用光合-蒸散耦合模型模拟冬小麦CO2通量的日变化

根据SPAC理论建立了一个冬小麦光合和蒸散的耦合模型.冬小麦CO2通量包括冠层光合、呼吸和土壤呼吸.冠层光合采用了Farquhar光合作用生化模型,并通过冠层阻力的参数化将光合作用与蒸腾作用耦合起来.用涡度相关方法观测了CO2通量,对模型进行了验证,结果显示模型可以较好地模拟CO2通量日变化过程.对模型的敏感性分析发现日间CO2通量最敏感的参数是初始量子效率.其次,CO2通量对光响应曲线凸度、CO2补偿点、凋萎点和叶面积指数的变化也有着较强的敏感性;夜间CO2通量敏感的参数是最适温度下Rubisco催化能力和暗呼吸参数.     

用光合-蒸散耦合模型模拟冬小麦CO2通量的日变化

根据 SPAC理论建立了一个冬小麦光合和蒸散的耦合模型。冬小麦 CO2 通量包括冠层光合、呼吸和土壤呼吸。冠层光合采用了 Farquhar光合作用生化模型 ,并通过冠层阻力的参数化将光合作用与蒸腾作用耦合起来。用涡度相关方法观测了 CO2通量 ,对模型进行了验证 ,结果显示模型可以较好地模拟 CO2 通量日变化过程。对模型的敏感性分析发现日间 CO2 通量最敏感的参数是初始量子效率。其次 ,CO2 通量对光响应曲线凸度、CO2 补偿点、凋萎点和叶面积指数的变化也有着较强的敏感性 ;夜间 CO2 通量敏感的参数是最适温度下 Rubisco催化能力和暗呼吸参数     

Escherichia coil growth dynamics: A three-pool biochemically based description

A three-pool growth model of an individual Escherichia coli cell is described herein. The model is based on a previously developed chemically structured complex single cell growth model. The reduction in model complexity and the identification of the essential modes of motion, over the time scale of growth, is achieved by temporal decomposition and analysis of hierarchy in relaxation times. The three-pool model faithfully simulates the changes in cell size, cell shape, cell macromolecular composition, DNA initiation and termination periods, and the dependence of cell growth under abiotic glucose limitation. The predictions made by the reduced model compare favorably with both the experimental data and those of the full single cell model (SCM) without any parameter adjustments. The three-pool model has very few significant parameters and has the potential to find immediate practical use in bioreactor design and process control strategies. The model development illustrates the use of modal analysis to yield reduced physiologically realistic dynamic model of complex microbial system such as E. coll.     

大兴安岭塔河地区林火发生的优势预测模型选择

选取在经济学和社会科学领域广泛应用的零膨胀模型(zero-inflated models)和栅栏模型(Hurdle models)对大兴安岭地区林火发生进行模拟,应用赤池准则(AIC)、似然比检验(LR)和模型残差平方和(SSR)对两类共4个回归模型——零膨胀泊松模型(ZIP)、零膨胀负二项模型(ZINB)、栅栏泊松模型(PH)、栅栏负二项模型(NBH)进行拟合分析,最终选取适合此林火发生特性的预测模型.模型的AIC和SSR值表明,ZINB模型对当地林火数据的拟合度最高.运用LR检验对嵌套模型(ZINB与ZIP,NBH与PH)进行检验,结果显示: ZINB和NBH均优于各自的嵌入模型,说明负二项(NB)模型对数据结构中的过度离散现象可以很好地模拟和解释.根据研究区林火实际发生规律和两类不同模型的应用假设条件判断,零膨胀模型更适合塔河地区的林火特性.     

气孔导度模型在北方农牧交错带的适用性评价——以马铃薯和油葵为例

基于北方农牧交错带主要作物马铃薯和油葵的叶片气孔导度、净光合速率和气象因子的平行观测数据,对常用气孔导度模型(Jarvis模型、Ball-Berry模型、Leuning模型和Medlyn模型)进行了适用性评价.结果表明:马铃薯的气孔导度与净光合速率呈现较强的线性关系,而油葵气孔导度与净光合速率的线性关系较弱.对于马铃薯气孔导度,Ball-Berry模型模拟效果最佳,Leuning模型和Medlyn模型次之,Jarvis模型模拟效果最差;各模型的模拟值与观测值的均方根误差(RMSE)分别为0.0331、0.0371、0.0456和0.0794 mol·m^-2·s^-1,归一化均方根误差(NRMSE)分别为26.8%、30.0%、36.9%和64.3%,拟合度(R²)分别为0.96、0.61、0.91和0.88.对于油葵的气孔导度,Jarvis模型模拟效果略好于Ball-Berry模型、Medlyn模型和Leuning模型,其RMSE分别为0.2221、0.2534、0.2547和0.2758 mol·m^-2·s^-1,NRMSE分别为40.3%、46.0%、46.2%和50.1%,R²分别为0.38、0.22、0.23和0.20.气象因子对气孔导度作用的通径分析表明,北方农牧交错带马铃薯和油葵气孔导度日变化主要受饱和水汽压差影响.模型评价结果表明用于油葵的气孔导度模型需要进一步改进.     

