Tests of the heterosis model

Summary An alternative to the classical model of self-incompatibility indicates that genetic control of self-incompatibility could involve more than one locus and function through passive failure of incompatible pollen tubes rather than through their active inhibition. Both aspects of the alternative model have been tested and, in each case, the data support the classical single-locus oppositional interpretation rather than the alternative. On the basis of these data, and others now available, we conclude that, in the Solanaceae, and presumably also in some others, self-incompatibility is better explained by the classical interpretation. Several points, however, remain to be resolved.     

用度量误差模型方法编制相容的生长过程表和材积表

指出了按照常规方法建立的生长模型和材积模型不相容的原因、利用两阶段度量误差模型方法估计生长模型和材积模型的参数,进而编制相容的生长过程表和材积表．     

Forecasting with the age-period-cohort model and the extended chain-ladder model

We consider forecasting from age-period-cohort models, as wellas from the extended chain-ladder model. The parameters of thesemodels are known only to be identified up to linear trends.Forecasts from such models may therefore depend on arbitrarylinear trends. A condition for invariant forecasts is proposed.A number of standard forecast models are analysed.     

On the mechanistic underpinning of discrete-time population models with complex dynamics

We present a mechanistic underpinning for various discrete-time population models that can produce limit cycles and chaotic dynamics. Specific examples include the discrete-time logistic model and the Hassell model, which for a long time eluded convincing mechanistic interpretations, and also the Ricker- and Beverton-Holt models. We first formulate a continuous-time resource consumption model for the dynamics within a year, and from that we derive a discrete-time model for the between-year dynamics. Without influx of resources from the outside into the system, the resulting between-year dynamics is always overcompensating and hence may produce complex dynamics as well as extinction in finite time. We recover a connection between various standard types of continuous-time models for the resource dynamics within a year on the one hand and various standard types of discrete-time models for the population dynamics between years on the other. The model readily generalizes to several resource and consumer species as well as to more than two trophic levels for the within-year dynamics.     

On the mechanistic underpinning of discrete-time population models with Allee effect

The Allee effect means reduction in individual fitness at low population densities. There are many discrete-time population models with an Allee effect in the literature, but most of them are phenomenological. Recently, Geritz and Kisdi [2004. On the mechanistic underpinning of discrete-time population models with complex dynamics. J. Theor. Biol. 228, 261-269] presented a mechanistic underpinning of various discrete-time population models without an Allee effect. Their work was based on a continuous-time resource-consumer model for the dynamics within a year, from which they derived a discrete-time model for the between-year dynamics. In this article, we obtain the Allee effect by adding different mate finding mechanisms to the within-year dynamics. Further, by adding cannibalism we obtain a higher variety of models. We thus present a generator of relatively realistic, discrete-time Allee effect models that also covers some currently used phenomenological models driven more by mathematical convenience.     

Score Test for Conditional Independence Between Longitudinal Outcome and Time to Event Given the Classes in the Joint Latent Class Model

Summary .  Latent class models have been recently developed for the joint analysis of a longitudinal quantitative outcome and a time to event. These models assume that the population is divided in  G  latent classes characterized by different risk functions for the event, and different profiles of evolution for the markers that are described by a mixed model for each class. However, the key assumption of conditional independence between the marker and the event given the latent classes is difficult to evaluate because the latent classes are not observed. Using a joint model with latent classes and shared random effects, we propose a score test for the null hypothesis of independence between the marker and the outcome given the latent classes versus the alternative hypothesis that the risk of event depends on one or several random effects from the mixed model in addition to the latent classes. A simulation study was performed to compare the behavior of the score test to other previously proposed tests, including situations where the alternative hypothesis or the baseline risk function are misspecified. In all the investigated situations, the score test was the most powerful. The methodology was applied to develop a prognostic model for recurrence of prostate cancer given the evolution of prostate-specific antigen in a cohort of patients treated by radiation therapy.     

