Quality-of-life indicators at different scales: Theoretical background

The article is presenting the general analysis of the systems approach and model approaches for the development of QoL indicators and indices. In our study we propose the method of response function as a method of the construction of purposeful, credible integrated models from data and prior knowledge or information. The method of response function implies credible models in the sense that they are identifiable, and, hopefully, explains system output behaviour satisfactorily.Using response function method for the development of QoL models, we are able to obtain QoL indices as the direct output of the models.     

Multi-scale modelling and the IUPS physiome project

We review the development of models of cellular and tissue function and in particular address issues of multi-scale modelling, including the transition from stochastic models to continuum models and the incorporation of cell and tissue structure. The heart is used as an example of linking models at the molecular level to cell, tissue and organ level function.     

The Input Signal Step Function (ISSF), a Standard Method to Encode Input Signals in SBML Models with Software Support, Applied to Circadian Clock Models

Time-dependent light input is an important feature of computational models of the circadian clock. However, publicly available models encoded in standard representations such as the Systems Biology Markup Language (SBML) either do not encode this input or use different mechanisms to do so, which hinders reproducibility of published results as well as model reuse. The authors describe here a numerically continuous function suitable for use in SBML for models of circadian rhythms forced by periodic light-dark cycles. The Input Signal Step Function (ISSF) is broadly applicable to encoding experimental manipulations, such as drug treatments, temperature changes, or inducible transgene expression, which may be transient, periodic, or mixed. It is highly configurable and is able to reproduce a wide range of waveforms. The authors have implemented this function in SBML and demonstrated its ability to modify the behavior of publicly available models to accurately reproduce published results. The implementation of ISSF allows standard simulation software to reproduce specialized circadian protocols, such as the phase-response curve. To facilitate the reuse of this function in public models, the authors have developed software to configure its behavior without any specialist knowledge of SBML. A community-standard approach to represent the inputs that entrain circadian clock models could particularly facilitate research in chronobiology.     

The theory of population dynamics—II. Physiological delays

Traditional population models describe changes in population size as a function of changes in the resources. Such first-order models cannot describe certain properties of population dynamics. General models with delays can account for all the observed dynamic complexities but are judged overgeneralized. It is proposed that the simplest model of intermediate complexity that explains such dynamic properties is a second-order model, which describes population dynamics as a function of a physiological variable, the dynamics of which in turn depends on resources. Data on accelerated decline of populations in the absence of food from experiments with brown and green hydra as well as literature data support the arguments.     

On the origin of DNA genomes: evolution of the division of labor between template and catalyst in model replicator systems

The division of labor between template and catalyst is a fundamental property of all living systems: DNA stores genetic information whereas proteins function as catalysts. The RNA world hypothesis, however, posits that, at the earlier stages of evolution, RNA acted as both template and catalyst. Why would such division of labor evolve in the RNA world? We investigated the evolution of DNA-like molecules, i.e. molecules that can function only as template, in minimal computational models of RNA replicator systems. In the models, RNA can function as both template-directed polymerase and template, whereas DNA can function only as template. Two classes of models were explored. In the surface models, replicators are attached to surfaces with finite diffusion. In the compartment models, replicators are compartmentalized by vesicle-like boundaries. Both models displayed the evolution of DNA and the ensuing division of labor between templates and catalysts. In the surface model, DNA provides the advantage of greater resistance against parasitic templates. However, this advantage is at least partially offset by the disadvantage of slower multiplication due to the increased complexity of the replication cycle. In the compartment model, DNA can significantly delay the intra-compartment evolution of RNA towards catalytic deterioration. These results are explained in terms of the trade-off between template and catalyst that is inherent in RNA-only replication cycles: DNA releases RNA from this trade-off by making it unnecessary for RNA to serve as template and so rendering the system more resistant against evolving parasitism. Our analysis of these simple models suggests that the lack of catalytic activity in DNA by itself can generate a sufficient selective advantage for RNA replicator systems to produce DNA. Given the widespread notion that DNA evolved owing to its superior chemical properties as a template, this study offers a novel insight into the evolutionary origin of DNA.     

