of the correlations when data are incomplete

This paper considers a modification of generalized estimating equations (GEE) for handling missing binary response data. The proposed method uses Gaussian estimation of the correlation parameters, i.e., the estimating function that yields an estimate of the correlation parameters is obtained from the multivariate normal likelihood. The proposed method yields consistent estimates of the regression parameters when data are missing completely at random (MCAR). However, when data are missing at random (MAR), consistency may not hold. In a simulation study with repeated binary outcomes that are missing at random, the magnitude of the potential bias that can arise is examined. The results of the simulation study indicate that, when the working correlation matrix is correctly specified, the bias is almost negligible for the modified GEE. In the simulation study, the proposed modification of GEE is also compared to the standard GEE, multiple imputation, and weighted estimating equations approaches. Finally, the proposed method is illustrated using data from a longitudinal clinical trial comparing two therapeutic treatments, zidovudine (AZT) and didanosine (ddI), in patients with HIV.     

Genetic differentiation among the Maculinea species (Lepidoptera: Lycaenidae) in eastern Central Europe

The present study aimed to analyse the level of genetic variation in the eastern Central European (Slovenia, Hungary, and Romania/Transylvania) populations of the Large Blues ( Maculinea ) to analyse the pattern of differentiation both between and within the species. One objective was to compare the level of differentiation between the two disputed species ( Maculinea alcon and Maculinea rebeli ) with that among the other species. Imagos were collected from 23 localities in eastern Central Europe in 2002. Enzyme polymorphism was analysed using polyacrylamide gel electrophoresis. Fourteen enzyme loci were studied in all samples. In the analysis of the data, F -statistics and Nei's genetic distances were calculated and a dendrogram (unweighted pair group method with arithmetic mean) was constructed on the basis of the distance matrix. A multivariate analysis of variance was performed to study the pattern of genetic differentiation among the samples. Principal component analysis analysis was also carried out using the allele frequency data of the samples. Our results indicated that the large blues are generally less polymorphic than other European lycaenid butterflies studied. At the same time, the level of genetic differentiation was high, even among local populations within the species. A low level of genetic variation within the populations coupled with strong differentiation among them implies the effect of genetic drift. Strong genetic differentiation of four Maculinea species ( M. alcon , Maculinea teleius, Maculinea nausithous , and Maculinea arion ) was confirmed. Significant differentiation was not found between M. alcon and M. rebeli .  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 91 , 11–21.     

Functional analysis of the Alternaria brassicicola non-ribosomal peptide synthetase gene AbNPS2 reveals a role in conidial cell wall construction

Alternaria brassicicola is a necrotrophic pathogen causing black spot disease on virtually all cultivated Brassica crops worldwide. In many plant pathosystems fungal secondary metabolites derived from non-ribosomal peptide synthetases (NPSs) are phytotoxic virulence factors or are antibiotics thought to be important for niche competition with other micro-organisms. However, many of the functions of NPS genes and their products are largely unknown. In this study, we investigated the function of one of the A. brassicicola NPS genes, AbNPS2 . The predicted amino acid sequence of AbNPS2 showed high sequence similarity with A. brassicae , AbrePsy1, Cochliobolus heterostrophus , NPS4 and a Stagonospora nodorum NPS. The AbNPS2 open reading frame was predicted to be 22 kb in length and encodes a large protein (7195 amino acids) showing typical NPS modular organization. Gene expression analysis of AbNPS2 in wild-type fungus indicated that it is expressed almost exclusively in conidia and conidiophores, broadly in the reproductive developmental phase. AbNPS2 gene disruption mutants showed abnormal spore cell wall morphology and a decreased hydrophobicity phenotype. Conidia of abnps2 mutants displayed an aberrantly inflated cell wall and an increase in lipid bodies compared with wild-type. Further phenotypic analyses of abnps2 mutants showed decreased spore germination rates both in vitro and in vivo , and a marked reduction in sporulation in vivo compared with wild-type fungus. Moreover, virulence tests on Brassicas with abnps2 mutants revealed a significant reduction in lesion size compared with wild-type but only when aged spores were used in experiments. Collectively, these results indicate that AbNPS2 plays an important role in development and virulence.     