The Continual Reassessment Method for Multiple Toxicity Grades: A Bayesian Model Selection Approach

Grade information has been considered in Yuan et al. (2007) wherein they proposed a Quasi-CRM method to incorporate the grade toxicity information in phase I trials. A potential problem with the Quasi-CRM model is that the choice of skeleton may dramatically vary the performance of the CRM model, which results in similar consequences for the Quasi-CRM model. In this paper, we propose a new model by utilizing bayesian model selection approach – Robust Quasi-CRM model – to tackle the above-mentioned pitfall with the Quasi-CRM model. The Robust Quasi-CRM model literally inherits the BMA-CRM model proposed by Yin and Yuan (2009) to consider a parallel of skeletons for Quasi-CRM. The superior performance of Robust Quasi-CRM model was demonstrated by extensive simulation studies. We conclude that the proposed method can be freely used in real practice.     

Emergence of oscillations in a model of weakly coupled two Bonhoeffer-van der Pol equations

Bifurcations of periodic solutions in a model of weakly coupled two Bonhoeffer-van der Pol equations are studied. The model realizes a half-center model with reciprocal inhibition, a typical model used in the field of neural motor control to account for the generation of alternating rhythmic bursts observed in motoneurons and spinal neural networks. Several oscillatory solutions such as in-phase, anti-phase as well as out-of-phase solutions emerge from the model's equilibrium as one of the parameters of the model changes. Among the variety of bifurcations exhibited by the model, we analyze Hopf bifurcations, by which several periodic solutions emerge, and illustrate generation mechanisms of alternating oscillations in the model.     

A Multiplicative Model Imposed More Restrictions on the Quasi-Symmetry Model for the Analysis of Square Contingency Tables

For the analysis of square contingency tables, this note proposes a multiplicative model imposed more restrictions on CAUSSINUS ' (1965) quasi-symmetry (QS) model. The model is not so strict as in the quasi-double symmetry model considered by TOMIZAWA (1985b). The proposed model has the structure of the QS about the main diagonal plus an extended QS about the reverse diagonal of the square contingency table. The model is applied to the data on unaided vision of students in a university in Japan.     

杭州西湖引水后生态系统中磷循环模型

报道了杭州西湖截污和引灌钱塘江水后的一个富营养化模型。它按照年度描述西湖生态系统中的磷循环。状态变量有浮游植物磷、正磷酸盐、碎屑磷和沉积物磷。模型校准和检验结果表明,对于系统给定的强制函数（引水量和水温等）的改变,模型作出的状态变量的描述是合理的。并且利用该模型模拟在不同引水量及挖泥量下西湖水质变化。模型对引水及挖泥的效益所作出的评估可供综合治理时参考。     

Interactions of small nonpolar molecules with biological membranes: an exactly solvable model

An exactly solvable model of the interaction of small nonpolar molecules with biological membranes is developed. This model, which is based upon a “decorated dimer model” extension of Nagle's membrane model, is demonstrated to qualitatively reproduce many of the changes in the order-disorder phase transition seen when biological membranes are exposed to anesthetic gases. The decorated dimer model is itself interesting because it provides an example of an exactly solvable monomer-dimer model in which phase transitions can occur in the presence of monomers.     

景观空间动态模型研究现状和应重点解决的问题

分析了景观空间动态模型研究的现状及今后的重点发展方向。论文重点介绍了随机景观模型、邻域规则模型和景观过程模型(包括渗透模型、个体行为模型和空间生态系统模型)3类景观空间模型的发展现状、存在的主要问题以及对这些模型途径进行完善的有关工作,并从确证性分析、有效性分析与敏感性分析等3个方面阐述了模型检验技术的发展现状。最后,总结了未来景观空间动态模型发展中应重点解决的主要问题,即模型算法的优化、尺度转换、模型的复杂化与简化、模型检验与评价,通用模型的建立以及传统模型与社会经济因素衔接问题。     

Towards the development of a minimal cell model by generalization of a model of Escherichia coli: use of dimensionless rate parameters.

