还原态氮源在微小原甲藻大规模赤潮中的重要性--动力学模型

1998年春末夏初,在美国的切萨皮克海湾的Choptank河出现了由微小原甲藻引发的大规模的赤潮。我们做了一系列与该藻赤潮发生机制有关的生理学特征实验。其中与氮吸收有关的生理学参数被应用于微小原甲藻赤潮发生动力学模型。为说明几个关键的生态及生理学过程在微小原甲藻赤潮发展和持续过程重的重要性,我们用该模型测试了几个关键过程点。模型测试的结果表明,河流输入充足的氮源是引起微小原甲藻赤潮的关键因素,而输入营养盐的组成结构对赤潮的发生并不起主要作用。然而在赤潮形成后,赤潮的维系依赖于还原态的氮源。在赤潮的维持过程中,微小原甲藻的倾向于吸收还原态的氮源的生理学特征起了很大作用。模型进一步表明微小原甲藻在低光照或黑暗条件下对氮的吸收仍然保持相当的吸收速率有利于该藻赤潮的发展。     

马尔可夫药物动力学模型B

本文建立的Markov模型B适于计算肾、心、脑、皮肤、脂肪、肌肉中的血药浓度,它具有生理药动学模型的优点,即动力学参数具有解剖学和生理学意义,又能象房室模型一样用简单、优美的形式表示模型的解.     

大数据-模型混合驱动下生物过程优化与放大的新机遇与挑战

当前,生物制造技术和产业是世界关注的热点。然而,生物过程优化与放大过程中普遍面临以下几个难题,包括:过程检测手段缺乏,难以满足关键指标参数的监控;细胞代谢认知匮乏,无法理性实现过程最优化调控;反应器环境差异大,导致逐级放大效率低下。文中针对以上亟待解决的关键问题,通过案例分析介绍发酵过程实时检测-动态调控-理性放大全链条关键技术创新。在未来,生物过程设计将以集成细胞生理学(时空多尺度细胞代谢模型)和流体动力学(CFD模型)的全生命周期模型为指导,推进计算机辅助设计与开发,加速生物过程实现大规模智能化生产,开启绿色生物制造新时代。     

基于BIOME-BGC模型的长白落叶松林净初级生产力模拟参数敏感性

基于植被生理生态过程的模型包含较多参数,合理的参数取值能够极大地提高模型的模拟能力.参数敏感性分析可以全面分析模型参数对模拟结果的影响程度,在筛选模型敏感参数过程中起到重要作用.本研究以模拟吉林省汪清林业局长白落叶松林净初级生产力（NPP）为例,分析了BIOME-BGC模型的参数敏感性.首先利用样地实测NPP数据与模拟值进行对比分析,检验模型对长白落叶松林NPP的模拟能力;然后利用Morris法和EFAST法筛选出BIOME-BGC模型中对长白落叶松林NPP影响较大的敏感参数.在此基础上,通过EFAST法对所有筛选出的参数进行定量的敏感性分析,计算了敏感参数的全局敏感性指数、一阶敏感性指数和二阶敏感性指数.结果表明： BIOME-BGC模型能够较好地模拟研究区内长白落叶松林NPP的变化趋势;Morris法可以在样本量较少的情况下实现对BIOME-BGC模型敏感参数的筛选,而EFAST法可以定量分析BIOME-BGC模型中单个参数以及不同参数之间交互作用对模拟结果的影响程度;BIOME-BGC模型中对长白落叶松林NPP影响较大的敏感参数为新生茎与叶片的碳分配比和叶片碳氮比,且二者之间的交互作用明显大于其他参数之间的交互作用.     

高山峡谷地区森林流域分布式降雨-径流模型的构建与验证

根据岷江上游杂谷脑河流域典型的高山峡谷地区主要水文特点,选择通用性较强的水文过程模式,构建高山峡谷地区森林流域分布式降雨-径流过程模型,避免过多复杂的区域性模型参数率定,保证模型在相似地区的可移植性;并选择杂谷脑水文站上游地区进行降雨-径流过程模拟,得到1999年和2000年模拟时段长度为1000 h的两个径流过程,对模拟与实测的径流过程、累积径流量、洪峰流量与峰现时间等进行比较,其拟合效果较好.该模型结构简单,引入的经验参数较少,可推广应用到其它尺度流域.     

