Using Bayesian networks to incorporate uncertainty in habitat suitability index models

Habitat suitability index (HSI) models rarely characterize the uncertainty associated with their estimates of habitat quality despite the fact that uncertainty can have important management implications. The purpose of this paper was to explore the use of Bayesian belief networks (BBNs) for representing and propagating 3 types of uncertainty in HSI models—uncertainty in the suitability index relationships, the parameters of the HSI equation, and measurement of habitat variables (i.e., model inputs). I constructed a BBN–HSI model, based on an existing HSI model, using Netica™ software. I parameterized the BBN's conditional probability tables via Monte Carlo methods, and developed a discretization scheme that met specifications for numerical error. I applied the model to both real and dummy sites in order to demonstrate the utility of the BBN–HSI model for 1) determining whether sites with different habitat types had statistically significant differences in HSI, and 2) making decisions based on rules that reflect different attitudes toward risk—maximum expected value, maximin, and maximax. I also examined effects of uncertainty in the habitat variables on the model's output. Some sites with different habitat types had different values for E[HSI], the expected value of HSI, but habitat suitability was not significantly different based on the overlap of 90% confidence intervals for E[HSI]. The different decision rules resulted in different rankings of sites, and hence, different decisions based on risk. As measurement uncertainty in habitat variables increased, sites with significantly different (α = 0.1) E[HSI] became statistically more similar. Incorporating uncertainty in HSI models enables explicit consideration of risk and more robust habitat management decisions. © 2012 The Wildlife Society.     

Niche Conservatism and Future Changes in the Potential Area Coverage of Arundina graminifolia,an Invasive Orchid Species from Southeast Asia

The Asian orchid, Arundina graminifolia, has been introduced to many locations over the last 50 yr, predominantly in South and Central America. A list of localities of A. graminifolia was compiled and used to model potential climatic niches based on the maximum entropy method. The differences are presented between niches occupied by native and invasive populations of A. graminifolia, and possible changes in the potential range of the species are discussed on the basis of various climate change scenarios. The coverage of habitats suitable for A. graminifolia will be reduced under future climate changes scenarios. The created niche distribution models indicated a more significant reduction in the potential ecological niches of the studied species in its invasive range. Nevertheless, areas with potentially suitable bioclimatic conditions for A. graminifolia should be monitored to prevent future uncontrolled invasion of the orchid into new habitats and to study its impact on the local ecosystems, as vast areas of its potential niche in the Americas are still unoccupied.     

Induced electric field and current density patterns in bone fractures

We have used the low frequency solver of the computer program SEMCAD‐X to model the induced electric field and current density patterns in simple models of a fractured femur embedded off‐center in cylindrical muscle tissue; a 1 cm fracture gap is filled with callus. The model is exposed to a 1 kHz, 1 mT sinusoidal magnetic field. The frequency chosen is typical of the major Fourier components of many waveforms used to stimulate fracture healing using pulsed magnetic fields; the intensity is also a typical level. Models include fractures perpendicular to the bone and at an angle from the perpendicular, each exposed to a field applied parallel to the bone or parallel to either of the two axes perpendicular to it. We find that all directions of applied magnetic fields produce essentially parallel induced electric fields and current densities through the plane of the callus, but that a magnetic field applied parallel to the bone induces considerably higher fields and currents than the same strength field applied in either perpendicular direction. Because investigations of pulsed‐field devices, including modeling of induced fields and currents, peaked more than a decade ago, this is the first application to our knowledge of the current capabilities of computer modeling systems to biological systems at low frequencies. Bioelectromagnetics 33:585–593, 2012. © 2012 Wiley Periodicals, Inc.     

