A Probabilistic Analysis of Regional Mercury Impacts on Wildlife

We investigate the uncertainties associated with modeling the potential health effects on piscivorous animals of mercury released to the atmosphere. The multimedia modeling system combines an atmospheric fate and transport model, an aquatic cycling model, and a terrestrial food web model. First, the modeling system is used to calculate point values of the animals' hazard quotients (i.e., measures of toxic dose). Next, we use a simplified version of the modeling system to conduct a probabilistic analysis for the Great Lakes region that takes into account input uncertainty, variability, and uncertainty and variability combined. The use of two different software packages for the combined uncertainty/variability analysis led to similar results except for high values (>90th percentile) where some differences were evident. A sensitivity study was performed on the combined uncertainty and variability analysis. Regional variability caused more than 70% of the variance in the results, with the fish bioaccumulation factor accounting for the majority of the variability. The major sources of uncertainty were the speciation of the mercury emissions, the lake pH, and the sediment burial rate.     

Stochastic and Subjective Uncertainty in the Assessment of Radiation Exposure at the Waste Isolation Pilot Plant

The Waste Isolation Pilot Plant (WIPP) is under development by the U.S. Department of Energy as a geologic (i.e., deep underground) disposal facility for transuranic waste. An analysis is presented of possible radiation exposures associated with inadvertent drilling intrusions through the WIPP using future drilling rates obtained in accordance with requirements specified by the U.S. Environmental Protection Agency (EPA) in 40 CFR 194, Subpart B. The analysis attempts to maintain a separation between stochastic (i.e., aleatory) and subjective (i.e., epistemic) uncertainty as implied in the EPA regulations 40 CFR 191, Subpart B, and 40 CFR 194. The results of the analysis are presented as distributions of complementary cumulative distribution functions (CCDFs) for radiation exposure to oil field workers, where the individual CCDFs arise from stochastic uncertainty (i.e., many possible patterns of drill ing intrusions are possible over the 10,000?yr period specified in 40 CFR 191, Subpart B) and the distributions of CCDFs arise from subjective uncertainty (i.e., many inputs to the analysis have fixed, but poorly known, values). The projected radiation exposures during the 10,000?yr period following decommissioning of the WIPP in the year 2033 were found to be small (typically less than 0.001 person-Sv), with the dominant exposure pathway being the incidental ingestion of contaminated dirt by drilling crew members.     

Treatments of Uncertainty and Variability in Ecological Risk Assessment of Single-Species Populations

The selection of the most appropriate model for an ecological risk assessment depends on the application, the data and resources available, the knowledge base of the assessor, the relevant endpoints, and the extent to which the model deals with uncertainty. Since ecological systems are highly variable and our knowledge of model input parameters is uncertain, it is important that models include treatments of uncertainty and variability, and that results are reported in this light. In this paper we discuss treatments of variation and uncertainty in a variety of population models. In ecological risk assessments, the risk relates to the probability of an adverse event in the context of environmental variation. Uncertainty relates to ignorance about parameter values, e.g., measurement error and systematic error. An assessment of the full distribution of risks, under variability and parameter uncertainty, will give the most comprehensive and flexible endpoint. In this paper we present the rationale behind probabilistic risk assessment, identify the sources of uncertainty relevant for risk assessment and provide an overview of a range of population models. While all of the models reviewed have some utility in ecology, some have more comprehensive treatments of uncertainty than others. We identify the models that allow probabilistic assessments and sensitivity analyses, and we offer recommendations for further developments that aim towards more comprehensive and reliable ecological risk assessments for populations.     

Selection of Stable Reference Genes for Quantitative Real-Time PCR on <i>Paeonia ostii</i> T. Hong et J. X. Zhang Leaves Exposed to Different Drought Stress Conditions

The definition of relatively stable expressed internal reference genes is essential in both traditional blotting quantification and as a modern data quantitative strategy. Appropriate internal reference genes can accurately standardize the expression abundance of target genes to avoid serious experimental errors. In this study, the expression profiles of ten candidate genes, ACT1, ACT2, GAPDH, eIF1, eIF2, α-TUB, β-TUB, TBP, RNA Pol II and RP II, were calculated for a suitable reference gene selection in Paeonia ostii T. Hong et J. X. Zhang leaves under various drought stress conditions. Data were processed by the four regularly used evaluation software. A comprehensive analysis revealed that RNA Pol II was the most stable gene and eIF2 was the least stable one. In addition, the geNorm program provided the optimal choice of two reference gene combination, RNA Pol II and β-TUB, for qRT-PCR normalization in P. ostii subjected to different drought stress levels. Our research provided convenience for gene expression analysis in P. ostii under drought stress and promoted research of effective methods to alleviate P. ostii drought stress in the future.     

