Maintenance requirements: energy supply from simultaneous endogenous respiration and substrate consumption

Abstract A model is presented that describes energy for maintenance purposes (ATP) as being obtained simultaneously from biomass degradation as well as from substrate degradation in excess of growth requirements. The ratio between both catabolic processes was taken to be growth rate dependent. As such, this approach is intermediate between established models; its significant features are negative growth and the absence of substrate consumption at zero substrate concentration, and the attainability of the maximum specific growth rate (the model parameter μ _max) at elevated substrate concentrations. As a simple case, the amounts of ATP obtained from direct substrate catabolism or from the degradation of an equivalent amount of biomass were taken as identical. Also, the maintenance demand in terms of ATP per unit time and biomass was taken to be constant. True growth rate dependency of maintenance can be implemented by relaxing either of these assumptions.     

Computational framework to model and design surgical meshes for hernia repair

Surgical procedures for hernia surgery are usually performed using prosthetic meshes. In spite of all the improvements in these biomaterials, the perfect match between the prosthesis and the implant site has not been achieved. Thus, new designs of surgical meshes are still being developed. Previous to implantation in humans, the validity of the meshes has to be addressed, and to date experimental studies have been the gold standard in testing and validating new implants. Nevertheless, these procedures involve long periods of time and are expensive. Thus, a computational framework for the simulation of prosthesis and surgical procedures may overcome some disadvantages of the experimental methods. The computational framework includes two computational models for designing and validating the behaviour of new meshes, respectively. Firstly, the beam model, which reproduces the exact geometry of the mesh, is set to design the weave and determine the stiffness of the surgical prosthesis. However, this implies a high computational cost whereas the membrane model, defined within the framework of the large deformation hyperelasticity, is a relatively inexpensive computational tool, which also enables a prosthesis to be included in more complex geometries such as human or animal bodies.     

Conventional and newly developed bioheat transport models in vascularized tissues: A review

Heat transfer in a biological system is a complex process and its analysis is difficult. Heterogeneous vascular architecture, blood flow in the complex network of arteries and veins, varying metabolic heat generation rates and dependence of tissue properties on its physiological condition contribute to this complexity. The understanding of heat transfer in human body is important for better insight of thermoregulatory mechanism and physiological conditions. Its understanding is also important for accurate prediction of thermal transport and temperature distribution during biomedical applications. During the last three decades, many attempts have been made by researchers to model the complex thermal behavior of the human body. These models, viz., blood perfusion, countercurrent, thermal phase-lag, porous-media, perturbation, radiation, etc. have their corresponding strengths and limitations. Along with their biomedical applications, this article reviews various contextual issues associated with these models. After brief discussion of early bioheat models, the newly developed bioheat models are discussed in detail. Dependence of these models on biological properties, viz., thermophysical and optical properties are also discussed.     

土壤-植物-大气连续体水热、CO2通量估算模型研究进展

土壤-植物-大气连续体(SPAC)水热、CO2通量的准确估算对理解陆地和大气的物质和能量交换过程有着重要意义.重点阐述了基于过程的土壤-植物-大气连续体水热、CO2通量模型,综述了统计模型、综合模型及基于遥感的模型的发展过程.其中水热通量统计模型包括基于温度和湿度以及基于温度和辐射的方法;CO2通量统计模型包括基于气候因子或蒸散因子以及基于光能利用率的方法.水热通量过程模型包括大叶、双源、多源和多层的水热传输物理模型;CO2通量过程模型包括叶片尺度及由大叶、双叶和多层方法扩展到冠层尺度的生理生态模型以及光合-蒸腾耦合模型.综合模型包括生物物理模型、生物化学模型和生物地理模型.统计模型形式简单,资料易得,对大范围的水热通量模拟具有指导意义;过程模型准确的揭示了水热和CO2通量传输的物理和生理过程,是大尺度综合模型的基础.未来生态系统水热、CO2通量估算模型将集成各种技术手段进行多尺度网络观测和大尺度机理模拟.     

