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.     

中国北方5种栎属树木多度分布及其对未来气候变化的响应

植物分布与气候之间的关系是预估未来气候变化对生态系统影响的实现基础。以往的物种分布模型通常以物种的分布区或者分布点的物种存在数据作为物种分布的响应变量。相较于物种存在数据, 多度反映了一个物种占用资源并把资源分配给个体的能力, 更能衡量物种对区域生态系统的影响。该研究通过野外调查获取了华北及周边地区1 045个样方的栎属树木多度, 利用广义线性模型、广义加性模型和随机森林模型模拟栓皮栎(Quercus variabilis)、麻栎(Q. acutissima)、槲栎(Q. aliena)、锐齿槲栎(Q. aliena var. acuteserrata)和蒙古栎(Q. mongolica) 5个树种多度的地理分布及未来2个不同时期(2050年和2070年)的潜在分布。结果表明: 随机森林模型对5个栎属树种的多度的拟合结果要优于广义线性模型和广义加性模型; 典型浓度路径(RCP) 8.5下的5个栎属树种在未来两个时期的多度变化幅度都要大于RCP 2.6下的变化, 在超过一半面积的区域中麻栎、槲栎、锐齿槲栎和蒙古栎的多度减少, 其中内蒙古东北部和黑龙江北部地区是5种栎属植物多度减少的集中分布地区。未来气候变化背景下, 需要加强对这几个区域的监测与物种保护。     

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.     

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.     

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。     

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.     

A critical assessment of comparative molecular modeling of tertiary structures of proteins*

In spite of the tremendous increase in the rate at which protein structures are being determined, there is still an enormous gap between the numbers of known DNA-derived sequences and the numbers of three-dimensional structures. In order to shed light on the biological functions of the molecules, researchers often resort to comparative molecular modeling. Earlier work has shown that when the sequence alignment is in error, then the comparative model is guaranteed to be wrong. In addition, loops, the sites of insertions and deletions in families of homologous proteins, are exceedingly difficult to model. Thus, many of the current problems in comparative molecular modeling are minor versions of the global protein folding problem. In order to assess objectively the current state of comparative molecular modeling, 13 groups submitted blind predictions of seven different proteins of undisclosed tertiary structure. This assessment shows that where sequence identity between the target and the template structure is high (> 70%), comparative molecular modeling is highly successful. On the other hand, automated modeling techniques and sophisticated energy minimization methods fail to improve upon the starting structures when the sequence identity is low (～30%). Based on these results it appears that insertions and deletions are still major problems. Successfully deducing the correct sequence alignment when the local similarity is low is still difficult. We suggest some minimal testing of submitted coordinates that should be required of authors before papers on comparative molecular modeling are accepted for publication in journals. © 1995 Wiley-Liss, Inc.     

疾病自然史的随机模型

1前言疾病自然史是指疾病的临床发展过程以及转归〔1〕．有些疾病如早期糖尿病,早期青光眼,肿瘤的临床前状态,往往自觉无症状,一旦自己感觉有症状或临床发现,此时已属于中、晚期,难以取得较好的治疗效果,特别是肿瘤,已经发生了转移．为此,必须早期发现、早期治疗．因此自然史研究有着重要意义．在肿瘤的预防中,它决定着二级预防,筛查方案的优化以及筛查效果的评价．国内外许多文献报道了宫颈癌、乳腺癌、AIDS等自然史的研究成果．在疾病自然史研究中,一般是将疾病分为几个阶段或几个状态,对肿瘤的研究一般是将癌前状态分为几…     

植被冠层尺度生理生态模型的研究进展

随着人们对植物生命活动各个过程研究的不断深入,以植物生理过程、物理过程为基础的各种生理生态学模型逐渐发展起来,而植被冠层尺度生理生态学过程模型已成为生态系统模型的核心之一。目前植被冠层尺度的大叶模型、多层模型、二叶模型以其成熟的理论基础及对植被冠层的光合作用、蒸腾作用较为成功的模拟,得到了广泛的应用。3个模型都以光合作用-气孔导度-蒸腾作用耦合模型为基础,但又具有各自的特点。本文对3种模型的结构及特点进行了总结,并对其进行了比较,简要介绍了目前植被冠层尺度生理生态学模型的应用及存在的问题和发展状况。     

流域水碳过程耦合模拟——WaSSI-C模型的率定与检验

在复杂的气候变化条件下, 利用水碳耦合模型进行生态水文学研究成为主要的研究手段和途径。该文以杂谷脑河上游流域为例, 在确定生态水文模型WaSSI-C模拟尺度的基础上, 探讨水碳耦合模型在中国西南湿润地区的适用性。杂古脑河上游流域位于岷江上游, 隶属于长江流域。在分析和讨论了模型结构和机理的基础上, 分别对模型蒸散和融雪计算进行了补充改进, 以提高模型的适用性。将1988-1996年作为模型的率定期, 1997-2006年作为模型的验证期, 分别在率定期和验证期利用实测的径流数据和中分辨率成像光谱仪数据的总初级生产力、蒸散(ET)数据, 对模拟结果进行对比验证。并利用决定系数(R²)和Nash-Sutcliffe效率系数(NS)两个指标对模拟效果进行评价。流域总径流率定期和验证期对比验证的R²分别为0.86和0.78; NS分别为0.82和0.67。总生态系统生产力和ET验证期的R²分别为0.89和0.78。可见模型模拟结果的两个评价指标都处于较为理想的区间内, 说明WaSSI-C模型在研究区内具有较好的适用性。并对模型的蒸散计算方法进行了讨论, 在此基础上提出了模型中存在的问题和改进的方向。     

