前列腺癌鼠模型

前列腺癌鼠模型是研究前列腺癌的重要工具,目前常见以下4类：自发和诱发鼠模型,异种移植鼠模型,转基因鼠模型和基因敲除鼠模型。简要综述了前列腺癌鼠模型的研究进展。     

A complete enumeration and classification of two-locus disease models

There are 512 two-locus, two-allele, two-phenotype, fully penetrant disease models. Using the permutation between two alleles, between two loci, and between being affected and unaffected, one model can be considered to be equivalent to another model under the corresponding permutation. These permutations greatly reduce the number of two-locus models in the analysis of complex diseases. This paper determines the number of nonredundant two-locus models (which can be 102, 100, 96, 51, 50, or 58, depending on which permutations are used, and depending on whether zero-locus and single-locus models are excluded). Whenever possible, these nonredundant two-locus models are classified by their property. Besides the familiar features of multiplicative models (logical AND), heterogeneity models (logical OR), and threshold models, new classifications are added or expanded: modifying-effect models, logical XOR models, interference and negative interference models (neither dominant nor recessive), conditionally dominant/recessive models, missing lethal genotype models, and highly symmetric models. The following aspects of two-locus models are studied: the marginal penetrance tables at both loci, the expected joint identity-by-descent (IBD) probabilities, and the correlation between marginal IBD probabilities at the two loci. These studies are useful for linkage analyses using single-locus models while the underlying disease model is two-locus, and for correlation analyses using the linkage signals at different locations obtained by a single-locus model.     

壤中流模型研究的现状及存在问题

对国内外壤中流模型与模拟进行了较为系统的介绍,并针对这些模型提出了一种壤中流模型分类的方法,即根据模型所依据的主要原理将壤中流模型分为三大类：１）Ｒｉｃｈａｒｄｓ模型;２）动力波模型;３）贮水泄流模型．Ｒｉｃｈａｒｄｓ模型又可分为一维Ｒｉｃｈａｒｄｓ模型、二维Ｒｉｃｈａｒｄｓ模型和三维Ｒｉｃｈａｒｄｓ模型;贮水泄流模型又可分为动力贮水泄流模型和Ｂｏｕｓｉｎｅｓｑ贮水泄流模型．同时,将这３类模型进行对比,指出了它们各自优点和不足．     

Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences

Although phylogenetic inference of protein-coding sequences continues to dominate the literature, few analyses incorporate evolutionary models that consider the genetic code. This problem is exacerbated by the exclusion of codon-based models from commonly employed model selection techniques, presumably due to the computational cost associated with codon models. We investigated an efficient alternative to standard nucleotide substitution models, in which codon position (CP) is incorporated into the model. We determined the most appropriate model for alignments of 177 RNA virus genes and 106 yeast genes, using 11 substitution models including one codon model and four CP models. The majority of analyzed gene alignments are best described by CP substitution models, rather than by standard nucleotide models, and without the computational cost of full codon models. These results have significant implications for phylogenetic inference of coding sequences as they make it clear that substitution models incorporating CPs not only are a computationally realistic alternative to standard models but may also frequently be statistically superior.     

Relationships among recent models for insect population dynamics with variable rates of development

A classification scheme for those population models which allow variation in development rates is proposed, based on two ways of modifying standard age-structured models. The resulting classes of models are termed development index models and sojourn time models. General formulations for the two classes of models are developed from two basic balance equations, and numerous specific models from the literature are shown to fit into the scheme. Concepts from competing risks theory are shown to be important in understanding the interplay between mortality and maturation. Relationships among the classes are investigated both for the most general forms of the models and for the simpler forms often used. The scheme can provide guidance in developing appropriate insect population models for specific modelling situations.Contribution 3878871     