温度与昆虫生长发育关系模型的发展与应用

昆虫作为变温动物,对温度变化更为敏感。研究温度变化对昆虫生长、发育的影响有重要理论和实践意义。目前已构建了多个描述温度与昆虫增长速率的关系模型,用于解释温度对昆虫发育速率的影响。这些模型大体可分为两类:没有热动力学基础的纯描述性模型和有热动力学基础的应用性模型。本文在对现有的有关温度变化与昆虫生长发育关系的11个模型进行评述的基础上,结合作者近年来的研究,重点介绍了迄今为止国际上最为合理的、用以反映温度对昆虫发育速率影响的Sharpe-Schoolfield-Ikemoto模型,并利用这些模型拟合了一组温发育速率数据用以展示这些模型的应用。     

Identifiability of single-index models and additive-index models

We provide a proof for the identifiability for both single-indexmodels and partially linear single-index models assuming onlythe continuity of the regression function, a condition muchweaker than the differentiability conditions assumed in theexisting literature. Our discussion is then extended to theidentifiability of the additive-index models.     

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.     

Meristems, metamers and modules and the development of shoot and root systems

BARLOW, P. W., 1989. Meristems, metamers and modules in the development of shoot and root systems . Root and shoot systems are hierarchical organizations whose levels are represented, in part, by cells and meristems. Meristems produce modules which in turn construct the architectural model. The latter is species specific and its structure depends on the geometrical interrelationships between the modular elements. The place of the metamer within this hierarchical scheme is discussed. Metamers derive directly from meristem activity and are externally recognizable as reiterated sub-units of the module. Another sub-unit of module construction, the cellular complex, or merophyte, is also a product of meristem activity, but, in contrast to the metamer, it is an internal, rather than an external, anatomical feature. Being cellular, it increases the ‘span’ of the cell level rather than constituting a level in its own right. Although the physical boundaries of metamer and merophyte can overlap, or even coincide, the two units belong to different conceptual schemes of module structure: the metamer is defined from a ‘classical’ morphological viewpoint, whereas the merophyte derives from a cellular conception of plant structure. Both the merophyte and the metamer have a role in clarifying the understanding of plant development since both provide insights into the functioning of the meristems from which they are derived and the structure of the module to which they contribute. For example, modules which lack an obvious metameric construction can usefully be analysed in terms of their merophytic organization. This is particularly true of roots of lower plants. Here, the merophytes reflect the presence and activity of a specialized meristematic apical cell. On the other hand, modules of higher plants, which lack such apical cells, also lack clearly defined merophytes, but their shoots have obvious metamers which reflect the activity of the meristem as a whole. It should be possible to represent the development of modules from cells, via their intermediate sub-structures of meristems and metamers, by means of formal languages of automata theory. One of these, a graphical algorithm (Petri net), is applied in this developmental context.     

A generalized diffusion model for growth and dispersal in a population

A reaction-diffusion model is presented in which spatial structure is maintained by means of a diffusive mechanism more general than classical Fickian diffusion. This generalized diffusion takes into account the diffusive gradient (or gradient energy) necessary to maintain a pattern even in a single diffusing species. The approach is based on a Landau-Ginzburg free energy model. A problem involving simple logistic kinetics is fully analyzed, and a nonlinear stability analysis based on a multi-scale perturbation method shows bifurcation to non-uniform states.Part of this work was done while at the Mathematical Institute, Oxford University as a Senior Visiting Fellow supported by the Science Research Council of Great Britain under grant GR/B31378     

工业微生物代谢网络模型的研究进展及应用

基因组规模代谢网络(Genome-scale metabolic network model,GSMM)是工业微生物菌株定向改造过程中一种极为重要的指导性工具,有助于研究者快速获取特定性状的工业微生物,因此越来越受到人们的关注。文中回顾了GSMM的发展历程,总结并评述了GSMM的构建方法,以4种重要工业微生物(枯草芽孢杆菌Bacillus subtilis、大肠杆菌Escherichia coli、谷氨酸棒杆菌Corynebacterium glutamicum和酿酒酵母Saccharomyces cerevisiae)为例,阐述了GSMM在工业微生物中的发展与应用。此外,还对GSMM未来的发展趋势进行了展望。     

Models and estimators linking individual-based and sample-based rarefaction,extrapolation and comparison of assemblages

