Thermodynamic view on decision-making process: emotions as a potential power vector of realization of the choice

This research is devoted to possible mechanisms of decision-making in frames of thermodynamic principles. It is also shown that the decision-making system in reply to emotion includes vector component which seems to be often a necessary condition to transfer system from one state to another. The phases of decision-making system can be described as supposed to be nonequilibrium and irreversible to which thermodynamics laws are applied. The mathematical model of a decision choice, proceeding from principles of the nonlinear dynamics considering instability of movement and bifurcation is offered. The thermodynamic component of decision-making process on the basis of vector transfer of energy induced by emotion at the given time is surveyed. It is proposed a three-modular model of decision making based on principles of thermodynamics. Here it is suggested that at entropy impact due to effect of emotion, on the closed system—the human brain,—initially arises chaos, then after fluctuations of possible alternatives which were going on—reactions of brain zones in reply to external influence, an order is forming and there is choice of alternatives, according to primary entrance conditions and a state of the closed system. Entropy calculation of a choice expectation of negative and positive emotion shows judgment possibility of existence of “the law of emotion conservation” in accordance with several experimental data.     

Reduced modeling and state observation of an activated sludge process

This article first proposes a reduction strategy of the activated sludge process model with alternated aeration. Initiated with the standard activated sludge model (ASM1), the reduction is based on some biochemical considerations followed by linear approximations of nonlinear terms. Two submodels are then obtained, one for the aerobic phase and one for the anoxic phase, using four state variables related to the organic substrate concentration, the ammonium and nitrate‐nitrite nitrogen, and the oxygen concentration. Then, a two‐step robust estimation strategy is used to estimate both the unmeasured state variables and the unknown inflow ammonium nitrogen concentration. Parameter uncertainty is considered in the dynamics and input matrices of the system. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Data reconciliation of concentration estimates from mid‐infrared and dielectric spectral measurements for improved on‐line monitoring of bioprocesses

Real‐time data reconciliation of concentration estimates of process analytes and biomass in microbial fermentations is investigated. A Fourier‐transform mid‐infrared spectrometer predicting the concentrations of process metabolites is used in parallel with a dielectric spectrometer predicting the biomass concentration during a batch fermentation of the yeast Saccharomyces cerevisiae. Calibration models developed off‐line for both spectrometers suffer from poor predictive capability due to instrumental and process drifts unseen during calibration. To address this problem, the predicted metabolite and biomass concentrations, along with off‐gas analysis and base addition measurements, are reconciled in real‐time based on the closure of mass and elemental balances. A statistical test is used to confirm the integrity of the balances, and a non‐negativity constraint is used to guide the data reconciliation algorithm toward positive concentrations. It is verified experimentally that the proposed approach reduces the standard error of prediction without the need for additional off‐line analysis. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Use of posterior predictive checks as an inferential tool for investigating individual heterogeneity in animal population vital rates

The investigation of individual heterogeneity in vital rates has recently received growing attention among population ecologists. Individual heterogeneity in wild animal populations has been accounted for and quantified by including individually varying effects in models for mark–recapture data, but the real need for underlying individual effects to account for observed levels of individual variation has recently been questioned by the work of Tuljapurkar et al. (Ecology Letters, 12, 93, 2009) on dynamic heterogeneity. Model‐selection approaches based on information criteria or Bayes factors have been used to address this question. Here, we suggest that, in addition to model‐selection, model‐checking methods can provide additional important insights to tackle this issue, as they allow one to evaluate a model's misfit in terms of ecologically meaningful measures. Specifically, we propose the use of posterior predictive checks to explicitly assess discrepancies between a model and the data, and we explain how to incorporate model checking into the inferential process used to assess the practical implications of ignoring individual heterogeneity. Posterior predictive checking is a straightforward and flexible approach for performing model checks in a Bayesian framework that is based on comparisons of observed data to model‐generated replications of the data, where parameter uncertainty is incorporated through use of the posterior distribution. If discrepancy measures are chosen carefully and are relevant to the scientific context, posterior predictive checks can provide important information allowing for more efficient model refinement. We illustrate this approach using analyses of vital rates with long‐term mark–recapture data for Weddell seals and emphasize its utility for identifying shortfalls or successes of a model at representing a biological process or pattern of interest.     

