Diffusivity of oxygen in aerobic granules

This work for the first time estimated apparent oxygen diffusivity (D(app)) of two types of aerobic granules, acetate-fed and phenol-fed, by probing the dissolved oxygen (DO) level at the granule center with a sudden change in the DO of the bulk liquid. With a high enough flow velocity across the granule to minimize the effects of external mass transfer resistance, the diffusivity coefficients of the two types of granules were estimated with reference to a one-dimensional diffusion model. The carbon source has a considerable effect on the granule diameter (d) and the oxygen diffusivity. The diffusivity coefficients were noted 1.24-2.28 x 10(-9) m2/s of 1.28-2.50 mm acetate-fed granules, and 2.50-7.65 x 10(-10) m2/s of 0.42-0.78 mm phenol-fed granules. Oxygen diffusivity declined with decreasing granule diameter, in particular, the diffusivity of acetate-fed granules is proportional to the size, whereas the diffusivity of phenol-fed granules is proportional to the square of granule diameter. The existence of large pores in granule, evidenced by FISH-CLSM imaging, was proposed to correspond to the noted size-dependent oxygen diffusivity. The phenol-fed granules exhibited a higher excellular polymer (ECP) content than the acetate-fed granules, hence yielding a lower oxygen diffusivity.     

Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints

Summary A new strategy for NMR structure calculations of proteins with the variable target function method (Braun, W. and Go, N. (1985)J. Mol. Biol.,186, 611) is described, which makes use of redundant dihedral angle constraints (REDAC) derived from preliminary calculations of the complete structure. The REDAC approach reduces the computation time for obtaining a group of acceptable conformers with the program DIANA 5-100-fold, depending on the complexity of the protein structure, and retains good sampling of conformation space.Dedicated to the memory of Professor V.F. Bystrov     

浙江省森林生物量动态

以浙江省1976至2004年森林资源连续清查资料为数据源,采用基于生物量与蓄积之间关系的生物量转换因子连续函数法,对全省林分生物量和包括林分在内的森林生物量动态进行估计。森林生物量为包括林分、疏林、灌木林、竹林、经济林和四旁树在内的所有林木生物量之和。结果表明,浙江省1976至2004年间森林生物量从1.00828×10^8Mg上升到2.44426×10^8Mg;其中,林分生物量由0.5712×10^8Mg上升到1.51128×10^8Mg。森林生物量和林分生物量的年平均增长速度分别为5.1%和9.1%。在1999至2004年间,森林生物量和林分生物量增长速度均明显加快,分别达到8.6%和10.1%。在1976至2004年间,全省森林面积年均增长速度为1.0%,森林平均生物量从16.50Mg·hm^-2上升到36.59Mg·hm^-2。但是,在森林资源总量不断增加的同时,全省林分质量仍维持较低水平。2004年全省林分单位面积生物量为38.40Mg·hm^-2,远低于全国平均水平（77.40Mg·hm^-2）。研究还表明,利用森林资源连续清查数据和基于单株测树因子的森林生物量模型能够估计大尺度范围内的森林生物量及其动态,但亟待在统一标准下建立和完善覆盖所有树种的生物量模型。     

基于VIC模型模拟的干旱区土壤水分及其时空变化特征

土壤水分在陆地水循环中起着十分重要的作用,大尺度、长时间及高精度的土壤水分监测是旱情预警、生态恢复与精准农业决策部署的重要指导依据,而陆面过程模式模拟在时空尺度上可获得更准确的土壤水分特征。以渭-库绿洲为目标靶区,结合VIC陆面过程模型和土地利用类型变化,探讨2009—2016年研究区年际间不同地类土壤水分时空变化规律,并用实测数据进行精度验证,结果表明:(1)东北区域土壤含水率模拟值较高,土壤含水量低值集中在研究区西部与南部区域。(2)盐渍土壤表层含水量高于耕地,每年雨季,灌丛土壤含水量高于其他3种地类,由于大量荒地转为耕地,绿洲荒地土壤含水量与耕地土壤相互接近,在28.784—53.741 mm之间。(3)渭-库绿洲近7年耕地与盐渍地面积大幅度增加,耕地与盐渍地面积增幅达35%以上,荒地面积相较2009年减少约46%,灌丛面积增幅约15%。(4)荒地土壤含水量伴随面积大幅度下降,土壤含水量数值集中在正态曲线28.6 mm以上区域。VIC模拟值与实测值均方根误差(RMSE)范围在1.4—2.80之间,RE范围在0.90—2.20之间,R~2范围在0.40—0.60之间,模拟效果较好。     

Model selection of generalized estimating equations with multiply imputed longitudinal data

Longitudinal data often encounter missingness with monotone and/or intermittent missing patterns. Multiple imputation (MI) has been popularly employed for analysis of missing longitudinal data. In particular, the MI‐GEE method has been proposed for inference of generalized estimating equations (GEE) when missing data are imputed via MI. However, little is known about how to perform model selection with multiply imputed longitudinal data. In this work, we extend the existing GEE model selection criteria, including the “quasi‐likelihood under the independence model criterion” (QIC) and the “missing longitudinal information criterion” (MLIC), to accommodate multiple imputed datasets for selection of the MI‐GEE mean model. According to real data analyses from a schizophrenia study and an AIDS study, as well as simulations under nonmonotone missingness with moderate proportion of missing observations, we conclude that: (i) more than a few imputed datasets are required for stable and reliable model selection in MI‐GEE analysis; (ii) the MI‐based GEE model selection methods with a suitable number of imputations generally perform well, while the naive application of existing model selection methods by simply ignoring missing observations may lead to very poor performance; (iii) the model selection criteria based on improper (frequentist) multiple imputation generally performs better than their analogies based on proper (Bayesian) multiple imputation.     