A model of a minimal cell would be a valuable tool in identifying the organizing principles that relate the static sequence information of the genome to the dynamic functioning of the living cell. Our approach for developing a minimal cell model is to first generalize an existing model of Escherichia coli by expressing reaction rates as ratios to a set of reference parameters. This generalized model is a prototype minimal cell model that will be developed by adding detail to explicitly include each chemical species. We tested the concept of a generalized model by testing the effect of scaling all enzyme-catalyzed reactions in the E. coli model. The scaling has little effect on cellular function for a wide range of kinetic ratios, where the kinetic ratio is defined as the rate of all enzyme-catalyzed reactions in a given model relative to those in the E. coli model.     

Statistical methods for estimating doubling time in in vitro cell growth

Summary Doubling time has been widely used to represent the growth pattern of cells. A traditional method for finding the doubling time is to apply gray-scaled cells, where the logarithmic transformed scale is used. As an alternative statistical method, the log-linear model was recently proposed, for which actual cell numbers are used instead of the transformed gray-scaled cells. In this paper, I extend the log-linear model and propose the extended log-linear model. This model is designed for extra-Poisson variation, where the log-linear model produces the less appropriate estimate of the doubling time. Moreover, I compare statistical properties of the gray-scaled method, the log-linear model, and the extended log-linear model. For this purpose, I perform a Monte Carlo simulation study with three data-generating models: the additive error model, the multiplicative error model, and the overdispersed Poisson model. From the simulation study, I found that the gray-scaled method highly depends on the normality assumption of the gray-scaled cells; hence, this method is appropriate when the error model is multiplicative with the log-normally distributed errors. However, it is less efficient for other types of error distributions, especially when the error model is additive or the errors follow the Poisson distribution. The estimated standard error for the doubling time is not accurate in this case. The log-linear model was found to be efficient when the errors follow the Poisson distribution or nearly Poisson distribution. The efficiency of the log-linear model was decreased accordingly as the overdispersion increased, compared to the extended log-linear model. When the error model is additive or multiplicative with Gamma-distributed errors, the log-linear model is more efficient than the gray-scaled method. The extended log-linear model performs well overall for all three data-generating models. The loss of efficiency of the extended log-linear model is observed only when the error model is multiplicative with log-normally distributed errors, where the gray-scaled method is appropriate. However, the extended log-linear model is more efficient than the log-linear model in this case.     

Boundary-element calculations for dielectric behavior of doublet-shaped cells

In order to simulate dielectric relaxation spectra (DRS) of budding yeast cells (Saccharomyces cerevisiae) in suspension, the complex polarization factor (Clausius-Mossotti factor) beta for a single cell and the complex permittivity of a cell suspension epsilon(sus)* were calculated with a doublet-shaped model (model RD), in which two spheres were connected with a part of a ring torus, using the boundary element method. The beta values were represented by a diagonal tensor consisting of components beta(z) parallel to the rotation axis (z axis) and beta(h) in a plane (h plane) perpendicular to the axis. The epsilon(sus)* values were calculated from the complex permittivity of the suspending medium epsilon(a)* and the components of beta. The calculation was compared with that of a conventional prolate spheroid model (model CP). It was found that model CP could be used as a first approximation to model RD. However, differences existed in beta(z) between models RD and CP; beta(z) showed three relaxation terms in the case of model RD in contrast with two terms in model CP. Narrowing the junction between the two spheres in model RD markedly decreased the characteristic frequency of one of the relaxation terms in beta(z). This suggests that the structure of the junction can be estimated from DRS. Effects of the shape change from model RD to a two-sphere model (model RD without the junction) were also examined. The behavior of beta(z) in the two-sphere model, the relaxation intensity of which was much lower than model RD, was quite similar to that in a single-sphere model. These simulations were consistent with the experimental observations of the dielectric behavior of the yeast cells during cell cycle progression.     

昆虫杆状病毒流行病模拟模型及Java模拟软件

研究昆虫杆状病毒流行病模拟模型,对确定基因工程改造杆状病毒的主攻方向,明确病毒病田间流行的机制与关键因素,以及制定生物防治策略,均具有重要的理论与实践意义.本研究研制了用于昆虫杆状病毒流行病模拟的数学模型和Java模拟软件,该模型包括描述种群动态的一个微分方程组,描述气温变化、作物生长及病毒动态的若干模型等.模拟软件用...     