Generalizability of neotropical bird abundance and richness models

Predicting the consequences of land-cover change on tropical biotas is a pressing task. However, testing the applicability of models developed with data from one region to another region has rarely been done. Bird faunas were sampled along 3.0-km routes in southern Costa Rica (Coto Brus) to develop statistical models to describe the abundance and richness of groups as a function of land-cover characteristics. The relative value of the land-cover models was assessed by comparing them with null models. The generalizability of the models was tested with data from north-western Costa Rica (Monteverde) to determine whether the models were applicable to another area that has undergone significant land-cover change in the last 60 years. The richness and abundance of understory, open-country and edge non-insectivore groups showed clear relationships with land-cover variables, and the land-cover models had lower prediction errors than the null models for Coto Brus. With one exception, useful models for canopy birds, edge insectivores and hummingbirds could not be developed. The land-cover models of abundance of canopy insectivores, understory insectivores and non-insectivores, and edge non-insectivores were generalizable to Monteverde whereas the land-cover models of abundance of open-country birds and species richness for any of the groups were not better than null models for Monteverde. The results indicate that land-cover models that describe the abundance or richness of various bird groups provide useful predictions in the area where the data were collected and that models of abundance of some canopy, understory and edge birds may perform well in areas that are similar in elevation, life zones and land use to the area from which data were collected. Land-cover models of the abundance of other groups, and of the richness of the majority of groups, may be less generalizable to other areas, or it may be difficult to develop models at all.     

乳腺癌实验动物模型的制备与应用

乳腺癌实验动物模型在研究人类乳腺癌的生物学行为及治疗等方面起着非常重要的作用。根据制备方法及研究目的的不同,乳腺癌实验动物模型可分为自发性、诱发性、移植性、转基因性及乳腺癌骨转移等动物模型,每种动物模型都有各自的特点和应用条件。     

Context-Dependent Evolutionary Models for Non-Coding Sequences: An Overview of Several Decades of Research and an Analysis of Laurasiatheria and Primate Evolution

The past decade has seen a growing interest in evolutionary models that relax the assumption of site-independent evolution for non-coding sequences. While phylogenetic inference using such so-called context-dependent models is currently computationally prohibitive, these models have been shown to yield significant increases in model fit compared to site-independent evolutionary models, which remain the most widely used evolutionary models to study substitution patterns and perform phylogenetic inference. Context-dependent models have been shown to be suited to study the spontaneous deamination of cytosine in mammalian sequences. In this paper, I discuss various approaches presented in recent years to model context-dependent evolution. I start with discussing the empirical research and results that have led to the development of these models. To accurately estimate the context-dependent substitution patterns that arise from these models, accurate sampling of substitution histories under such models is required. Further, appropriate model selection techniques to assess model performance has become more important than ever, given the drastic increase in parameters of context-dependent models and the tendency of older model selection techniques to prefer parameter-rich models. I also present new results on two mammalian datasets (Primate and Laurasiatheria data) to shed a light on so-called lineage-dependent context-dependent evolution. I conclude this paper with a discussion on current challenges in the development of context-dependent modeling approaches.     

Shapes and functions of species–area curves (II): a review of new models and parameterizations

This paper has extended and updated my earlier list and analysis of candidate models used in theoretical modelling and empirical examination of species–area relationships (SARs). I have also reviewed trivariate models that can be applied to include a second independent variable (in addition to area) and discussed extensively the justifications for fitting curves to SARs and the choice of model. There is also a summary of the characteristics of several new candidate models, especially extended power models, logarithmic models and parameterizations of the negative-exponential family and the logistic family. I have, moreover, examined the characteristics and shapes of trivariate linear, logarithmic and power models, including combination variables and interaction terms. The choice of models according to best fit may conflict with problems of non-normality or heteroscedasticity. The need to compare parameter estimates between data sets should also affect model choice. With few data points and large scatter, models with few parameters are often preferable. With narrow-scale windows, even inflexible models such as the power model and the logarithmic model may produce good fits, whereas with wider-scale windows where inflexible models do not fit well, more flexible models such as the second persistence (P2) model and the cumulative Weibull distribution may be preferable. When extrapolations and expected shapes are important, one should consider models with expected shapes, e.g. the power model for sample area curves and the P2 model for isolate curves. The choice of trivariate models poses special challenges, which one can more effectively evaluate by inspecting graphical plots.     