Bayesian nonparametric centered random effects models with variable selection

In a linear mixed effects model, it is common practice to assume that the random effects follow a parametric distribution such as a normal distribution with mean zero. However, in the case of variable selection, substantial violation of the normality assumption can potentially impact the subset selection and result in poor interpretation and even incorrect results. In nonparametric random effects models, the random effects generally have a nonzero mean, which causes an identifiability problem for the fixed effects that are paired with the random effects. In this article, we focus on a Bayesian method for variable selection. We characterize the subject‐specific random effects nonparametrically with a Dirichlet process and resolve the bias simultaneously. In particular, we propose flexible modeling of the conditional distribution of the random effects with changes across the predictor space. The approach is implemented using a stochastic search Gibbs sampler to identify subsets of fixed effects and random effects to be included in the model. Simulations are provided to evaluate and compare the performance of our approach to the existing ones. We then apply the new approach to a real data example, cross‐country and interlaboratory rodent uterotrophic bioassay.     

The immunoglobulin superfamily: An insight on its tissular, species, and functional diversity

The immunoglobulin superfamily (IgSF) is a heterogenic group of proteins built on a common fold, called the Ig fold, which is a sandwich of two β sheets. Although members of the IgSF share a similar Ig fold, they differ in their tissue distribution, amino acid composition, and biological role. In this paper we report an up-to-date compilation of the IgSF where all known members of the IgSF are classified on the basis of their common functional role (immune system, antibiotic proteins, enzymes, cytokine receptors, etc.) and their distribution in tissue (neural system, extracellular matrix, tumor marker, muscular proteins, etc.), or in species (vertebrates, invertebrates, bacteria, viruses, fungi, and plants). The members of the family can contain one or many Ig domains, comprising two basic types: the constant domain (C), with seven strands, and the variable domain (V), with eight, nine, or ten strands. The different overviews of the IgSF led to the definition of new domain subtypes, mainly concerning the C type, based on the distribution of strands within the two sheets. The wide occurrence of the Ig fold and the much less conserved sequences could have developed from a common ancestral gene and/or from a convergent evolutionary process. Cell adhesion and pattern recognition seem to be the common feature running through the entire family. Received: 4 June 1997 / Accepted: 15 September 1997     

A simple correlation for predicting effective diffusivities in immobilized cell systems

A simple correlation method has been developed to predict effective diffusivities of small molecules in heterogeneous materials such as immobilized cell systems. This correlation uses a single diffusivity measurement at one cell volume fraction to predict diffusivities for any other volume fraction of cell. The method has been applied to 20 sets of published diffusivity measurements in immobilized cell systems and accurately predicts affective diffusivities of molecules for the full range of cell fractions. It may also be used to predict effective diffusivities in heterogeneous materials in which the diffusivity of a molecule in each phase and the volume fraction of each phase are known. (c) 1996 John Wiley & Sons, Inc.     

An experimental study of mass diffusion and reaction rate in an anaerobic biofilm

An experimental reactor consisting of two chambers, separated by a porous ceramic immobilization matrix, was constructed to measure the effective diffusivity of different compounds and the consumption rates of acetate in developing biofilms. In initial experiments, effective diffusivities for acetate, propionate, isopropanol, and lithium salt through the ceramic immobilization matrix in the absence of biofilm were determined to be 40% to 50% less than in water at infinite dilution. The effective diffusivity of the lithium salt was similar to that of acetate. The effective diffusivity of the lithium salt through biofilms of thickness in the range of 200 to 1200 mum was essentially constant with a value of approximately 7% of that in water at infinite dilution. Acetate consumption in the biofilm was linearly proportional to biofilm thickness up to a biofilm depth of 800 mum. Deviation from linearity appeared in biofilm thicknesses greater than 800 mum. Results of these experiments support previous reports that immobilized cell reactors have significantly higher bioconversion rates than suspended cell systems.     

满江红鱼腥藻的相对耐热性

利用加温处理引起藻丝叶绿素a可变荧光强度的变化,以测定满江红鱼腥藻(Anabaena azollae imbricata)的相对耐热性。藻丝在25℃下可变荧光和固定荧光的比值为0.35±0.05;在37℃下(5分钟),相应的比值为0.27;在45℃下比值降至0.11。在50℃下,叶绿素a可变荧光几乎完全消失。较高温度可能引起光合电子传递链成分的构象和功能的变化,减少了光能的利用。结果表明满江红鱼腥藻可以忍受37℃的温度。