物种分布模型在海洋潜在生境预测的应用研究进展

海洋生物的栖息分布与环境要素的关联性一直是海洋生态学研究的热点之一.近年来,物种分布模型被广泛应用于预测海洋物种分布、潜在适宜性生境评价等研究,为保护海洋生物多样性、防治外来物种入侵及制定渔业管理措施等提供了一条有效途径.物种分布模型主要包括生境适宜性指数模型、机理模型和统计模型.本文对物种分布模型的理论基础进行了归纳和总结,回顾了物种分布模型在预测海洋物种潜在地理分布研究中的开发与应用,重点介绍了不同类型统计模型在海洋物种潜在分布预测中的研究实例.比较各种选取变量和模型验证方法,认为赤池信息准则对于选取模型变量具有优势,Kappa系数和受试者操作特征曲线下面积在验证模型精度中应用最广泛.阐述了物种分布模型存在的问题及未来发展趋势,随着海洋生物生理机制研究的进一步深入,机理模型将是今后物种分布模型发展的重点.     

Numerical model (switchable/dual model) of the human head for rigid body and finite elements applications

In this paper, a methodology for the development and validation of a numerical model of the human head using generic procedures is presented. All steps required, starting with the model generation, model validation and applications will be discussed. The proposed model may be considered as a dual one due to its capabilities to switch from deformable to a rigid body according to the application's requirements. The first step is to generate the numerical model of the human head using geometry files or medical images. The required stiffness and damping for the elastic connection used for the rigid body model are identified by performing a natural frequency analysis. The presented applications for model validation are related to impact analysis. The first case is related to Nahum's (Nahum and Smith 1970) experiments pressure data being evaluated and a pressure map generated using the results from discrete elements. For the second case, the relative displacement between the brain and the skull is evaluated according to Hardy's (Hardy WH, Foster CD, Mason, MJ, Yang KH, King A, Tashman S. 2001.Investigation of head injury mechanisms using neutral density technology and high-speed biplanar X-ray. Stapp Car Crash J. 45:337–368, SAE Paper 2001-22-0016) experiments. The main objective is to validate the rigid model as a quick and versatile tool for acquiring the input data for specific brain analyses.     

Randomization and Additivity in the Two-Period Crossover Clinicial Trial

In certain areas of medical research, the two-period crossover design is a frequent choice for comparing treatments A and B in a randomized clinical trial. Earlier work by Grizzle and by Brown was based upon a parametric theory linear model. Recently, the present authors employed D. R. Cox's additive randomization models and, for the case of zero residual effect, found a discrepancy between it and the parametric model with respect to the precision of period effects. In the present note, this divergence is accounted for by allowing for the possibility of non-additivity through the use of a completely general randomization model. It is concluded that the structure of the crossover design is such that use of the parametric theory linear model is required if a single, consistent model is desired.     

On the Use of Bayesian Methods for Evaluating Compartmental Neural Models

Computational modeling is being used increasingly in neuroscience. In deriving such models, inference issues such as model selection, model complexity, and model comparison must be addressed constantly. In this article we present briefly the Bayesian approach to inference. Under a simple set of commonsense axioms, there exists essentially a unique way of reasoning under uncertainty by assigning a degree of confidence to any hypothesis or model, given the available data and prior information. Such degrees of confidence must obey all the rules governing probabilities and can be updated accordingly as more data becomes available. While the Bayesian methodology can be applied to any type of model, as an example we outline its use for an important, and increasingly standard, class of models in computational neuroscience—compartmental models of single neurons. Inference issues are particularly relevant for these models: their parameter spaces are typically very large, neurophysiological and neuroanatomical data are still sparse, and probabilistic aspects are often ignored. As a tutorial, we demonstrate the Bayesian approach on a class of one-compartment models with varying numbers of conductances. We then apply Bayesian methods on a compartmental model of a real neuron to determine the optimal amount of noise to add to the model to give it a level of spike time variability comparable to that found in the real cell.     