Making more sense of the order: A review of Canoco for Windows 4.5, PC‐ORD version 4 and SYN‐TAX 2000

Abstract. Personal computers of ever‐increasing speed have motivated programmers of multivariate software to adapt their programs to be run in Microsoft Windows and Macintosh platforms. Updated versions of these multivariate programs appear more and more frequently and are marketed intensively. In this review we provide a comparative analysis of the most recent versions of three analytical software packages –Canoco for Windows 4.5, PC‐ORD version 4 and SYN‐TAX 2000. The three packages share two characteristics. First, the most recent versions are now compatible with the most recent Windows platforms and should therefore be accessible for use by virtually all vegetation scientists. Second, they have capabilities for numerous multivariate techniques, although each package has some unique techniques. Thus, any one of the packages will have much to offer the user.     

Public Reactions to Risk Messages Communicating Different Sources of Uncertainty: An Experimental Test

There is an abundant literature on the challenge of integrating uncertainties in experts’ risk assessments, but the evidence on the way they are understood by the public is scarce and mixed. This study aims to better understand the effect of communicating different sources of uncertainty in risk communication. A causal design was employed to test the effect of communicating risk messages varying in type of advisory warning (no risk and suggests no protective measure, or risk and recommends a protective measure) and sources of uncertainty (no uncertainty, divergence between experts, contradictory data, or lack of data) on public reactions. Participants from the general public (N = 434) were randomly assigned to read and react to variants of a fictitious government message discussing the presence of a new micro-organism found in tap water. Multiple analysis of variance showed that to report uncertainty from divergence between experts or from contradictory data reduced the adherence to the message, but not to mention the lack of data. Moreover, the communication of diverse sources of uncertainty did not affect trust in the government when the advisory warning stated there was a risk and recommended a protective measure. These findings have important implications for risk communication.     

Selective separation and enrichment of peptides for MS analysis using the microspheres composed of Fe3O4@nSiO2 core and perpendicularly aligned mesoporous SiO2 shell

In this work, we report the development of a novel enrichment protocol for peptides by using the microspheres composed of Fe₃O₄@nSiO₂ Core and perpendicularly aligned mesoporous SiO₂ shell (designated Fe₃O₄@nSiO₂@mSiO₂). The Fe₃O₄@nSiO₂@mSiO₂ microspheres possess useful magnetic responsivity which makes the process of enrichment fast and convenient. The highly ordered nanoscale pores (2 nm) and high‐surface areas of the microspheres were demonstrated to have good size‐exclusion effect for the adsorption of peptides. An increase of S/N ratio over 100 times could be achieved by using the microspheres to enrich a standard peptide, and the application of the microspheres to enrich universal peptides was performed by using myoglobin tryptic digest solution. The enrichment efficiency of re‐used Fe₃O₄@nSiO₂@mSiO₂ microspheres was also studied. Large‐scale enrichment of endogenous peptides in rat brain extract was achieved by the microspheres. Automated nano‐LC‐ESI‐MS/MS was applied to analyze the sample after enrichment, and 60 unique peptides were identified in total. The facile and low‐cost synthesis as well as the convenient and efficient enrichment process of the novel Fe₃O₄@nSiO₂@mSiO₂ microspheres makes it a promising candidate for selectively isolation and enrichment of endogenous peptides from complex biological samples.     

A Practical Plan for Public Works of Art Heckman Summer School at Woodstock

The 1957 launch of Sputnik and the 1983 publication of A Nation at Risk shifted national education policy. Music educators promoted an “intrinsic value” of music philosophy following Sputnik and music advocacy through politics and public performances following A Nation at Risk. Examining the history of both the intrinsic value philosophy and advocacy reveals that music educators responded to Sputnik and A Nation at Risk by continuing to work within their existing language and practices rather than reacting to and transforming after either event. The political, social, and cultural contexts of these events may explain music educators’ responses.     