Role of host fruit color in the behavior of the walnut fly Rhagoletis juglandis

Observations and sticky-trap tests were used to assess the effect of fruit color on the behavior of adult male and female Rhagoletis juglandis Cresson (Diptera: Tephritidae), a tephritid that infests husks of Arizona walnut in southeastern Arizona. In the first experiment, during which flies were observed foraging among walnut models suspended from small walnut trees, models were painted green to appear ripe and uninfested or yellow with brown patches to appear ripe and infested. Flies used for this first experiment were also of two types: prior to observations, one group of flies had access to real walnuts for 1.5 days (prior experience) while the other group of flies was held without real walnut fruits (no prior experience). Regardless of prior experience with real walnut fruits, female flies landed on green models more than yellow/brown models. Experienced males also were more likely to land on green models than on yellow/brown models. More interactions also occurred on green models, because there were more landings.In the field behavioral assay, flies from a natural population given a choice of green, yellow, and yellow/brown models landed most often on green models, and all interactions and oviposition attempts occurred on green models. Flies also distinguished models by color in field sticky trap assays.These results suggest that female response to ripeness cues is innate, while males develop a preference for green based on their encounter rate with females.     

On the generality of habitat distribution models: a case study of capercaillie in three Swiss regions

Predictive habitat distribution models are normally assumed to sacrifice generality for precision and reality. Nevertheless, such models are often applied to predict the distribution of a species outside the area for which the model has been calibrated.
We investigated how the geographic extent of the data used for calibration influenced the performance of habitat distribution models applied on independent data. We took a multi-scale logistic regression approach by varying the grain size to develop six habitat models for capercaillie Tetrao urogallus in Switzerland: three regional models, for the northern Pre-Alps, eastern Central Alps and Jura mountains, respectively, and three pooled models, each using data from two of the three regions. The six models were validated with data from the region(s) not used for model building. We used Cohen's Kappa and the area under the receiver operating characteristics curve as accuracy measures. The regional models performed well in the region where they had been calibrated, but poorly to moderately well in the other regions. The pooled models classified almost as well in their calibration regions as the corresponding regional models, but generally better when validated on data from the independent region. Hence, models built with data from single regions provide less certain predictions of species' distributions in other regions. We recommend building more general models using data pooled from several regions, when the aim is to predict species' distributions in independent regions.     

Comparative modeling and protein-like features of hydrophobic-polar models on a two-dimensional lattice

Lattice models of proteins have been extensively used to study protein thermodynamics, folding dynamics, and evolution. Our study considers two different hydrophobic-polar (HP) models on the 2D square lattice: the purely HP model and a model where a compactness-favoring term is added. We exhaustively enumerate all the possible structures in our models and perform the study of their corresponding folds, HP arrangements in space and shapes. The two models considered differ greatly in their numbers of structures, folds, arrangements, and shapes. Despite their differences, both lattice models have distinctive protein-like features: (1) Shapes are compact in both models, especially when a compactness-favoring energy term is added. (2) The residue composition is independent of the chain length and is very close to 50% hydrophobic in both models, as we observe in real proteins. (3) Comparative modeling works well in both models, particularly in the more compact one. The fact that our models show protein-like features suggests that lattice models incorporate the fundamental physical principles of proteins. Our study supports the use of lattice models to study questions about proteins that require exactness and extensive calculations, such as protein design and evolution, which are often too complex and computationally demanding to be addressed with more detailed models.     

Numerical simulations of stochastic circulatory models

Properties of two of the stochastic circulatory models theoretically introduced by Smith et al., 1997, Bull. Math. Biol. 59, 1–22 were investigated. The models assumed the gamma distribution of the cycle time under either the geometric or Poisson elimination scheme. The reason for selecting these models was the fact that the probability density functions of the residence time of these models are formally similar to those of the Bateman and gamma-like function models, i.e., the two common deterministic models. Using published data, the analytical forms of the probability density functions of the residence time and the distributions of the simulated values of the residence time were determined on the basis of the deterministic models and the stochastic circulatory models, respectively. The Kolmogorov-Smirnov test revealed that even for 1000 xenobiotic particles, i.e., a relatively small number if the particles imply drug molecules, the probability density functions of the residence time based on the deterministic models closely matched the distributions of the simulated values of the residence time obtained on the basis of the stochastic circulatory models, provided that parameters of the latter models fulfilled selected conditions.     