腹主动脉瘤生长过程的蠕变力学模型

基于增强对腹主动脉瘤生长过程的理解、为腹主动脉瘤临床手术提供参考的目的,本文根据腹主动脉瘤的生长物理机制,提出了以蠕变力学为基础模拟腹主动脉瘤生长过程的模型.建立了腹主动脉瘤简化模型,利用有限元方法进行模拟计算.结果显示蠕变模型能够有效模拟腹主动脉瘤生长过程中的形态变化.参数优化模型模拟结果符合临床统计数据所示的腹主动脉瘤生长过程.本文还讨论了腹主动脉材料力学参数对模型的影响.     

基于实码遗传算法的湖泊水质模型参数优化

参数的合理取值决定着模型的模拟效果,因此确定研究区域的模型结构后,需要对模型的参数进行优化.湖泊水质模型(Simulation by means of an Analytical Lake Model,SALMO)利用常微分方程描述湖泊的营养物质循环和食物链动态,考虑了多个生态过程,包含104个参数.由于参数较多,不适宜采用传统参数优化方法进行优化.利用太湖梅梁湾2005年数据,采用实码遗传算法优化了SALMO模型中相对敏感的参数,运用优化后的模型,模拟了梅梁湾2006年的水质.对比分析参数优化前后模型的效果表明遗传算法能高效地对SALMO进行参数优化,优化后的模拟精度得到了显著提高,能更好地模拟梅梁湾的水质变化.     

神经放电节律转化的分岔序列模式

神经元接受到的外界信号是动态变化的,神经放电节律模式则会依据一定的规律动态转化来反映这种变化,以往确定性理论模型(如Chay模型和Rose-Hindmarsh模型)模拟出了部分神经放电模式转化的整体分岔规律。利用Chay模型仿真,通过调节具有生理学意义的参数,模拟出了神经元放电的一系列分岔序列,同时在神经起步点的实验中,应用与模型对应的参数进行调节,观察到了与仿真结果整体上一致的分岔序列,印证了数值模拟的结果,展现了真实的神经元放电整体分岔结构的基本规律,为理解具体的生理调节活动中神经放电节律的转化提供了理论基础。     

利用模拟退火算法优化Biome-BGC模型参数

生态过程模型建立在明确的机理之上,能够较好地模拟陆地生态系统的行为和特征,但模型众多的参数,成为模型具体应用的瓶颈。本文以Biome-BGC模型为例,采用模拟退火算法,对其生理、生态参数进行优化。在优化过程中,先对待优化参数进行了选择,然后采取逐步优化的方法进行优化。结果表明,使用优化后的参数,模型模拟结果与实际观测更为接近,参数优化能有效地降低模型模拟的不确定性。文中参数优化的过程和方法,可为生态模型的参数识别和优化提供一种实例和思路,有助于生态模型应用区域的扩展。     

语音处理的神经电生理学基础研究进展

解码大脑在语音处理过程中涉及的信息加工层级结构、皮质响应机制及功能连接模式,是神经语言学领域的研究重点.以语音信息加工时序为依据,可将该认知过程划分为:初级声学信号时频编码(spectrotemporal analysis of primary acoustic signals)、音素处理(phonemic processing)以及词汇-语义加工(lexical-semantic processing) 3个处理阶段.目前,研究者已对各阶段的神经机制进行了广泛且深入的研究,但不同模型理论/假说难以整合互补,有必要进行梳理与总结.本文将以大脑处理语音信息的3个阶段为主线,以电生理学方法为侧重范式,对各阶段下的皮质映射、神经振荡模式以及事件相关响应机制等神经基础研究现状进行总结评述,以期为进一步了解语音信号如何在人脑中进行处理和表达等相关研究提供一定的参考.     