Network Meta-Analysis Using R: A Review of Currently Available Automated Packages

Network meta-analysis (NMA) – a statistical technique that allows comparison of multiple treatments in the same meta-analysis simultaneously – has become increasingly popular in the medical literature in recent years. The statistical methodology underpinning this technique and software tools for implementing the methods are evolving. Both commercial and freely available statistical software packages have been developed to facilitate the statistical computations using NMA with varying degrees of functionality and ease of use. This paper aims to introduce the reader to three R packages, namely, gemtc, pcnetmeta, and netmeta, which are freely available software tools implemented in R. Each automates the process of performing NMA so that users can perform the analysis with minimal computational effort. We present, compare and contrast the availability and functionality of different important features of NMA in these three packages so that clinical investigators and researchers can determine which R packages to implement depending on their analysis needs. Four summary tables detailing (i) data input and network plotting, (ii) modeling options, (iii) assumption checking and diagnostic testing, and (iv) inference and reporting tools, are provided, along with an analysis of a previously published dataset to illustrate the outputs available from each package. We demonstrate that each of the three packages provides a useful set of tools, and combined provide users with nearly all functionality that might be desired when conducting a NMA.     

Regional material flow behaviors of agro‐food processing craft villages in Red River Delta,Vietnam

The economic reform “??i M?i” in 1986 has rapidly increased the number of craft villages in Vietnam, especially in the Red River Delta (RRD) leading to environmental degradation. This article presents an assessment of environmental and resource issues of agro‐Food Processing Craft Villages (FPCVs) in RRD using a refined approach to material flow analysis focusing on consistent quantification of uncertainty with particular attention to secondary and empirical data that are often faced in material flow analyses in transition economies. Material flows of agro‐Food Processing including eight types of production were examined and linked to activities of private Households, Rice Cultivation, and Pig Farming in a model called Red River Delta. Materials investigated were Goods (i.e., total materials), organic carbon (org.C), nitrogen (N), and phosphorus (P). The findings reveal material cycles are almost entirely open, that is, the materials used in FPCVs do not recycle within the region. From ～10.5 million tons/year of imported Goods used for agro‐Food Processing, final products and utilized materials account for minor fractions (～5%, by weight). Conversely, the majority (88%) is directly discharged. Materials accumulated as stocks represent 1% of Goods (100,000 tons/year), 21% of org.C (～34,000 tons/year), 42% of N (～1,300 tons/year), and 57% of P (～300 tons/year), whose substance concentrations vastly exceed natural resilience capacities. Although agro‐Food Processing accounts for negligible material shares in Red River Delta, FPCVs pollution is severe at local levels due to the location of home‐based production. Several options for closing material loops at various system scales are recommended for environmental and resource management of FPCVs. The material flow analysis results provide a database that may be used as a decision support tool for production establishments in craft villages and relevant authorities in setting priorities on environmental planning and resource management. This article met the requirements for a gold – silver JIE data openness badge described at http://jie.click/badges .     

Consumer adoption of personalised nutrition services from the perspective of a risk–benefit trade-off

Through a Privacy Calculus (i.e. risk–benefit trade-off) lens, this study identifies factors that contribute to consumers’ adoption of personalised nutrition services. We argue that consumers’ intention to adopt personalised nutrition services is determined by perceptions of Privacy Risk, Personalisation Benefit, Information Control, Information Intrusiveness, Service Effectiveness, and the Benevolence, Integrity, and Ability of a service provider. Data were collected in eight European countries using an online survey. Results confirmed a robust and Europe-wide applicable cognitive model, showing that consumers’ intention to adopt personalised nutrition services depends more on Perceived Personalisation Benefit than on Perceived Privacy Risk. Perceived Privacy Risk was mainly determined by perceptions of Information Control, whereas Perceived Personalisation Benefit primarily depended on Perceived Service Effectiveness. Services that required increasingly intimate personal information, and in particular DNA, raised consumers’ Privacy Risk perceptions, but failed to increase perceptions of Personalisation Benefit. Accordingly, to successfully exploit personalised nutrition, service providers should convey a clear message regarding the benefits and effectiveness of personalised nutrition services. Furthermore, service providers may reduce Privacy Risk by increasing consumer perceptions of Information Control. To enhance perceptions of both Information Control and Service Effectiveness, service providers should make sure that consumers perceive them as competent and reliable.     