The relationship between the transition matrix model and the diffusion model

The diffusion equation model and the Lefkovitch matrix model have been employed independently in plant population ecology in order to analyze the dynamics of growth and size structure. The two models describe the dynamics of size structure in biological populations, and thus there must be some relationship between them. In the present paper, we examine the theoretical relationship between these two models. We demonstrate, on a certain assumption, that the one-step Lefkovitch matrix model corresponds to a difference equation of the diffusion equation and that the two- and three-step Lefkovitch matrix model correspond to difference equations of the 4th- and 6th-order Kramers-Moyal expansions, respectively. It is also shown that 2n moments (the first to the 2n-th moments) of growth rate are necessary and sufficient to rewrite uniquely the n-step Lefkovitch matrix model in terms of the linear combination of the moments. We finally discuss the relationship between the species characteristics of census data and the appropriate types of the Lefkovitch matrix.     

A model evaluating the contribution of environmental factors to the production of resting eggs in the rotifer Brachionus plicatilis

The production of resting eggs by the rotifer Brachionus plicatilis was tested at four salinities (9, 18, 27 and 36\%) and six concentrations of the alga Chlorella stigmatophora (0.25, 0.5, 1.0, 2.0, 4.0 and 6.0 × 10⁶ cells ml^–1). The results indicated that resting eggs were produced only at two salinities (9\% and 18\%) and that their number was affected by the amount of food provided. A model consisting of two generalized linear sub-models was built to evaluate the contribution of each of the tested food concentrations at the two salinities. The sub-models were used to distinguish between two different components of resting egg production: one related to the presence or absence of resting egg production, and the other to the number of resting eggs produced, given that production had occurred. Besides indicating the best combination of salinity and food concentration for obtaining large numbers of resting eggs, they revealed the contribution of internal population factors that were not controlled in the course of the experiment. The model identified the positive contribution of the relative number of females to males, and the negative association between high rotifer densities and the production of resting eggs. The results of the present study help in defining the optimal conditions for mass production of resting eggs, which are of potential importance in aquaculture.Deceased, September 1991.     

相关遗传力抽样方差的估计

本文给出了单因子组和系统模型下有关相关传力及相关环境力抽样方差的估计方法。有关该参数在育种中的潜在应用其它与遗传相关之产间的相互关系也给予了一定的讨论。概括地来讲,相关遗传力具有遗传力和遗传相关的双重特征。遗传力是相关遗传力的一个特例而相关遗传力则是遗传力概念本身的扩展。用相关遗传力来表达性状间的相关遗传变异要比通常所用的遗传相关更准确一些。     

Genetic admixture in the Late Pleistocene

The replacement hypothesis of modern human origins holds that the original population of modern humans expanded throughout the world, replacing existing archaic populations as it went. If this expanding population interbred with the peoples it replaced, then some archaic mitochondria might have been introduced into the early modern gene pool. Such mitochondria would be recognizable today because they should differ from other modern mitochondria at several times the number of sites that we are used to seeing in pairwise comparisons. In this paper we ask what can be inferred from the absence of these “divergent” mitochondria from modern samples. We show that if the effective number of females in our species has been large for the past 40,000 years, then the level of admixture must have been low. For example, if this effective number exceeded 1.6 million, then we can reject the hypothesis that more more than 2/1,000 of the mitochondria in the early modern population derived from admixture with archaic peoples. We argue elsewhere that regional continuity would be detectable in the fossil record only if the rate of admixture exceeded 76%. Here, we show that this level of admixture would require the effective female size of the human population to have been less than 1,777 for the past 40,000 years. © 1996 Wiley-Liss, Inc.     