Optimization and mathematical modeling of the transtubular bioreactor for the production of monoclonal antibodies from a hybridoma cell line

This report describes the use of a transtubular bioreactor to study the relative effects of diffusion versus perfusion of medium on antibody production by a hybridoma cell line. The study was performed with a high-density cell culture maintained in a serum-free, low-protein medium for 77 days. It was determined that the reactor possessed a macro-mixing pattern residence time distribution similar to a continuous stirred tank reactor (CSTR). However, due to the arrangement of the medium lines in the reactor, the flow patterns for nutrient distribution consist of largely independent medium path lengths ranging from short to long. When operated with cyclic, reversing, transtubular medium flow, some regions of the reactor (with short residence times) are more accessible to medium than others (with long residence times). From this standpoint, the reactor can be divided into three regions: a captive volume, which consists of medium primarily delivered via diffusion; a lapped volume, which provides nutrients through unilateral convection; and a swept volume, which operates through bilateral convection. The relative sizes of these three volumes were modified experimentally by changing the period over which the direction of medium flow was reversed from 15 min (larger captive volume) to 9 h (larger swept volume). The results suggest that antibody concentration increases as the size of the diffusion-limited (captive) volume is increased to a maximum at around 30 min with a sharp decrease thereafter. As reflected by changes in measured consumption of glucose and production of lactate, no significant difference in cellular metabolism occurred as the reactor was moved between these different states. These results indicate that the mode of operation of the transtubular bioreactor may influence antibody productivity under serum-free, low-protein conditions with minimal effects on cellular metabolism.     

天山林区六种灌木生物量的建模及其器官分配的适应性

灌木全株生物量估算模型的构建仍存在一定困难,对灌木生物量在器官分配上所体现的适应性研究也不够充分。以天山林区6种常见灌木为研究对象,在天山的东段、中段、西段林区分别设置样地进行群落调查,由此以全株收获法取得6种常见灌木若干标准株的全株、根、枝、叶及各径级根的生物量,将D~2H(地径平方与高度的乘积)与V(冠幅面积与高度的乘积)分别选为估测模型的自变量,通过回归分析法建立了各种灌木全株生物量的最优估算模型,然后比较了此6种灌木全株生物量在营养器官上分配差异以及根系生物量在径级上的分配差异。结果表明:(1)天山林区6种常见灌木中,小檗(Berberis heteropoda Schrenk)、忍冬(Lonicera hispida Pall.ex Roem.et Schuet.)、栒子(Cotoneaster melanocarpus Lodd.)的全株生物量约为8.48—9.01 kg,蔷薇(Rosa spinosissima L.)、绣线菊(Spiraea hypericifolia L.)、方枝柏(Juniperus pseudosabina Fisch.et Mey.)的全株生物量约为2.71—3.20 kg;(2)蔷薇、绣线菊、栒子的全株生物量最优估测模型是以V为自变量的函数,小檗、忍冬、方枝柏的全株生物量最优估测模型是以D~2H为自变量的函数,各模型R~2值均在0.850以上,且在P0.05水平上达到显著,模型模拟结果达到了较高的准确度;(3)6种灌木全株生物量在根、枝上的分配比重差异不显著,仅在叶上的分配比重有差异(P0.05);根系生物量在径级上的分配均呈现随根系径级下降而减少的规律,6种灌木在径级大于2 mm根上的分配比重存在差异(P0.05,径级大于20 mm根为P0.01水平);(4)6种灌木全株生物量在营养器官上的分配差异以及根系生物量在径级上的分配差异均体现了各物种对其生境选择的适应策略。     

DECA,A Comprehensive,Automatic Post-processing Program for HDX-MS Data*

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Highlights

• •Open source software for comprehensive HDX-MS data analysis.
• •Automatic back-exchange correction options.
• •Rigorous statistical analysis of the significance of uptake differences.
• •High quality visualization tools.

     

Introducing “best single template” models as reference baseline for the Continuous Automated Model Evaluation (CAMEO)

Critical blind assessment of structure prediction techniques is crucial for the scientific community to establish the state of the art, identify bottlenecks, and guide future developments. In Critical Assessment of Techniques in Structure Prediction (CASP), human experts assess the performance of participating methods in relation to the difficulty of the prediction task in a biennial experiment on approximately 100 targets. Yet, the development of automated computational modeling methods requires more frequent evaluation cycles and larger sets of data. The “Continuous Automated Model EvaluatiOn (CAMEO)” platform complements CASP by conducting fully automated blind prediction evaluations based on the weekly pre-release of sequences of those structures, which are going to be published in the next release of the Protein Data Bank (PDB). Each week, CAMEO publishes benchmarking results for predictions corresponding to a set of about 20 targets collected during a 4-day prediction window. CAMEO benchmarking data are generated consistently for all methods at the same point in time, enabling developers to cross-validate their method's performance, and referring to their results in publications. Many successful participants of CASP have used CAMEO—either by directly benchmarking their methods within the system or by comparing their own performance to CAMEO reference data. CAMEO offers a variety of scores reflecting different aspects of structure modeling, for example, binding site accuracy, homo-oligomer interface quality, or accuracy of local model confidence estimates. By introducing the "bestSingleTemplate" method based on structure superpositions as a reference for the accuracy of 3D modeling predictions, CAMEO facilitates objective comparison of techniques and fosters the development of advanced methods.     