PRIMO/PRIMONA: A coarse‐grained model for proteins and nucleic acids that preserves near‐atomistic accuracy

The new coarse graining model PRIMO/PRIMONA for proteins and nucleic acids is proposed. This model combines one to several heavy atoms into coarse‐grained sites that are chosen to allow an analytical, high‐resolution reconstruction of all‐atom models based on molecular bonding geometry constraints. The accuracy of proposed reconstruction method in terms of structure and energetics is tested and compared with other popular reconstruction methods for a variety of protein and nucleic acid test sets. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

Large scale demonstration of a process analytical technology application in bioprocessing: Use of on‐line high performance liquid chromatography for making real time pooling decisions for process chromatography

Process Analytical Technology (PAT) has been gaining a lot of momentum in the biopharmaceutical community because of the potential for continuous real time quality assurance resulting in improved operational control and compliance. In previous publications, we have demonstrated feasibility of applications involving use of high performance liquid chromatography (HPLC) and ultra performance liquid chromatography (UPLC) for real‐time pooling of process chromatography column. In this article we follow a similar approach to perform lab studies and create a model for a chromatography step of a different modality (hydrophobic interaction chromatography). It is seen that the predictions of the model compare well to actual experimental data, demonstrating the usefulness of the approach across the different modes of chromatography. Also, use of online HPLC when the step is scaled up to pilot scale (a 2294 fold scale‐up from a 3.4 mL column in the lab to a 7.8 L column in the pilot plant) and eventually to manufacturing scale (a 45930 fold scale‐up from a 3.4 mL column in the lab to a 158 L column in the manufacturing plant) is examined. Overall, the results confirm that for the application under consideration, online‐HPLC offers a feasible approach for analysis that can facilitate real‐time decisions for column pooling based on product quality attributes. The observations demonstrate that the proposed analytical scheme allows us to meet two of the key goals that have been outlined for PAT, i.e., “variability is managed by the process” and “product quality attributes can be accurately and reliably predicted over the design space established for materials used, process parameters, manufacturing, environmental, and other conditions”. The application presented here can be extended to other modes of process chromatography and/or HPLC analysis. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

SELECTION FOR MECHANICAL ADVANTAGE UNDERLIES MULTIPLE CRANIAL OPTIMA IN NEW WORLD LEAF‐NOSED BATS

Selection for divergent performance optima has been proposed as a central mechanism underlying adaptive radiation. Uncovering multiple optima requires identifying forms associated with different adaptive zones and linking those forms to performance. However, testing and modeling the performance of complex morphologies like the cranium is challenging. We introduce a three‐dimensional finite‐element (FE) model of the cranium that can be morphed into different shapes by varying simple parameters to investigate the relationship between two engineering‐based measures of performance, mechanical advantage and von Mises stress, and four divergent adaptive zones occupied by New World Leaf‐nosed bats. To investigate these relationships, we tested the fit of Brownian motion and Ornstein–Uhlenbeck models of evolution in mechanical advantage and von Mises stress using dated multilocus phylogenies. The analyses revealed three performance optima for mechanical advantage among species from three adaptive zones: bats that eat nectar; generalized insectivores, omnivores and some frugivores; and bats that specialize on hard canopy fruits. Only two optima, one corresponding to nectar feeding, were consistently uncovered for von Mises stress. These results suggest that mechanical advantage played a larger role than von Mises stress in the radiation of New World Leaf‐nosed bats into divergent adaptive zones.     

The impact of participatory forest management (PFM) on forest integrity and biodiversity in Arabuko‐Sokoke forest,Kenya

Bird communities composed of habitat specialists suffer considerable loss of species following disturbance (Ecol. Monogr. 41 , 1971, 207–233). Participatory forest management (PFM) aims to ensure local ownership and support for forest conservation. This study determined if forest birds and forest quality in places under PFM is significantly higher than areas without PFM in Arabuko‐Sokoke forest. Forest quality data were collected in the PFM and no PFM zones in the Mixed forest (MF) and Cynometra Woodland (CW). Plot‐based approach was used to collect vegetation data along 1 km transects at intervals of 1 km sampling twenty transects and 200 plots in each of the study zones. Birds’ data were collected using 10‐min point‐counts along 88, 1 km long transects placed 1‐km apart sampling in 30 m radius‐plots at intervals of 100 m. Data were collected in 2008 and 2009. The results showed higher measures of forest quality in PFM zones than no PFM zones which showed higher measures of forest disturbance. The results did not show statistical differences in birds’ diversity indexes between PFM and no PFM zones indicating that the human‐induced disturbance has not reached critical ecological thresholds to affect birds’ species diversity. It can be deduced that PFM investment is leading to improved forest management.     

