An evolutionary computing approach for parameter estimation investigation of a model for cholera

We consider the problem of using time-series data to inform a corresponding deterministic model and introduce the concept of genetic algorithms (GA) as a tool for parameter estimation, providing instructions for an implementation of the method that does not require access to special toolboxes or software. We give as an example a model for cholera, a disease for which there is much mechanistic uncertainty in the literature. We use GA to find parameter sets using available time-series data from the introduction of cholera in Haiti and we discuss the value of comparing multiple parameter sets with similar performances in describing the data.     

Estimation of a Secondary Parameter in a Group Sequential Clinical Trial

In this article, we investigate estimation of a secondary parameter in group sequential tests. We study the model in which the secondary parameter is the mean of the normal distribution in a subgroup of the subjects. The bias of the naive secondary parameter estimator is studied. It is shown that the sampling proportions of the subgroup have a crucial effect on the bias: As the sampling proportion of the subgroup at or just before the stopping time increases, the bias of the naive subgroup parameter estimator increases as well. An unbiased estimator for the subgroup parameter and an unbiased estimator for its variance are derived. Using simulations, we compare the mean squared error of the unbiased estimator to that of the naive estimator, and we show that the differences are negligible. As an example, the methods of estimation are applied to an actual group sequential clinical trial, The Beta-Blocker Heart Attack Trial.     

Temperature‐dependent demography of Agriphila aeneociliella (Lepidoptera: Crambidae), a new insect pest of wheat in China

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Using regression coefficient as a stability parameter in plant breeding programs

Summary Expanding the regression coefficient as stability parameter (Finlay and Wilkinson 1963) requires an unbiased interpretation of the parameter. Information on the covariances among the genotypes of the population must be specific, particularly when the assumed relatedness of the genotypes appears questionable. Such a problem, however, is not expected when the covariances between the genotypes are either zero or equal and possibly non zero.     

Simultaneous identification of growth law and estimation of its rate parameter for biological growth data: a new approach

Scientific formalizations of the notion of growth and measurement of the rate of growth in living organisms are age-old problems. The most frequently used metric, “Average Relative Growth Rate” is invariant under the choice of the underlying growth model. Theoretically, the estimated rate parameter and relative growth rate remain constant for all mutually exclusive and exhaustive time intervals if the underlying law is exponential but not for other common growth laws (e.g., logistic, Gompertz, power, general logistic). We propose a new growth metric specific to a particular growth law and show that it is capable of identifying the underlying growth model. The metric remains constant over different time intervals if the underlying law is true, while the extent of its variation reflects the departure of the assumed model from the true one. We propose a new estimator of the relative growth rate, which is more sensitive to the true underlying model than the existing one. The advantage of using this is that it can detect crucial intervals where the growth process is erratic and unusual. It may help experimental scientists to study more closely the effect of the parameters responsible for the growth of the organism/population under study.     

胶州湾生物-物理耦合模型参数灵敏度分析

参数灵敏度分析旨在评价模型中各参数对模拟结果的影响程度,是参数优化和模型校正的基础步骤,也是认识模型行为的重要工具。所建的胶州湾生物-物理耦合模型包括浮游植物、浮游动物、营养盐、碎屑和溶解氧5类状态变量,对其涉及的50个参数进行灵敏度分析,得到3个非常灵敏性参数、2个灵敏性参数、11个比较灵敏性参数和34个不太灵敏性参数。非常灵敏及灵敏性参数包括浮游植物生长速率(μPRPC)、暗反应修正因子(FAC)、光饱和强度(α)、浮游植物死亡率(μDEPC)和水体消光系数(bla),主要影响浮游植物生长和死亡过程,反映了浮游植物在生态系统中的基础性和重要性作用。这5个参数显著地影响碳和营养盐循环,是整个胶州湾生态系统最主要的影响参数,应优先进行优化。比较灵敏性参数的影响主要表现在营养盐对浮游植物生长或死亡的限制以及温度对光饱和量的限制,浮游动物生长、牧食和死亡过程以及浮游植物生物量对牧食的限制,叶绿素a的生产,缺氧条件下沉积物释放磷以及浮游植物对磷的摄取等过程,这些参数对于各状态变量的灵敏性存在不同程度的差异,从而表征不同的特点。与不太灵敏性参数相关的过程主要为叶绿素a和碎屑消光作用,温度对浮游植物生长、浮游动物牧食、碎屑和沉积物矿化的限制,碎屑和沉积物矿化与沉降,与无机氮相关的大部分过程,溶解氧浓度变化等,这些过程除了受模型内部参数影响外,还在很大程度上受水深、海水温度和陆源污染等外部因素影响。比较灵敏及不太灵敏性参数影响模型局部过程,是模型校正的重要依据,除了非常灵敏及灵敏性参数以外,叶绿素a、浮游动物、碎屑和无机磷四种状态变量可分别根据叶绿素a最大生产系数(K CHmax)、浮游动物一级死亡率(μDEZC1)、有机碎屑矿化率(μREDC)和浮游植物磷摄取的半饱和常数(h UPPP)进行校正。与营养盐相关参数的灵敏度分析表明,胶州湾浮游植物处于磷限制,无机氮主要受陆源排污影响。因此,对无机氮的校正主要通过合理设置沿岸河流径流量或陆源污染物浓度与比例以及无机氮初始场。溶解氧对各参数均不太灵敏。     