Modelling the effect of urbanization on the transmission of an infectious disease

This paper models the impact of urbanization on infectious disease transmission by integrating a CA land use development model, population projection matrix model and CA epidemic model in S-Plus. The innovative feature of this model lies in both its explicit treatment of spatial land use development, demographic changes, infectious disease transmission and their combination in a dynamic, stochastic model. Heuristically-defined transition rules in cellular automata (CA) were used to capture the processes of both land use development with urban sprawl and infectious disease transmission. A population surface model and dwelling distribution surface were used to bridge the gap between urbanization and infectious disease transmission. A case study is presented involving modelling influenza transmission in Southampton, a dynamically evolving city in the UK. The simulation results for Southampton over a 30-year period show that the pattern of the average number of infection cases per day can depend on land use and demographic changes. The modelling framework presents a useful tool that may be of use in planning applications.     

Reliability Analysis of the Groundwater Conceptual Model

The hydrologic model is the foundation of water resource management and planning. Conceptual model is the essential component of groundwater model. Due to limited understanding of natural hydrogeological conditions, the conceptual model is always constructed incompletely. Therefore, the uncertainty in the model's output is evitable when natural groundwater field is simulated by a single groundwater model. A synthetic groundwater model is built and regarded as the true model, and three alternative conceptual models are constructed by considering incomplete hydrogeological conditions. The outputs (groundwater budget terms from boundary conditions) of these groundwater models are analyzed statistically. The results show that when the conceptual model is closer to the true hydrogeological conditions, the distributions of outputs of the groundwater model are more concentrated on the true outputs. Therefore, the more reliable the structure of the conceptual model is, the more reliable the output of the groundwater model is. Moreover, the uncertainty caused by the conceptual model cannot be compensated by parameter uncertainty.     

A simple model of the eco-hydrodynamics of the epilimnion of Lake Tanganyika

1. The ecosystem response of Lake Tanganyika was studied using a four-component, nutrient–phytoplankton–zooplankton–detritus, phosphorus-based ecosystem model coupled to a nonlinear, reduced-gravity, circulation model. The ecosystem model, an improved version of the earlier eco-hydrodynamics model developed for Lake Tanganyika, was used to estimate the annual primary production of Lake Tanganyika and its spatial and temporal variability. The simulations were driven with the National Centres for Environmental Protection (NCEP) records for winds and solar radiation forcing.
2. The simulated annual cycles of the four ecosystem variables and the daily net primary production were compared with the observations. The comparison showed that simulations reproduced realistically the general features of the annual cycles of epilimnial phosphate, net primary production and plankton dynamics.
3. The climatic simulations for the years 1970–2006 yielded a daily averaged integrated upper layer net production ranging from 0.11 to 1.78 g C m⁻² day⁻¹ and daily averaged chlorophyll- a (chl- a ) from 0.16 to 4.3 mg m⁻³. Although the nutrient concentrations in the epilimnion during the strong wind years were high, the net production was low, which is partly because of the greater vertical mixing, produced by strong winds, exposing the phytoplankton to low light conditions in deeper waters. The simulated annual net production and chl- a agreed quite well with observed production available in the literature.
4. We envisage using this model to predict the future scenarios of primary productivity in the lake.     

模式动物斑马鱼在神经系统疾病研究中的应用

近年来,斑马鱼作为一种新型模式动物被广泛地应用于发育学、遗传学、行为学和分子生物学等研究领域。其具有繁殖能力强、发育迅速且同步、体外受精和幼体透明等生物学和形态学特点,经广泛培养和筛选突变品种,目前斑马鱼品系资源丰富。与其他非脊椎模式动物相比,它与人类有更高的同源性。本文主要介绍斑马鱼作为一种理想的模式动物,结合其特殊的行为学检测手段和分子生物学特点,在研究神经系统疾病的发病机制、构建疾病模型和相应药物筛选等方面的应用。     

Equivariant Estimation for the Parameters of an Exponential Model Based on Censored Sampling

Lehmann (1983) provides a detailed discussion on equivariant estimation of the parameters of location, scale and location-scale models. Edwin Prabakaran and Chandrasekar (1994) developed simultaneous equivariant estimation approach and illustrated the method with examples. In this paper, we consider exponential models and obtain minimum risk equivariant estimators of the parameters based on Type II censored samples. The equivariant method of estimation is illustrated with biological and reliability applications.