基于景观安全格局的建设用地管制分区

旨在探索如何构建一种生态与经济发展兼顾的建设用地管制分区工作体系.以扬州市为例,选择防洪、水土保持、生物保护、乡土文化保护和游憩安全5个要素构建区域多层次综合生态安全格局,利用神经网络CA模型模拟无生态约束下的区域城镇建设用地扩展格局,将二者耦合得到优先建设区、有条件建设区、调整建设区、限制建设区和禁止建设区,并为每类管制区编制相应的管制规则.结果表明:①利用景观安全格局与城镇建设用地扩展格局耦合来进行建设用地管制区划分,优先考虑生态环境保护,再进行建设用地的安排,实现了生态与经济的双赢;②通过调整建设区的划定,为地方政府提供了新增建设用地适宜调整的区域,在建设用地管制的基础上,给予地方政府充分的自主权.     

Sensitivity Analysis of Environmental Process Modeling in a Life Cycle Context: A Case Study of Hemp Crop Production

The aim of this article is to develop a methodological approach allowing to assess the influence of parameters of one or more elementary processes in the foreground system, on the outcomes of a life cycle assessment (LCA) study. From this perspective, the method must be able to: (1) include foreground process modeling in order to avoid the assumption of proportionality between inventory data and reference flows; (2) quantify influences of foreground processes’ parameters (and, possibly, interactions between parameters); and (3) identify trends (either increasing or decreasing) for each parameter on each indicator in order to determine the most favorable direction for parametric variation. These objectives can be reached by combining foreground system modeling, a set of two different sensitivity analysis methods (each one providing different and complementary information), and LCA. The proposed method is applied to a case study of hemp‐based insulation materials for buildings. The present study will focus on the agricultural stage as a foreground system and as a first step encompassing the entire life cycle. A set of technological recommendations were identified for hemp farmers in order to reduce the crop's environmental impacts (from –11% to –89% according to the considered impact category). One of the main limitations of the approach is the need for a detailed model of the foreground process. Further, the method is, at present, rather time‐consuming. However, it offers long‐term advantages given that the higher level of model detail adds robustness to the LCA results.     

Ultrastructure and the importance of wear in the dentition of the halfbeak (Pisces: Hemiramphidae) pharyngeal mill

To assess how tooth microstructure and composition might facilitate the pharyngeal mill mechanism of halfbeaks, apatite structure and iron content were determined by scanning electron microscopy and energy dispersive X‐ray analysis for Hyporhamphus regularis ardelio, Arrhamphus sclerolepis krefftii, and Hemiramphus robustus. Iron was present in developing teeth and was concentrated along the shearing edge of spatulate incisiform teeth, which dominate the occlusive wear zone in all three species. A model based on tooth structure and wear rate is proposed to explain how halfbeaks maintain a fully functional occlusion zone throughout growth and consequent tooth addition and replacement. Replacement teeth erupt and wear rapidly so that a constant occlusion plane is always present. Iron within the tooth tissue reduces the wear rate of the cutting edge while simultaneously maintaining its sharpness and efficiency. J. Morphol. 2009. © 2008 Wiley‐Liss, Inc.     

基于“无废理念”的纺织服装工业区绿色化改造模式研究

通过对中国工业区,特别是纺织服装工业区"产废"情况的梳理,明确针对污染严重,经济效益不高的工业区进行改造的必要性。为实现对纺织服装工业区绿色化改造,从"无废理念"出发,重点研究纺织服装工业区绿色化改造的可实施路径。在研究方法上将纺织服装工业区作为研究整体,基于可持续发展思想,构建纺织服装工业区经济、社会、环境复合生态系统,运用层次分析法,选取对于该类工业园区具有代表性的经济、社会、环境指标进行评价,通过评价后总的分值,结合生命周期规律,将需要改造的纺织服装工业区进行初步筛选。同时,利用经济、社会、环境各子系统的分值,对具体改造模式加以判别。文章通过对纺织服装工业区不可持续性的内涵挖掘,将工业区绿色化改造模式与改造内容建立关联,可以通过产业绿色化改造和建成空间绿色化改造,来实现工业园区的升级与转型,进而实现可持续发展。最后,根据模式判别结果,针对不同模式在产业与建成空间的不同特征,提出相应的绿色化改造方法和政策建议。在结论中总结基于"无废理念"纺织服装工业区绿色化改造与可持续发展的辩证关系。此方法适用于其他类型的工业区改造模式判别,以促进工业区的可持续发展。     

Estimation and Inference for the Causal Effect of Receiving Treatment on a Multinomial Outcome: An Alternative Approach

Summary Recently, Cheng (2009 , Biometrics 65, 96–103) proposed a model for the causal effect of receiving treatment when there is all‐or‐none compliance in one randomization group, with maximum likelihood estimation based on convex programming. We discuss an alternative approach that involves a model for all‐or‐none compliance in two randomization groups and estimation via a perfect fit or an expectation–maximization algorithm for count data. We believe this approach is easier to implement, which would facilitate the reproduction of calculations.     