Estimation of kinetic parameters for substrate and inhibitor in a reaction with an enzyme sample containing different types of inhibitor

The method of kinetic analysis is developed to obtain the maximum velocity (V_m), the Michaelis constant (K_m) and the parameters characterizing the inhibitors in an impure enzyme reaction, contaminated with one of four types of inhibitor (competitive, noncompetitive, uncompetitive and mixed-type). Although the reaction rate decreases with the increasing concentration of the enzyme sample containing an inhibitor, the double-reciprocal plot of the rate against the sample concentration becomes linear. The slopes of these linear plots at several different concentrations of substrate provide K_m and the specific enzyme activity, which is proportional to V_m, in the sample. These linear straight lines intersect in a point, of which the coordinates give the unique parameters for the inhibitor. To prove the validity of this kinetic method, the model experiments were carried out with acetylcholinesterase and its inhibitors, phenyltrimethylammonium and trimethylammonium. The present method was applied to the measurement of the specific activity of galactosylceramide galactosidase in the mouse cerebral homogenate. In addition, a kinetic method is indicated for the inhibition of an enzymatic reaction by a contaminant which binds the substrate to reduce the fraction available to the enzyme.     

Morphology of Aulacoseira filaments as indicator of the aquatic environment in a large subtropical river: The Pearl River,China

To identify new indicators of aquatic environmental parameters, both qualitative (the percentages of curved filaments and filaments with ending separation spines) and quantitative morphological parameters (filament and cell size) of a dominant chain colony-forming planktonic diatom (Aulacoseira granulata) were determined in the large, subtropical Pearl River, China. The qualitative parameters mainly exhibited a spatial pattern. The percentage of curved filaments was a good bioindicator of spatial patterns because it varied along the nutrient gradient. Furthermore, the percentage of filaments with ending separation spines was a good bioindicator of seasonal variation. Although the quantitative parameters exhibited a clear temporal pattern, no single parameter could be used as a bioindicator of either spatial or temporal patterns. The link between qualitative and quantitative parameters reflected the internal adaptation mechanism of filamentous diatoms to the external environment. The methods of the present study can also be applied to ecological indicators in other aquatic ecosystems dominated by chain colony-forming diatoms.     

Marginal regression analysis of a multivariate binary response

We propose the use of the mean parameter for regression analysisof a multivariate binary response. We model the associationusing dependence ratios defined in terms of the mean parameter,the components of which are the joint success probabilitiesof all orders. This permits flexible modelling of higher-orderassociations, using maximum likelihood estimation. We reanalysetwo data sets, one with variable cluster size and the othera longitudinal data set with constant cluster size.     

Crown profile of foliage area characterized with the Weibull distribution in a hinoki (Chamaecyparis obtusa) stand

Summary Thirten sample trees of various sizes in a 29-year-old hinoki [Chamaecyparis obtusa (Sieb, et Zucc.) Endl.] plantation were felled and subjected to the stratified clip technique. Crown profile of foliage area fitted well with the Weibull distribution. The crown profile tended to be more skewed toward the top of crowns in smaller trees than in larger trees. This tendency was reflected in the value of the shape parameter of the Weibull distribution. The shape parameter ranged from 1.73 to 3.23 and gradually increased up to an asymptotic value with an increase of stem diameter at breast height. The scale parameter of the distribution ranged from 1.0 to 4.2 and tended to increase in proportion to stem diameter at breast height. Foliage area of a tree correlated well with stem diameter at breast height through an ordinary allometric equation. Tree height could be approximated fairly well by a generalized allometric equation as a function of stem diameter at breast height. On the basis of the census of stem diameter at breast height, canopy profile could be constructed synthesizing crown profiles of foliage area for individual trees in the stand. Leaf area index was estimated to be 6.6 ha ha^–1.     