A comparison of the peri-implant bone stress generated by the preload with screw tightening between ‘bonded’ and ‘contact’ model

A number of finite element analyses (FEAs) for the dental implant were performed without regard for preload and with all interfaces ‘fixed-bonded’. The purpose of this study was comparing the stress distributions between the conventional FEA model with all contacting interfaces ‘fixed-bonded’ (bonded model) and the model with the interfaces of the components in ‘contact’ with friction simulated as a preloaded implant (contact model). We further verified the accuracy of the result of the FEA using model experiment. In the contact model, the stress was more widely distributed than in the bonded model. From the model study, the preload induced by screw tightening generated strain at the peri-implant bone, even before the application of external force. As a result, the bonded model could not reproduce the mechanical phenomena, whereas the contact model is considered to be appropriate for analysing mechanical problems.     

Patient-derived orthotopic xenograft (PDOX) mouse model of adult rhabdomyosarcoma invades and recurs after resection in contrast to the subcutaneous ectopic model

Rhabdomyosarcoma (RMS) is a rare mesenchymal tumor. The aim of the present study was to develop a patient-derived orthotopic xenograft (PDOX) mouse model of RMS and compare the PDOX model to a subcutaneous (s.c.)-transplant model. A patient RMS from a striated muscle was grown orthotopically in the right biceps femoris muscle and right quadriceps muscle of nude mice to establish a PDOX model, as well as under the skin to establish an s.c. model. PDOX tumors grew at a statistically-significant faster rate compared to the s.c. tumors. Recurrence after surgical resection occurred only in PDOX tumors, not in the s.c. model. Histologically, only the PDOX model was shown to be invasive. In conclusion, these results indicate that the PDOX model of adult RMS is malignant and the subcutaneous model is benign. These results emphasize that a proper tumor microenvironment is necessary for patient-like behavior of a tumor in a mouse model.     

Parametric and non-parametric modeling of short-term synaptic plasticity. Part II: Experimental study

This paper presents a synergistic parametric and non-parametric modeling study of short-term plasticity (STP) in the Schaffer collateral to hippocampal CA1 pyramidal neuron (SC) synapse. Parametric models in the form of sets of differential and algebraic equations have been proposed on the basis of the current understanding of biological mechanisms active within the system. Non-parametric Poisson–Volterra models are obtained herein from broadband experimental input–output data. The non-parametric model is shown to provide better prediction of the experimental output than a parametric model with a single set of facilitation/depression (FD) process. The parametric model is then validated in terms of its input–output transformational properties using the non-parametric model since the latter constitutes a canonical and more complete representation of the synaptic nonlinear dynamics. Furthermore, discrepancies between the experimentally-derived non-parametric model and the equivalent non-parametric model of the parametric model suggest the presence of multiple FD processes in the SC synapses. Inclusion of an additional set of FD process in the parametric model makes it replicate better the characteristics of the experimentally-derived non-parametric model. This improved parametric model in turn provides the requisite biological interpretability that the non-parametric model lacks.     

A multi-body model for comparative study of cervical traction simulation – development,improvement and validation

A computer simulation model was developed to study the dynamic behavior of the cervical spine during cervical traction therapy in inclined and sitting traction positions. The model improved upon an old model with additional components to represent the behavior of the intervertebral discs and the posterior ligaments. The simulation result of the new model was compared against the cervical traction data from a radiographic experiment in both positions. The simulation results of the old model and new model were compared to illustrate the improvement. Using the new model, we compared the timing response of cervical traction in the inclined and sitting positions.     

A musculo-skeletal model of rat ankle motion and its experimental test on rat

A biomechanical musculo-skeletal model of functional electrical stimulation (FES)-induced rat ankle motion was implemented and tested in rat experiments. The muscle model is a new Hill-based model which includes established physiological relations of force-velocity and force-length-frequency. However, the series-elastic component and the activation component of previous Hill-based models are replaced by a new component which accounts for dynamic time delays and recruitment that occur in real muscle force generation during limb movements. The skeletal model includes gravity and dynamic forces that occur in real rat ankle motions. In computer simulations, various FES patterns were applied to the tibialis anterior (TA) and soleus (SO) model muscles to produce walk-like ankle motions. In lab experiments, the same stimulation patterns were applied by epimysial electrodes implanted in the TA and SO muscles of live rats cordotomized at level T7. The resulting rat motions were recorded by video camera. Video data was converted to ankle angle-vs-time files for comparison with corresponding model angle-vs-time files. Over a physiologically significant range of ankle motions, model parameters were adjustable to yield model motions that agreed with rat motions to within 2 degrees (root mean square differences of rat and model ankle angles). This is shown in plots of model and rat motions presented here for representative cases of FES. The accuracy of our model in reproducing real ankle motions supports the hypothesis that our new muscle model generates correct muscle forces over a useful range of limb motions. It suggests that the model may be useful in the design of FES neural prostheses.