Stochastic S-system modeling of gene regulatory network

Microarray gene expression data can provide insights into biological processes at a system-wide level and is commonly used for reverse engineering gene regulatory networks (GRN). Due to the amalgamation of noise from different sources, microarray expression profiles become inherently noisy leading to significant impact on the GRN reconstruction process. Microarray replicates (both biological and technical), generated to increase the reliability of data obtained under noisy conditions, have limited influence in enhancing the accuracy of reconstruction . Therefore, instead of the conventional GRN modeling approaches which are deterministic, stochastic techniques are becoming increasingly necessary for inferring GRN from noisy microarray data. In this paper, we propose a new stochastic GRN model by investigating incorporation of various standard noise measurements in the deterministic S-system model. Experimental evaluations performed for varying sizes of synthetic network, representing different stochastic processes, demonstrate the effect of noise on the accuracy of genetic network modeling and the significance of stochastic modeling for GRN reconstruction . The proposed stochastic model is subsequently applied to infer the regulations among genes in two real life networks: (1) the well-studied IRMA network, a real-life in-vivo synthetic network constructed within the Saccharomycescerevisiae yeast, and (2) the SOS DNA repair network in Escherichiacoli.     

一类生物系统平衡点的稳定性

本文利用Logistic模型和稳定性理论,建立了一类生物系统竞争和排斥的数学模型,并且讨论了模型平衡点稳定的条件。     

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.     

Sensitivity analysis of an energetic muscle model applied at whole body level in recumbent pedalling

Musculoskeletal models are used in order to describe and analyse the mechanics of human movement. In order to get a complete evaluation of the human movement, energetic muscle models were developed and were shown to be promising.

The aim of this work is to determine the sensitivity of muscle mechanical and energetic model estimates to changes in parameters during recumbent pedalling.

Inputs of the model were electromyography and joint angles, collected experimentally on one participant. The sensitivity analysis was performed on muscle-specific tension, physiological cross-sectional area, muscle maximal force, tendon rest length and percentage of fast-twitch fibres using an integrated sensitivity ratio. Soleus, gastrocnemius, vasti, gluteus and medial hamstrings were selected for the analyses.

The energetic model was found to be always less sensitive to parameter changes than the mechanical model. Tendon slack length was found to be the most critical parameter for both energetic and mechanical models even if the effect on the energetic output was smaller than on muscle force and joint moments.     

生理房室药动学模型

生理药动学模型较ｎ房室模型能更准确地描述药物在体内的处置过程,但在实际应用中由于其计算结果有较大的误差而限制其应用和推广．在生理模型中,某一组织器官中血液分布容积相对于单位时间的血流量来说,如果太大,就去给计算结果带来较大的误差．本文提出的生理房室模型可以减小这种误差,从而更准确地模拟药物在体内的处置过程．文中对一组模拟的生理和生化参数分别求出了生理房室模型和生理模型的数值解．通过两组解的比较,说明生理房室模型可以描述药物在体内处置过程中的细微变化．     

青藏高原东缘生态过渡带碳中和评估与预测

青藏高原东缘生态过渡带是我国重要的生态功能区和碳库,对该区域碳中和的评估和预测对于中国乃至亚洲的碳排放管理具有重要意义。基于率定的CASA模型估算了2001-2019年青藏高原东缘生态过渡带栅格尺度碳汇量,结合中国碳排放数据库分析近20年碳排放时空演变规律;然后,采用STIRPAT模型和岭回归建立碳排放与人口等6个社会经济指标的弹性关系,并讨论库兹涅兹曲线对碳排放的影响。之后采用情景分析法,设计包括绿色发展等5种不同经济发展情景预测研究区2020-2060年碳排放变化特征;最后,提出假性碳中和并进行定义,结合GM （1,1）模型预测所得碳汇量,探究青藏高原东缘生态过渡带净碳汇量未来不同情景演变趋势,预测与评估不同发展情景研究区碳中和状况。结果表明：研究区碳汇量在2001-2019年间呈波动缓慢上升趋势,研究区碳汇量东南部高西北部较低;而碳排放量增长速率迅速,于2019年达到108Mt左右,是2001年的3.07倍;近20年,研究区碳汇量均大于碳排放量,但二者差距呈减少趋势。STIRPAT模型岭回归系数表明,研究区内存在城镇化率环境库兹涅兹曲线（EKC）效应,随着城镇化率的提升,区域碳排放呈先增加后减少趋势,而对于富裕度无显著EKC效应;在6个影响因素中,人口变量对碳排放的影响最显著,每增加1%的人口,碳排放将增加1.03%左右;在预测的五种不同发展情景中,可持续发展情景（ST）与基准情景（BL）、节能情景（ES）与绿色发展情景（GD）分别在2050年、2040年实现碳达峰,碳达峰时间随着能耗的减少逐渐提前。粗放情景（ETS）在2060年仍未实现碳达峰,并且其碳排放将于2040年左右超过碳汇量,而其余四种情景预测2020-2060年碳汇量始终大于碳排放量,但其净碳汇量均呈先减少后增加的趋势。因此,青藏高原东缘生态过渡带具有较强固碳能力,但如采用不加管制的发展模式,其碳汇量将无法抵消其碳排放量。因此,在规划发展模式与保护生态的同时,应重点控制人口、畜牧业等因素,提高人民与产业的节能减排意识。     

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。     

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．