Structure is more important than physiology for estimating intracanopy distributions of leaf temperatures

Estimating leaf temperature distributions (LTDs) in canopies is crucial in forest ecology. Leaf temperature affects the exchange of heat, water, and gases, and it alters the performance of leaf‐dwelling species such as arthropods, including pests and invaders. LTDs provide spatial variation that may allow arthropods to thermoregulate in the face of long‐term changes in mean temperature or incidence of extreme temperatures. Yet, recording LTDs for entire canopies remains challenging. Here, we use an energy‐exchange model (RATP) to examine the relative roles of climatic, structural, and physiological factors in influencing three‐dimensional LTDs in tree canopies. A Morris sensitivity analysis of 13 parameters showed, not surprisingly, that climatic factors had the greatest overall effect on LTDs. In addition, however, structural parameters had greater effects on LTDs than did leaf physiological parameters. Our results suggest that it is possible to infer forest canopy LTDs from the LTDs measured or simulated just at the surface of the canopy cover over a reasonable range of parameter values. This conclusion suggests that remote sensing data can be used to estimate 3D patterns of temperature variation from 2D images of vegetation surface temperatures. Synthesis and applications. Estimating the effects of LTDs on natural plant–insect communities will require extending canopy models beyond their current focus on individual species or crops. These models, however, contain many parameters, and applying the models to new species or to mixed natural canopies depends on identifying the parameters that matter most. Our results suggest that canopy structural parameters are more important determinants of LTDs than are the physiological parameters that tend to receive the most empirical attention.     

Amazon forest carbon dynamics predicted by profiles of canopy leaf area and light environment

Tropical forest structural variation across heterogeneous landscapes may control above‐ground carbon dynamics. We tested the hypothesis that canopy structure (leaf area and light availability) – remotely estimated from LiDAR – control variation in above‐ground coarse wood production (biomass growth). Using a statistical model, these factors predicted biomass growth across tree size classes in forest near Manaus, Brazil. The same statistical model, with no parameterisation change but driven by different observed canopy structure, predicted the higher productivity of a site 500 km east. Gap fraction and a metric of vegetation vertical extent and evenness also predicted biomass gains and losses for one‐hectare plots. Despite significant site differences in canopy structure and carbon dynamics, the relation between biomass growth and light fell on a unifying curve. This supported our hypothesis, suggesting that knowledge of canopy structure can explain variation in biomass growth over tropical landscapes and improve understanding of ecosystem function.     

Estimation of carbon storage based on individual tree detection in <Emphasis Type="Italic">Pinus densiflora</Emphasis> stands using a fusion of aerial photography and LiDAR data

The objective of this study was to estimate the carbon storage capacity of Pinus densiflora stands using remotely sensed data by combining digital aerial photography with light detection and ranging (LiDAR) data. A digital canopy model (DCM), generated from the LiDAR data, was combined with aerial photography for segmenting crowns of individual trees. To eliminate errors in over and under-segmentation, the combined image was smoothed using a Gaussian filtering method. The processed image was then segmented into individual trees using a marker-controlled watershed segmentation method. After measuring the crown area from the segmented individual trees, the individual tree diameter at breast height (DBH) was estimated using a regression function developed from the relationship observed between the field-measured DBH and crown area. The above ground biomass of individual trees could be calculated by an image-derived DBH using a regression function developed by the Korea Forest Research Institute. The carbon storage, based on individual trees, was estimated by simple multiplication using the carbon conversion index (0.5), as suggested in guidelines from the Intergovernmental Panel on Climate Change. The mean carbon storage per individual tree was estimated and then compared with the field-measured value. This study suggested that the biomass and carbon storage in a large forest area can be effectively estimated using aerial photographs and LiDAR data.     