Blood pressure and blood flow variation during postural change from sitting to standing: model development and validation.

Short-term cardiovascular responses to postural change from sitting to standing involve complex interactions between the autonomic nervous system, which regulates blood pressure, and cerebral autoregulation, which maintains cerebral perfusion. We present a mathematical model that can predict dynamic changes in beat-to-beat arterial blood pressure and middle cerebral artery blood flow velocity during postural change from sitting to standing. Our cardiovascular model utilizes 11 compartments to describe blood pressure, blood flow, compliance, and resistance in the heart and systemic circulation. To include dynamics due to the pulsatile nature of blood pressure and blood flow, resistances in the large systemic arteries are modeled using nonlinear functions of pressure. A physiologically based submodel is used to describe effects of gravity on venous blood pooling during postural change. Two types of control mechanisms are included: 1) autonomic regulation mediated by sympathetic and parasympathetic responses, which affect heart rate, cardiac contractility, resistance, and compliance, and 2) autoregulation mediated by responses to local changes in myogenic tone, metabolic demand, and CO(2) concentration, which affect cerebrovascular resistance. Finally, we formulate an inverse least-squares problem to estimate parameters and demonstrate that our mathematical model is in agreement with physiological data from a young subject during postural change from sitting to standing.     

栀子水提取物对实验性2型糖尿病大鼠血糖及同型半胱氨酸水平的影响

观察栀子提取物对实验性2型糖尿病大鼠血糖、血脂及同型半胱氨酸水平的影响.采用Wistar雄性大鼠70只,随机抽取10只作为正常对照组,喂以普通维持饲料,其余60只高糖高脂饲料喂养4周后,ip链脲佐菌素(STZ)30 mg/kg建立2型糖尿病模型,7d后选取成模大鼠50只随机分为模型对照组(生理盐水)、盐酸二甲双胍对照组、栀子提取物低、中、高剂量组(0.2、0.4、0.6 g/kg),每组10只.连续ig给药4周后,观察各组大鼠血糖、血脂及同型半胱氨酸水平等变化.栀子提取物ig能降低糖尿病大鼠的血糖、甘油三酯(TG)、胆固醇(TC)、低密度脂蛋白(LDLC),同时能升高高密度脂蛋白(HDLC),降低同型半胱氨酸水平.     

根据外部形态特征试论披碱草属3组植物间的系统关系

通过对披碱草属中小颖组、宽颖组和长颖组种类外部形态的观察,总结了3组植物外部形态特征的异同,探讨了形态学特征的分类学意义。同时,根据3组植物外部形态性状—花序、小穗、小花、以及内稃的演化趋势,分析了各组的演化关系和系统位置。结果表明：小颖组最原始,宽颖组较进化,长颖组最高级;小颖组可能直接派生了较进化的宽颖组,并在宽颖组的基础上进而产生了最高级的长颖组。此外,本文对披碱草属参试种的系统关系也作了一定程度的探讨,结果显示圆锥披碱草最原始,墨西哥披碱草最进化,其余参试种居于两者之间。上述研究工作为整个披碱草属系统与进化方面的探讨提供了形态学方面的理论证据。     

A note on permutation tests for variance components in multilevel generalized linear mixed models

In many applications of generalized linear mixed models to multilevel data, it is of interest to test whether a random effects variance component is zero. It is well known that the usual asymptotic chi-square distribution of the likelihood ratio and score statistics under the null does not necessarily hold. In this note we propose a permutation test, based on randomly permuting the indices associated with a given level of the model, that has the correct Type I error rate under the null. Results from a simulation study suggest that it is more powerful than tests based on mixtures of chi-square distributions. The proposed test is illustrated using data on the familial aggregation of sleep disturbance.