Ecological interpretations of the mid-domain effect

The suggestion that spatial gradients in species richness are influenced by geometric constraints resulting in the mid‐domain effect has been investigated by null models. The technical aspects of making such null models are well explored, but the implicit ecological assumptions behind these models are less explored. Four ecological models that all assume that species ranges are constrained by hard boundaries are made: evolutionary model, source‐sink model, dynamic‐environment model, and range‐size model. These models give different predictions that make it possible to separate the models from each other, and from a model that assumes that hard boundaries are not important.     

陆地植被净第一性生产力的研究

回顾了当前国内外陆地植被净第一性生产力（ＮＰＰ） 的研究现状，分析了３ 种生产力模型（ 气候相关模型、过程模型和光能利用率模型） 在应用于全球和区域生产力研究时的长处及不足：气候相关模型在气候变化研究中应用比较多，但计算的只是潜在ＮＰＰ；过程模型着重于植物生长的生理生态过程，但过于复杂，模型中的参数不易获得；光能利用率模型因为可直接利用遥感数据成为ＮＰＰ模型发展的一个主要方面．对国内ＮＰＰ的研究及遥感手段在ＮＰＰ研究中的应用进行了分析．     

Models of foot-and-mouth disease

During the 2001 foot-and-mouth disease outbreak in the UK, three very different models were used in an attempt to predict the disease dynamics and inform control measures. This was one of the first times that models had been used during an epidemic to support the decision-making process. It is probable that models will play a pivotal role in any future livestock epidemics, and it is therefore important that decision makers, veterinarians and farmers understand the uses and limitations of models. This review describes the utility of models in general before focusing on the three foot-and-mouth disease models used in 2001. Finally, the future of modelling is discussed, analysing the advances needed if models are to be successfully applied during any subsequent epidemics.     

Three dimensional printing as an effective method of producing anatomically accurate models for studies in thermal ecology

Hollow copper models painted to match the reflectance of the animal subject are standard in thermal ecology research. While the copper electroplating process results in accurate models, it is relatively time consuming, uses caustic chemicals, and the models are often anatomically imprecise. Although the decreasing cost of 3D printing can potentially allow the reproduction of highly accurate models, the thermal performance of 3D printed models has not been evaluated. We compared the cost, accuracy, and performance of both copper and 3D printed lizard models and found that the performance of the models were statistically identical in both open and closed habitats. We also find that 3D models are more standard, lighter, durable, and inexpensive, than the copper electroformed models.     

On the Use of Enterprise Models

This paper presents the results of a field study designed to determine how enterprise models are used. The paper begins with an introduction to enterprise models then provides an overview of the survey method used. No known empirical studies have been conducted to determine how enterprise models actually are used by industry. The research is designed to answer this question. A screening sample and complete web-based survey of 72 enterprise modelers was conducted. The primary research question of this survey was on the use of enterprise models, with particular focus on the three dimensions of living models: scope, enactment, and dynamicity. Half the respondents claim that their enterprise models were of their entire division, multiple divisions, and even multiple enterprises. It is encouraging to see that enterprise models are used on such a wide scope. The enactment of the enterprise models was not as large as was expected. Of the respondents, 75% claimed that their models did not receive information from the enterprise more frequently than quarterly. The same was true for how often the models provided information to the enterprise. Seventy-five percent did not update their models more than five times (although, 32% did update the model three to five times). Finally, additional areas of research are proposed.     

The uses of epidemic models.

This paper is concerned with models formulated to describe the spread of infectious diseases through a community. Some standard epidemic models are introduced and an overview of their uses is provided. The paper includes a discussion of the advantages of simple models over complex ones and the advantages of stochastic models over deterministic ones. The role that epidemic models can play in helping us to understand the spread of diseases and to plan control policies for diseases is explained. The paper also contains a review of some major insights gained from a study of epidemic models and from statistical analyses of disease data using epidemic models. Some explicit suggestions for future research projects are made.