Good modeling practice for PAT applications: Propagation of input uncertainty and sensitivity analysis

The uncertainty and sensitivity analysis are evaluated for their usefulness as part of the model‐building within Process Analytical Technology applications. A mechanistic model describing a batch cultivation of Streptomyces coelicolor for antibiotic production was used as case study. The input uncertainty resulting from assumptions of the model was propagated using the Monte Carlo procedure to estimate the output uncertainty. The results showed that significant uncertainty exists in the model outputs. Moreover the uncertainty in the biomass, glucose, ammonium and base‐consumption were found low compared to the large uncertainty observed in the antibiotic and off‐gas CO₂ predictions. The output uncertainty was observed to be lower during the exponential growth phase, while higher in the stationary and death phases ‐ meaning the model describes some periods better than others. To understand which input parameters are responsible for the output uncertainty, three sensitivity methods (Standardized Regression Coefficients, Morris and differential analysis) were evaluated and compared. The results from these methods were mostly in agreement with each other and revealed that only few parameters (about 10) out of a total 56 were mainly responsible for the output uncertainty. Among these significant parameters, one finds parameters related to fermentation characteristics such as biomass metabolism, chemical equilibria and mass‐transfer. Overall the uncertainty and sensitivity analysis are found promising for helping to build reliable mechanistic models and to interpret the model outputs properly. These tools make part of good modeling practice, which can contribute to successful PAT applications for increased process understanding, operation and control purposes. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

基于HJ1B和ALOS/PALSAR数据的森林地上生物量遥感估算

森林地上生物量的精确估算能够减小碳储量估算的不确定性。为了探寻一种有效地提高森林生物量估算精度的方法,探讨了基于遥感物理模型和经验统计模型估算山地森林地上生物量的方法。首先,基于Li-Strahler几何光学模型和多元前向模式(MFM)进行模型模拟,结合查找表算法(LUT)从多光谱图像HJ1B估算贺兰山研究区的森林地上生物量。其次,采用统计方法建立了2种回归模型:(1)多光谱图像HJ1B进行混合像元分解(SMA),并与雷达图像ALOS/PALSAR进行图像融合建立生物量回归模型;(2)雷达图像ALOS/PALSAR后向散射系数和实测生物量建立了生物量回归模型。用实测数据对3种算法估算结果进行精度验证。研究结果表明:采用几何光学模型和MFM算法估算的森林地上生物量精度最好(决定系数R2=0.61,均方根误差RMSE=8.33 t/hm2,P0.001),其估算地上生物量与实测值一致性较好,估算生物量精度略优于SMA估算的精度(R2=0.60,RMSE=9.417 t/hm2);ALOS/PALSAR多元回归估算的精度最差(R2=0.39,RMSE=14.89 t/hm2)。由此可见,采用几何光学模型和混合像元分解SMA适合估算森林地上生物量,利用这2种方法进行森林地上生物量遥感监测研究具有一定的应用潜力。     

Multivariate control of plant species richness and community biomass in blackland prairie

Recent studies have shown that patterns of plant species richness and community biomass are best understood in a multivariate context. The objective of this study was to develop and evaluate a multivariate hypothesis about how herbaceous biomass and richness relate to gradients in soil conditions and woody plant cover in blackland prairies. Structural equation modeling was used to investigate how soil characteristics and shade by scattered Juniperus virginiana trees relate to standing biomass and species richness in 99 0.25 m² quadrats collected in eastern Mississippi, USA. Analysis proceeded in two stages. In the first stage, we evaluated the hypothesis that correlations among soil parameters could be represented by two underlying (latent) soil factors, mineral content and organic content. In the second stage, we evaluated the hypothesis that richness and biomass were related to (1) soil properties, (2) tree canopy extent, and (3) each other (i.e. reciprocal effects between richness and biomass). With some modification to the details of the original model, it was found that soil properties could be represented as two latent variables. In the overall model, 51% and 53% of the observed variation in richness and biomass were explained. The order of importance for variables explaining variations in richness was (1) soil organic content, (2) soil mineral content, (3) community biomass, and (4) tree canopy extent. The order of importance for variables explaining biomass was (1) tree canopy and (2) soil organic content, with neither soil mineral content nor species richness explaining significant variation in biomass. Based on these findings, we conclude that variations in richness are uniquely related to both variations in soil conditions and variations in herbaceous biomass. We further conclude that there is no evidence in these data for effects of species richness on biomass.     