16S rDNA-based characterization of BTX-catabolizing microbial associations isolated from a South African sandy soil

In the presence of different selection pressures, particularly pHand electron donor concentration, indigenous microbial associations which catabolize selected petroleum hydrocarbon components (benzene, toluene and o-, m- and p-xylene (BTX)) were enriched and isolated from a petroleum hydrocarbon-contaminated KwaZulu-Natal sandy soil. Electron microscopy revealed that, numerically, rods constituted the majority of the populations responsible for BTX catabolism. Molecular techniques (polymerase chain reaction (PCR) and 16S rDNA fingerprinting by denaturing-gradient gel electrophoresis (DGGE)) were employed to explore the diversities and analyze the structures of the isolated microbial associations. Pearson product-moment correlation indicated that the different, but chemically similar, petroleum hydrocarbon molecules, effectedthe isolation of different associations. However, some similar numerically-dominant bands characterized the associations. A 30% similarity was evident between the m- and o-xylene-catabolizing associations regardless of the molecule concentration and the enrichment pH. PCR-DGGE was also used to complement conventional culture-based microbiological procedures for environmental parameter optimization. Band pattern differencesindicated profile variations of the isolated associations which possibly accounted for the growth rate changes recorded in response to pH and temperature perturbations.     

Protein: A proposal for a standard parameter to express cyanobacterial biomass in laboratory experiments

This study aims to check if the protein content of a cyanobacterial culture is a reliable biomass parameter for cyanobacteria in laboratory experiments, and therefore can be proposed as a standard biomass parameter in culture work to facilitate comparison of results from different studies. For this purpose, the cyanobacteria Microcystis aeruginosa PCC 7806 and Planktothrix agardhii PT2 were grown in 10-L batch cultures with O2 medium and under iron-, nitrate- or phosphate-limited conditions. A linear correlation was found between protein and biovolume in all cultures during exponential growth. We conclude that protein is a suitable biomass parameter for cyanobacteria in laboratory experiments during balanced growth.     

粉质质量指数在冬小麦面团品质及烘烤品质中的应用价值研究

为了进一步了解粉质质量指数在小麦面团品质和烘烤品质评价中的作用,对90份冬小麦样品的粉质质量指数(FQN)与揉混仪参数、拉伸仪参数和面包品质参数之间的相关关系进行了研究。结果表明：FQN与揉混仪参数(峰值时间、峰值面积、8min尾高和斜率)有极显著的正相关关系,且以线性相关为主,可以用于评价小麦粉的耐揉性和筋力;FQN与拉伸曲线面积和最大拉伸阻力有较好的相关关系,但与延伸度相关性较小,且以非线性相关为主。因此,FQN不能很好地进行评价面团的拉伸特性;FQN与面包体积、面包评分和面包坚实度有一定的非线性相关关系,FQN可以用作评价面包烘烤品质的参数指标。     

Parametric sensitivity analysis and reduction of a detailed nutritional model of plant cell cultures

A kinetic model of plant nutrition described by Cloutier et al. (Cloutier et al., 2008. Biotechnol Bioeng 99:189-200) is progressively simplified so as to obtain a predictive model that describes the evolution of the biomass and the extracellular and intracellular concentrations of three determining nutrients, that is, free intracellular nitrogen, phosphate, and carbohydrate compounds. Three techniques of global sensitivity analysis are successively applied to assess the model parameter influence and potential correlation. The resulting dynamic model is able to predict plant growth for the two most encountered plant bioprocesses, namely suspension cells and hairy roots.     

马尾松毛虫高海拔种群发生对光周期的响应:基于年龄-时期、两性生命表分析

马尾松毛虫Dendrolimus punctatus Walker是南方林业重大害虫,目前对其在高海拔区(>700 m)的发生特点仍不清楚。本研究从湖南绥宁(26.35°N,110.09°E)高海拔区采虫,放在5个光周期处理下饲养,以年龄-时期、两性生命表法计算种群参数,揭示光周期对该种群发生的影响。结果显示:L∶D=15.5∶8.5(15.5 h)和L∶D=14.5∶9.5(14.5 h)光周期处理组种群发生正常,而L∶D=11.5∶12.5(11.5 h)、L∶D=12.5∶11.5(12.5 h)和L∶D=13.5∶10.5(13.5 h)光周期处理组未观察到成虫发生。15.5 h组内禀增长率(r)为0.057 d-1,净生殖力(R0)为55.73粒,单雌产卵力(fecundity)为241.5粒,平均世代时间T为71.05 d,14.5 h组r为0.018 d-1,R0为6.29粒,显著低于15.5 h组。该种群在14.5 h光周期处理下表现出分散繁殖行为,即出现两个繁殖期,时差1个月左右。与15.5 h处理组相比,14.5 h处理组成虫寿命显著缩短。该研究表明:马尾松毛虫高海拔种群对光周期变化响应强烈,而湖南绥宁光周期在7月底就开始变短,当地马尾松毛虫在这种光周期诱导下较早进入滞育发育,因而种群年发生仅一代。