单木生物量模型估计区域尺度生物量的不确定性

采用系统抽样体系江西省固定样地杉木连续观测数据和生物量数据,通过Monte Carlo法反复模拟由单木生物量模型推算区域尺度地上生物量的过程,估计了江西省杉木地上总生物量。基于不同水平建模样本量n及不同决定系数R~2的设计,分别研究了单木生物量模型参数变异性及模型残差变异性对区域尺度生物量估计不确定性的影响。研究结果表明:2009年江西省杉木地上生物量估计值为(19.84±1.27)t/hm~2,不确定性占生物量估计值约6.41%。生物量估计值和不确定性值达到平稳状态所需的运算时间随建模样本量及决定系数R~2的增大而减小;相对于模型参数变异性,残差变异性对不确定性的影响更小。     

JUICE,software for vegetation classification

Abstract. The program JUICE was designed as a Microsoft® WINDOWS® application for editing, classification and analysis of large phytosociological tables and databases. This software, with a current maximum capacity of 30 000 relevés in one table, includes many functions for easy manipulation of table and header data. Various options include classification using COCKTAIL and TWINSPAN methods, calculation of interspecific associations, fidelity measures, average Ellenberg indicator values, preparation of synoptic tables, automatic sorting of relevé tables, and export of table data into other applications (word processors, spreadsheet programs or mapping packages). JUICE is optimized for use in association with TURBOVEG which is the most widespread database program for storing phytosociological data in Europe.     

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     

Essential‐Oil Diversity of Three Calamintha Species from Greece

The aim of the present study was to contribute to the knowledge of the essential‐oil composition of the Calamintha officinalis‐nepeta complex in Greece and to clarify the main patterns of its variation. The oils obtained from 22 wild‐growing populations of C. glandulosa, C. nepeta, and C. menthifolia were studied. They could be classified into two different chemotypes, which correspond to the main biosynthetic routes of the C(3)‐oxygenated p‐menthane compounds. Chemotype I includes oils rich in trans‐piperitone oxide, cis‐piperitone oxide, and piperitenone oxide, while Chemotype II comprises oils rich in pulegone and menthone or menthone and isomenthone. Within both chemotypes, quantitative fluctuations of the main components were observed. Comparison with published data showed that the presence of Chemotype II has not been observed before in C. menthifolia, while Chemotype I has been reported in C. nepeta plants from Greece for the first time.     

An attempt to apply ligand field theory to positronium reactions with 3d complexes

Positronium, Ps, the bound state between an electron, e, and a positron, c⁺, may have two spin states: theortho,o-Ps, and thepara,p-Ps, states, which differ for the spin orientation of the two particles. The two types of Ps atoms may be inter-converted by collision with paramagnetic compounds, such as several3d complexes. By investigating about 90 complexes of V^II, Cr^II, Cr^III, Mn^II, Fe^II, Co^II and Ni^II as a function of temperature, it was found that the rate constants k_CR of theo-Ps intop-Ps conversion reactions, CR, are linearly correlated to the delocalization β of metal electrons caused by the ligands. Therefore, if β known, k_CR may be estimated andvice versa. This suggests a new method for the experimental determination of β. The rate constants of the Ps oxidation reactions by Co^III complexes were also investigated and discussed. The paper is preceded by four sections dealing with: 1) the positron and positronium formation; 2) the positron annihilation modes; 3) the methods for measuring the Ps rate constants and establishing the Ps reaction types; 4) the application of the Smoluchowski equation to Ps reactions. Moreover, an attempt is made to ascertain the standard electrochemical potential of Ps atoms. The positron reactions and the formation of positronides are also taken into consideration. Presentata nella seduta del 13 dicembre 2002 dal Socio F. Calderazzo.     

Mutation analysis of the different<Emphasis Type="Italic"> tfd</Emphasis> genes for degradation of chloroaromatic compounds in<Emphasis Type="Italic"> Ralstonia eutropha</Emphasis> JMP134