基于GreenLab原理构建油松成年树的结构-功能模型

 林木的结构-功能模型(functional-structural tree modeling, FSTMs)是基于器官级组件构建的将植物结构和功能结合起来的一类模型, 在应用于成年树时需要解决拓扑结构复杂性和年轮分配模式普适性的问题。该文以18年生和41年生的油松 (Pinus tabulaeformis)成年树为研究对象, 将GreenLab模型应用到成年树的模拟中。采用破坏性取样, 实测了2株油松成年树的形态结构, 利用子结构模型解决成年树拓扑结构复杂性的问题, 引入年轮影响系数λ, 将全局分配模式和Pressler模式结合起 来, 解决年轮分配模式在不同年龄和环境条件下不同的问题。模型的直接参数通过实测数据获得, 隐含参数利用非线性最小二乘法拟合反求获得。通过实测数据与模拟数据的对比、模拟数据与经验模型模拟数据的对比, 对模型的模拟效果进行了评估, 发现节间总重、针叶总重、树高、树干节间重观测值和模型模拟值建立的回归方程的决定系数为0.84–0.98, 结构-功能模型与经验模型对总生物量模拟的决定系数为0.95, 表明该模型能较真实地反映油松的结构和生长过程。     

ORCHIDEE‐STICS,a process‐based model of sugarcane biomass production: calibration of model parameters governing phenology

Agro‐Land Surface Models (agro‐LSM) combine detailed crop models and large‐scale vegetation models (DGVMs) to model the spatial and temporal distribution of energy, water, and carbon fluxes within the soil–vegetation–atmosphere continuum worldwide. In this study, we identify and optimize parameters controlling leaf area index (LAI) in the agro‐LSM ORCHIDEE‐STICS developed for sugarcane. Using the Morris method to identify the key parameters impacting LAI, at eight different sugarcane field trial sites, in Australia and La Reunion island, we determined that the three most important parameters for simulating LAI are (i) the maximum predefined rate of LAI increase during the early crop development phase, a parameter that defines a plant density threshold below which individual plants do not compete for growing their LAI, and a parameter defining a threshold for nitrogen stress on LAI. A multisite calibration of these three parameters is performed using three different scoring functions. The impact of the choice of a particular scoring function on the optimized parameter values is investigated by testing scoring functions defined from the model‐data RMSE, the figure of merit and a Bayesian quadratic model‐data misfit function. The robustness of the calibration is evaluated for each of the three scoring functions with a systematic cross‐validation method to find the most satisfactory one. Our results show that the figure of merit scoring function is the most robust metric for establishing the best parameter values controlling the LAI. The multisite average figure of merit scoring function is improved from 67% of agreement to 79%. The residual error in LAI simulation after the calibration is discussed.     

Improving predictions of tropical forest response to climate change through integration of field studies and ecosystem modeling

Tropical forests play a critical role in carbon and water cycles at a global scale. Rapid climate change is anticipated in tropical regions over the coming decades and, under a warmer and drier climate, tropical forests are likely to be net sources of carbon rather than sinks. However, our understanding of tropical forest response and feedback to climate change is very limited. Efforts to model climate change impacts on carbon fluxes in tropical forests have not reached a consensus. Here, we use the Ecosystem Demography model (ED2) to predict carbon fluxes of a Puerto Rican tropical forest under realistic climate change scenarios. We parameterized ED2 with species‐specific tree physiological data using the Predictive Ecosystem Analyzer workflow and projected the fate of this ecosystem under five future climate scenarios. The model successfully captured interannual variability in the dynamics of this tropical forest. Model predictions closely followed observed values across a wide range of metrics including aboveground biomass, tree diameter growth, tree size class distributions, and leaf area index. Under a future warming and drying climate scenario, the model predicted reductions in carbon storage and tree growth, together with large shifts in forest community composition and structure. Such rapid changes in climate led the forest to transition from a sink to a source of carbon. Growth respiration and root allocation parameters were responsible for the highest fraction of predictive uncertainty in modeled biomass, highlighting the need to target these processes in future data collection. Our study is the first effort to rely on Bayesian model calibration and synthesis to elucidate the key physiological parameters that drive uncertainty in tropical forests responses to climatic change. We propose a new path forward for model‐data synthesis that can substantially reduce uncertainty in our ability to model tropical forest responses to future climate.