玉米叶片三维形态的数学模拟研究

根据玉米叶片三维形态特征,应用悬臂梁模型来描述玉米叶曲线,对描述玉米叶片边缘扭曲的数学模型进行改进后,提出了基于特征参数的玉米叶片三维形态数学模型及其实现方法,本模型大大减少了描述全米叶片三维形态的信息量,并具有较高的逼真性,同时适用于描述其它禾谷类作物叶片的三维形态。     

High‐throughput protein refolding screening method using zeolite

We established a 96‐well‐plate‐based refolding screening system using zeolite. In this system, protein denatured and solubilized with 6 M guanidine hydrochloride is adsorbed onto zeolite placed in a 96‐well plate. The refolding conditions can be tested by incubating the samples with refolding buffers under various conditions of pH, salts, and additives. In this study, we chose green fluorescent protein as the model protein. Green fluorescent protein was expressed as inclusion bodies, and we tested the effects of four pH conditions and six additives on its refolding. The results demonstrate that green fluorescent protein was more efficiently refolded with zeolite than with the conventional dilution method. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Linking flux network measurements to continental scale simulations: ecosystem carbon dioxide exchange capacity under non-water-stressed conditions

This paper examines long‐term eddy covariance data from 18 European and 17 North American and Asian forest, wetland, tundra, grassland, and cropland sites under non‐water‐stressed conditions with an empirical rectangular hyperbolic light response model and a single layer two light‐class carboxylase‐based model. Relationships according to ecosystem functional type are demonstrated between empirical and physiological parameters, suggesting linkages between easily estimated parameters and those with greater potential for process interpretation. Relatively sparse documentation of leaf area index dynamics at flux tower sites is found to be a major difficulty in model inversion and flux interpretation. Therefore, a simplification of the physiological model is carried out for a subset of European network sites with extensive ancillary data. The results from these selected sites are used to derive a new parameter and means for comparing empirical and physiologically based methods across all sites, regardless of ancillary data. The results from the European analysis are then compared with results from the other Northern Hemisphere sites and similar relationships for the simplified process‐based parameter were found to hold for European, North American, and Asian temperate and boreal climate zones. This parameter is useful for bridging between flux network observations and continental scale spatial simulations of vegetation/atmosphere carbon dioxide exchange.     

Soft‐modeling based spectrofluorimetric study of simultaneous equilibria

A two‐way soft resolution method will fail when applied to a simultaneous equilibria system due to rank deficiency in its concentration profiles. Increasing the dimensionality of measurements from two‐way to three‐way data can be used to overcome this problem. Simultaneous dissociation of two weak acids is considered as a model for simultaneous equilibria. Three‐way data obtained from excitation–emission spectrofluorimetric monitoring of a pH‐metric titration is analyzed using a proper combination of well‐known soft‐modeling methods. Multivariate curve resolution‐alternating least squares is used for calculating the excitation and emission spectral profiles of involved species and rank annihilation factor analysis for obtaining the contribution of each species in measured excitation–emission matrices at different pHs. The results of simulated and real simultaneous acids dissociation equilibria showed that the proposed combined method performs well even in situation when the equilibrium constants are close to each other. The applicability of method for study of an acidic dissociation is also shown. Copyright © 2009 John Wiley & Sons, Ltd.     

Growth behavior of number distributed adherent MDCK cells for optimization in microcarrier cultures

An assay for measuring the number of adherent cells on microcarriers that is independent from dilution errors in sample preparation was used to investigate attachment dynamics and cell growth. It could be shown that the recovery of seeded cells is a function of the specific rates of cell attachment and cell death, and finally a function of the initial cell‐to‐bead ratio. An unstructured, segregated population balance model was developed that considers individual classes of microcarriers covered by 1–220 cells/bead. The model describes the distribution of initially attached cells and their growth in a microcarrier system. The model distinguishes between subpopulations of dividing and nondividing cells and describes in a detailed way cell attachment, cell growth, density‐dependent growth inhibition, and basic metabolism of Madin‐Darby canine kidney cells used in influenza vaccine manufacturing. To obtain a model approach that is suitable for process control applications, a reduced growth model without cell subpopulations, but with a formulation of the specific cell growth rate as a function of the initial cell distribution on microcarriers after seeding was developed. With both model approaches, the fraction of growth‐inhibited cells could be predicted. Simulation results of two cultivations with a different number of initially seeded cells showed that the growth kinetics of adherent cells at the given cultivation conditions is mainly determined by the range of disparity in the initial distribution of cells on microcarriers after attachment. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009