The shifts in species composition and ecological modelling in hydrobiology

Ecosystems have an enormous flexibility to meet changes in external factors and still maintain their functions. If present species are not able to cope with the conditions, given by the external factors, new species are waiting in the wings ready to take over. It is a serious shortcoming of our present ecological models, that they are not able to describe these changes in species composition. However, it seems that the thermodynamic function exergy may be used as goal function in ecological models to incorporate the flexibility of real ecosystems and the selection of species into our models of ecosystems. The application of exergy in modelling may be considered a translation of Darwin's selection into thermodynamics. The theoretical basis for the application of exergy as goal function is presented, and applications of exergy in ecological models are illustrated by several case studies.     

人类疾病动物模型是医药创新研究的前沿

人类疾病动物模型对医药研究起着支撑作用,是进行医药研究的必备工具之一.本文阐述了人类疾病动物模型在医药研究中所能发挥的作用,以及在医药研究的历史中所做出的贡献.最后,对疾病动物模型在医药创新研究中应用的前沿进行了展望.     

A general class of Bayesian survival models with zero and nonzero cure fractions

We propose a new class of survival models which naturally links a family of proper and improper population survival functions. The models resulting in improper survival functions are often referred to as cure rate models. This class of regression models is formulated through the Box-Cox transformation on the population hazard function and a proper density function. By adding an extra transformation parameter into the cure rate model, we are able to generate models with a zero cure rate, thus leading to a proper population survival function. A graphical illustration of the behavior and the influence of the transformation parameter on the regression model is provided. We consider a Bayesian approach which is motivated by the complexity of the model. Prior specification needs to accommodate parameter constraints due to the non-negativity of the survival function. Moreover, the likelihood function involves a complicated integral on the survival function, which may not have an analytical closed form, and thus makes the implementation of Gibbs sampling more difficult. We propose an efficient Markov chain Monte Carlo computational scheme based on Gaussian quadrature. The proposed method is illustrated with an example involving a melanoma clinical trial.     

Hypothesis testing in semiparametric additive mixed models

We consider testing whether the nonparametric function in a semiparametric additive mixed model is a simple fixed degree polynomial, for example, a simple linear function. This test provides a goodness-of-fit test for checking parametric models against nonparametric models. It is based on the mixed-model representation of the smoothing spline estimator of the nonparametric function and the variance component score test by treating the inverse of the smoothing parameter as an extra variance component. We also consider testing the equivalence of two nonparametric functions in semiparametric additive mixed models for two groups, such as treatment and placebo groups. The proposed tests are applied to data from an epidemiological study and a clinical trial and their performance is evaluated through simulations.     

陆地碳循环研究中植物生理生态过程模拟进展

植物生理生态过程的模拟是陆地碳循环模型研究中的关键过程之一,就与碳循环过程密切相关的3个关键的植物生理生态过程;光合作用,碳分配和物候等过程的数学模式进行分类：（1）光合作用模式,根据光合作用模式基础的不同把光合作用模式分为：半经验模式;机理模式和使用卫星遥感资料的模式等;（2）植物碳分配模式介绍了功能平衡模式;运输-阻力模式;光合作用与生长模式;环境反应模式和大尺度生态系统模式等5类。（3）植被物候模式;根据观测和参数化方法的不同可以将现有的物候数值模式分为两类;观测统计模式和使用卫星遥感资料的物候模式,对各类模式的主要控制方程,研究进展和应用分别进行了简要评述。     

Rodent models based on endolysosomal genes involved in Parkinson's disease

Genes associated with endolysosomal function have been recently associated with familial Parkinson's disease and described as risk factors for sporadic cases. This indicates that deficits in this pathway predispose to parkinsonism. To better understand the role of these genes in disease development, rodent models have been created by targeting genes playing a role in endolysosomal function, such as LRRK2, DNAJC6, SYNJ1, VPS35, GBA1, ATP13A2 and TMEM175. Here, we review the latest findings describing parkinsonian features in these animal models secondary to endolysosomal dysfunction. Also, we provide suggestions for further development and application of these animal models to better understand the contribution of endolysosomal dysfunction in Parkinson's disease and provide novel models for testing therapeutic approaches.     