Ralstonia eutropha JMP134 possesses two sets of similar genes for degradation of chloroaromatic compounds, tfdCDEFB (in short: tfd _I cluster) and tfdD _II C _II E _II F _II B _II (tfd _II cluster). The significance of two sets of tfd genes for the organism has long been elusive. Here, each of the tfd genes in the two clusters on the original plasmid pJP4 was replaced by double recombination with a gene fragment in which a kanamycin resistance gene was inserted into the respective tfd genes reading frame. The insertion mutants were all tested for growth on 2,4-dichlorophenoxyacetic acid (2,4-D), 2-methyl-4-chlorophenoxyacetic acid (MCPA), and 3-chlorobenzoate (3-CBA). None of the tfdD _II C _II E _II F _II B _II genes appeared to be essential for growth on 2,4-D or on 3-CBA. Mutations in tfdC, tfdD and tfdF also did not abolish but only retarded growth on 2,4-D, indicating that they were redundant to some extent as well. Of all tfd genes tested, only tfdE and tfdB were absolutely essential, and interruption of those two reading frames abolished growth on 2,4-D, 3-CBA (tfdE only), and MCPA completely. Interestingly, strains with insertion mutations in the tfd _I cluster and those in tfdD _II , tfdC _II , tfdE _II and tfdB _II were severely effected in their growth on MCPA, compared to the wild-type. This indicated that not only the tfd _I cluster but also the tfd _II cluster has an essential function for R. eutropha during growth on MCPA. In contrast, insertion mutation of tfdD _II resulted in better growth of R. eutropha JMP134 on 3-CBA, which is most likely due to the prevention of toxic metabolite production in the absence of TfdD_II activity.     

Economic analysis of pilot‐scale production of B‐phycoerythrin

β‐Phycoerythrin is a color protein with several applications, from food coloring to molecular labeling. Depending on the application, different purity is required, affecting production cost and price. Different production and purification strategies for B‐phycoerythrin have been developed, the most studied are based on the production using Porphyridium cruentum and purified using chromatographic techniques or aqueous two‐phase systems. The use of the latter can result in a less expensive and intensive recovery of the protein, but there is lack of a proper economic analysis to study the effect of using aqueous two‐phase systems in a scaled‐up process. This study analyzed the production of B‐Phycoerythrin using real data obtained during the scale‐up of a bioprocess using specialized software (BioSolve, Biopharm Services, UK). First, a sensitivity analysis was performed to identify critical parameters for the production cost, then a Monte Carlo analysis to emulate real processes by adding uncertainty to the identified parameters. Next, the bioprocess was analyzed to determine its financial attractiveness and possible optimization strategies were tested and discussed. Results show that aqueous two‐phase systems retain their advantages of low cost and intensive recovery (54.56%); the costs of production per gram calculated (before titer optimization: US$15,709 and after optimization: US$2,374) allowed to obtain profit (in the range of US$millions in a 10‐year period) for a potential company taking this production method by comparing the production cost against commercial prices. The bioprocess analyzed is a promising and profitable method for the generation of a highly purified B‐phycoerythrin. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1472–1479, 2016     

Evidence for two chemosensory pathways in Rhodobacter sphaeroides

In contrast to enteric bacteria, chemotaxis in Rhodobacter sphaeroides requires transport and partial metabolism of chemoattractants. Although a chemotaxis operon has been identified containing homologues of the enteric cheA, cheW, cheR genes and two homologues of the cheY gene, deletion of the entire chemotaxis operon had only minor effects on chemotactic behaviour under the conditions tested. Responses to sugars were enhanced in tethered cells but in all other chemotaxis assays behaviour of the operon deletion mutant was wild type. The mutant also showed wild-type responses to weak organic acids such as acetate and propionate, the dominant chemoattractants for this organism, under all conditions. This is in direct contrast to the enterics in which CheA, CheW and CheY are absolutely essential for taxis to PTS sugars, oxygen and MCP-dependent chemoeffectors. The operon deletion mutant was subjected to Tn5 transposon mutagenesis and new mutants selected using a chemotaxis and phototaxis screen. One mutant, JPA203, was non-chemotactic on swarm plates and showed inverted responses when tethered or subjected to changes in light intensity. Characterization of the Tn5 insertion in JPA203 identified a second chemotaxis operon in R. sphaeroides that contains homologues of cheY, cheA and cheR, the first homologue of cheB and two homologues of cheW. The new genes were labelled orf10, cheY_III, cheA_II, cheW_II, cheW_III, cheR_II, cheB and tlpC. When introduced into a wild-type background, deletion of cheA_II produced a chemotaxis minus phenotype in R. sphaeroides, suggesting that cheA_II forms part of a dominant chemotactic pathway, whereas the earlier identified operon plays only a minor role under laboratory conditions. The data presented here support the existence of two chemosensory pathways in R. sphaeroides, a feature that so far is unique in bacterial chemotaxis.