竞争和景观格局相互作用对外来入侵物种传播影响的动态模拟

通过中性景观模型和元胞自动机模型模拟了不同景观格局、不同竞争力和关键种群特征的外来入侵物种的传播动态,模拟结果表明:(1)竞争力强的外来入侵物种,可利用生境面积越大,集聚度越高,越有利于其入侵和传播,而对竞争力弱的外来入侵物种来说,可利用生境面积越小,越分散,越有利于其生存。竞争力强可以有效利用整块的高集聚度的资源,而弱竞争力的外来入侵物种为了逃避土著种的竞争往往趋向于分布在分散的小生境中;(2)可利用生境面积大于50%时,景观格局集聚度越小,竞争力弱的外来入侵物种适应环境的弛豫时间越长;(3)外来入侵物种的传播与种子产量呈正相关关系,与繁殖年龄呈负相关关系,拟合关系因景观格局和竞争而异;(4)平均迁移距离对外来入侵物种传播的影响最大,在管理过程中应根据不同的目标,不同的景观格局、竞争力和种群特征选择合适的管理措施。     

A Dynamic Model for Determining the Temporal Distribution of Environmental Burden

Abstract: In an article on the role of temporal information in life-cycle assessment in this journal, Field and colleagues argued that frequently it is not the single product but the "fleet" (or cohort) of products that "is the appropriate unit of analysis," and that in focusing on the fleet one "explicitly introduces the notion of time as a critical element of comparative life-cycle assessments. …" Major transitions, such as replacement of one fleet of products by an alternative fleet, correspond to a system in a transient rather than steady state, and explicit consideration of time is central to transient analysis.
One tool increasingly used as part of life-cycle assessment, economic input-output (EIO) analysis, at best deals with time in an implicit fashion. This article illustrates how the sequential interindustry model (SIM), a formulation of the EIOmodel that explicitly represents time, might be utilized in life-cycle assessment. SIM introduces this temporal component by explicitly accounting for the time required by production activities and the resulting sequencing of the inputs. This can be thought of as engineering rather than accounting information. The data demands of such a model are not likely to be met at present or at any time in the near future. Even so, simulation methods and the use of so-called synthetic data have a history of productive use in a number of fields, including the social sciences.
SIM also utilizes the contribution of Joshi on the application of the EIO model to environmental impact and the inclusion of the use as well as the production phases of a product in EIO analysis. The possibility of accounting for discounting of future events, with its impact on decision making, is also briefly discussed.     

Cloning,characterization, and mutational analysis of a highly active and stable <Emphasis Type="SmallCaps">l</Emphasis>-arabinitol 4-dehydrogenase from <Emphasis Type="Italic">Neurospora crassa</Emphasis>

An NAD⁺-dependent l-arabinitol 4-dehydrogenase (LAD, EC 1.1.1.12) from Neurospora crassa was cloned and expressed in Escherichia coli and purified to homogeneity. The enzyme was a homotetramer and contained two Zn²⁺ ions per subunit, displaying similar characteristics to medium-chain sorbitol dehydrogenases (SDHs). High enzymatic activity was observed for substrates l-arabinitol, adonitol, and xylitol and no activity for d-mannitol, d-arabinitol, or d-sorbitol. The enzyme showed strong preference for NAD⁺ but also displayed a very low yet detectable activity with NADP⁺. Mutational analysis of residue F59, the single different substrate-binding residue between LADs and d-SDHs, failed to confer the enzyme the ability to accept d-sorbitol as a substrate, suggesting that the amino acids flanking the active site cleft may be responsible for the different activity and affinity patterns between LADs and SDHs. This enzyme should be useful for in vivo and in vitro production of xylitol and ethanol from l-arabinose. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.