利用线性混合效应模型模拟杉木人工林枝条生物量

基于福建省将乐林场45株人工杉木解析木的572组枝条生物量数据,采用线性混合效应模型方法,建立杉木人工林枝条总生物量和枝、叶生物量的预测模型,并利用独立样本数据对模型进行检验.结果表明： 线性混合效应模型比传统多元线性回归模型的拟合精度高.不同随机效应参数的组合,其混合模型的精度不同.考虑异方差结构的混合模型能够消除数据间的异方差性,其精度更高,其中,对于枝条总生物量和叶生物量模型,以指数函数作为异方差结构时的模型精度最高;对于枝生物量模型,以常数加幂函数作为异方差结构时的模型精度最高.模型检验结果表明：对于杉木人工林枝条生物量预测模型,考虑随机效应和异方差结构的线性混合模型的检验精度比传统多元线性回归模型的精度有明显提高.     

Experimental tests of sex allocation theory with two species of simultaneously hermaphroditic acorn barnacles

Sex allocation theory for simultaneous hermaphrodites predicts increases in relative allocation to male-specific function as competition for fertilizations increases. Theoretical models developed specifically for competing acorn barnacles predict that the proportional allocation to male function increases toward an asymptote of 50% as the number of competitors for fertilizations increases. Experimental manipulations were used to investigate how mate competition affected both relative and absolute allocation to the sex functions for two species of acorn barnacle: Semibalanus balanoides and Balanus glandula. The ratio of male to female allocation did not increase with the number of competitors for either species. However, both species showed increased allocation to male function (estimated as total mass of sex-specific tissues) with increased crowding. Allocation to female function seemed to be limited by other factors and did not vary with mating group size as predicted. Allocation to male and female function were both positively related to body size, but a trade-off between male and female function, a key assumption of prior models, was not observed.     

The effect of intracortical competition on the formation of topographic maps in models of Hebbian learning

Correlation-based learning (CBL) models and self-organizing maps (SOM) are two classes of Hebbian models that have both been proposed to explain the activity-driven formation of cortical maps. Both models differ significantly in the way lateral cortical interactions are treated, leading to different predictions for the formation of receptive fields. The linear CBL models predict that receptive field profiles are determined by the average values and the spatial correlations of the second order of the afferent activity patterns, wheras SOM models map stimulus features. Here, we investigate a class of models which are characterized by a variable degree of lateral competition and which have the CBL and SOM models as limit cases. We show that there exists a critical value for intracortical competition below which the model exhibits CBL properties and above which feature mapping sets in. The class of models is then analyzed with respect to the formation of topographic maps between two layers of neurons. For Gaussian input stimuli we find that localized receptive fields and topographic maps emerge above the critical value for intracortical competition, and we calculate this value as a function of the size of the input stimuli and the range of the lateral interaction function. Additionally, we show that the learning rule can be derived via the optimization of a global cost function in a framework of probabilistic output neurons which represent a set of input stimuli by a sparse code. Received: 23 June 1999 / Accepted in revised form: 05 November 1999     

Sensitivity of model predictions of muscle function to changes in moment arms and muscle-tendon properties: a Monte-Carlo analysis

Hill-type muscle models are commonly used in musculoskeletal models to estimate muscle forces during human movement. However, the sensitivity of model predictions of muscle function to changes in muscle moment arms and muscle-tendon properties is not well understood. In the present study, a three-dimensional muscle-actuated model of the body was used to evaluate the sensitivity of the function of the major lower limb muscles in accelerating the whole-body center of mass during gait. Monte-Carlo analyses were used to quantify the effects of entire distributions of perturbations in the moment arms and architectural properties of muscles. In most cases, varying the moment arm and architectural properties of a muscle affected the torque generated by that muscle about the joint(s) it spanned as well as the torques generated by adjacent muscles. Muscle function was most sensitive to changes in tendon slack length and least sensitive to changes in muscle moment arm. However, the sensitivity of muscle function to changes in moment arms and architectural properties was highly muscle-specific; muscle function was most sensitive in the cases of gastrocnemius and rectus femoris and insensitive in the cases of hamstrings and the medial sub-region of gluteus maximus. The sensitivity of a muscle's function was influenced by the magnitude of the muscle's force as well as the operating region of the muscle on its force-length curve. These findings have implications for the development of subject-specific models of the human musculoskeletal system.     

Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies

A set of software tools for building and distributing models of macromolecular assemblies uses an integrative structure modeling approach, which casts the building of models as a computational optimization problem where information is encoded into a scoring function used to evaluate candidate models.