Aims In ecology and conservation biology, the number of species counted in a biodiversity study is a key metric but is usually a biased underestimate of total species richness because many rare species are not detected. Moreover, comparing species richness among sites or samples is a statistical challenge because the observed number of species is sensitive to the number of individuals counted or the area sampled. For individual-based data, we treat a single, empirical sample of species abundances from an investigator-defined species assemblage or community as a reference point for two estimation objectives under two sampling models: estimating the expected number of species (and its unconditional variance) in a random sample of (i) a smaller number of individuals (multinomial model) or a smaller area sampled (Poisson model) and (ii) a larger number of individuals or a larger area sampled. For sample-based incidence (presence–absence) data, under a Bernoulli product model, we treat a single set of species incidence frequencies as the reference point to estimate richness for smaller and larger numbers of sampling units.Methods The first objective is a problem in interpolation that we address with classical rarefaction (multinomial model) and Coleman rarefaction (Poisson model) for individual-based data and with sample-based rarefaction (Bernoulli product model) for incidence frequencies. The second is a problem in extrapolation that we address with sampling-theoretic predictors for the number of species in a larger sample (multinomial model), a larger area (Poisson model) or a larger number of sampling units (Bernoulli product model), based on an estimate of asymptotic species richness. Although published methods exist for many of these objectives, we bring them together here with some new estimators under a unified statistical and notational framework. This novel integration of mathematically distinct approaches allowed us to link interpolated (rarefaction) curves and extrapolated curves to plot a unified species accumulation curve for empirical examples. We provide new, unconditional variance estimators for classical, individual-based rarefaction and for Coleman rarefaction, long missing from the toolkit of biodiversity measurement. We illustrate these methods with datasets for tropical beetles, tropical trees and tropical ants.Important findings Surprisingly, for all datasets we examined, the interpolation (rarefaction) curve and the extrapolation curve meet smoothly at the reference sample, yielding a single curve. Moreover, curves representing 95% confidence intervals for interpolated and extrapolated richness estimates also meet smoothly, allowing rigorous statistical comparison of samples not only for rarefaction but also for extrapolated richness values. The confidence intervals widen as the extrapolation moves further beyond the reference sample, but the method gives reasonable results for extrapolations up to about double or triple the original abundance or area of the reference sample. We found that the multinomial and Poisson models produced indistinguishable results, in units of estimated species, for all estimators and datasets. For sample-based abundance data, which allows the comparison of all three models, the Bernoulli product model generally yields lower richness estimates for rarefied data than either the multinomial or the Poisson models because of the ubiquity of non-random spatial distributions in nature.     

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.     

人工模拟胃肠道模型在食源性致病菌耐受及致病机理中的应用

人工模拟胃肠道模型是研究食源性致病菌耐受及致病机理的一种重要工具,其本质是在实验室模拟的条件下,重现人体消化过程中的化学、物理及生物作用,以研究食源性致病菌的耐受性、致病机理、肠道菌群互作及疫苗开发,对食源性致病菌的控制和治疗具有十分重要的意义。文中综述了人工模拟胃肠道模型在食源性致病菌研究中的应用,将现有胃肠道模型系统地划分为体外静态模型、体外动态模型、普通动物模型及人源化动物模型,并详细介绍了各类模型的概念及特性。在此基础之上,进一步分析了现有模型的不足,并对未来人工模拟胃肠道模型的研究方向进行了展望,以期为食源性致病菌耐受及致病机理的研究奠定扎实的研究基础。     

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．     

Chromosomes and the origins of apes and australopithecins

Comparison of molecular data suggests that the higher apes (Gorilla, Pan) and humankind (Homo) are closely related and that they diverged from the common ancestor through two speciation events situated very closely together in time. Examination of the chromosomal formulas of the living species reveals a paradox in the distribution of mutated chromosomes which can only be resolved by a model of trichotomic diversification. This new model of divergence from the common ancestor is characterized by the transition from (1) a monotypic phase to (2) a polytypic phase of three sub-species — pre-gorilla, pre-chimpanzee and preaustralopithecine. The quadruped ancestors ofAustralopithecus appear to have been one of the three components of the common ancestor. The question is whetherramidus is an australopithecine or a pre-australopithecine representative of the common ancestor. The new model of diversification of the common ancestor is resituated in the paleogeographic and paleoclimatic context which, through the north-south pattern of extension of aridity, provides a coherent scenario for the formation of extant species and subspecies of theGorilla andPan genera.     

一种新的DNA复制和转录模型

DNA复制和转录有两种模型,一种是传统的滑动模型,复制和转录发生时参与反应的蛋白质沿DNA模板滑动.在另一种新提出的工厂模型中,固定在核结构上的蛋白质拉动模板来完成DNA的复制和转录.来自生物化学、生物物理学和细胞生物学等的实验证据表明,新的工厂模型是生物活体细胞内真实的复制和转录模式.