Some insights into protein structural class prediction

It has been quite clear that the success rate for predicting protein structural class can be improved significantly by using the algorithms that incorporate the coupling effect among different amino acid components of a protein. However, there is still a lot of confusion in understanding the relationship of these advanced algorithms, such as the least Mahalanobis distance algorithm, the component-coupled algorithm, and the Bayes decision rule. In this communication, a simple, rigorous derivation is provided to prove that the Bayes decision rule introduced recently for protein structural class prediction is completely the same as the earlier component-coupled algorithm. Meanwhile, it is also very clear from the derivative equations that the least Mahalanobis distance algorithm is an approximation of the component-coupled algorithm, also named as the covariant-discriminant algorithm introduced by Chou and Elrod in protein subcellular location prediction (Protein Engineering, 1999; 12:107-118). Clarification of the confusion will help use these powerful algorithms effectively and correctly interpret the results obtained by them, so as to conduce to the further development not only in the structural prediction area, but in some other relevant areas in protein science as well.     

Optimization of the chiral separation of some 2-arylpropionic acids on an avidin column by modeling a combined response

The enantiomeric separation of some nonsteroidal antiinflammatory drugs was investigated on an avidin column. An experimental design approach (central composite design) was used to evaluate the effects of three method parameters (pH, concentration of organic modifier, and buffer concentration) on the analysis time and the resolution, as well as to model these responses. This revealed that the organic modifier concentration and sometimes the pH are significant parameters to control because of their influence on both analysis time and resolution. Furthermore, the central composite design results were combined in a multicriteria decision-making approach in order to obtain a set of optimal experimental conditions leading to the most desirable compromise between resolution and analysis time.     

Evidence for a pre-restriction point Cdk3 activity

We have examined the activity of cyclin-dependent kinase 3 (cdk3) during G1-phase of the cell cycle in Chinese Hamster Ovary (CHO) fibroblasts. Histone H1 kinase activity associated with anti-cdk3 immunoprecipitates peaked during a brief window of time, 2-3 h prior to the restriction point. In vitro cdk3 activity was sensitive to roscovitine, a drug previously shown to inhibit cdks 1, 2, and 5, but not cdk4 or 6. Early G1-phase activation of cdk3 was downregulated by treatment of cells with MG132, an inhibitor of the proteasome, and by the protein synthesis inhibitor cycloheximide. These results provide evidence for a pre-restriction point cdk3 activity that requires both the synthesis of a regulatory subunit and degradation of an inhibitor.     

Aid for aggregating the impacts in Life Cycle assessment

Background and Objectives  Multiple Criteria Decision Aid (MCDA) methods may be employed in a great number of fields. Life Cycle Assessment (LCA) is a specific method among the MCDA Methods. A stage of MCDA methods to be respected in LCA is the comparative evaluation of the environmental impacts. This stage is the most difficult to implement because it is a question of estimating the global environmental impact of the life cycles studied. To achieve this purpose, it is necessary to model the environmental impacts and to apply a Multicriteria Analysis (MCA) method. The problem is to choose the most suitable among the available MCA methods. The objective of this paper is to help the LCA practitioner to make this choice. Methodology  The MCA methods are compared according to their non-compensatory degree, their sensitivity to thresholds, their practicability and their workability. Results and Conclusion  The protocol presented in this paper allows to choose the most appropriate MCA method for a given LCA according to the four previous criteria. This choice will depend on the priorities of the decision maker with concern to the comparison criteria.     

A colicin-tolerant Escherichia coli mutant that confers hfl phenotype carries two mutations in the region coding for the C-terminal domain of FtsH (HflB)

An Escherichia coli mutant, ER437, which was originally isolated for colicin tolerance, was found to carry two amino acid changes in the C-terminal portion of FtsH (HflB). These mutations were demonstrated to reduce the ability of FtsH to degrade the phage lambda CII protein in vivo and in vitro, providing a rationalization for the mutant Hfl phenotype.     

Are life cycle assessments a threat to sound public policy making?

This paper deals with the question of whether Life Cycle Assessments (LCAs), with their focus on objective and quantitative results, are the best way to support public policy processes. The public policy making process is characterized as a continuous discoursive struggle. Criteria are defined to distinguish between good and bad public policy discourses to judge the effects of LCA on the public policy process. Many policy scientists argue that methodologies that emphasize quantification and the use of formal methods are not beneficial for sound public policy making. An empirical report of the role LCAs played in public policy making processes on PVC and chlorine in the Netherlands is made to evaluate the contribution of LCAs to public policy making processes and to identify the main limitations of the current LCA methodologies and practices. It appears that political actors tend to use LCAs in a polarizing way. LCAs are easily misused due to their apparent objectivity, and the quantitative and black box nature of their results. LCAs contain an implicit, normative frame that does not match the environmentalists’ perception on the kind of evidence needed on toxic effects of organochlorines, which reduced the open nature of the Dutch PVC debate. It is recommended to develop a methodology for product evaluation that approaches the issue in a more open and emergent way to prevent “premature closure” of the analysis. It is expected that a focus on the development of balanced, rich arguments on facts and values in the study process will be more fruitful than the calculation of integral, quantitative indicators.     

Evaluating options in LCA: The emergence of conflicting paradigms for impact assessment and evaluation

LCA aims to help direct decisions in an environmentally sustainable direction. It indicates the environmental effects of choices and evaluates these against this background. Approaches to evaluation in LCA differ substantially, related to the way of modelling environmental effects and to the way these effects are combined into an overall judgement on alternative options. Several approaches are now operational, which are linked to different paradigms in decision making. It is shown that the choice of paradigm is quite decisive on the outcome of the analysis. Also within similar paradigms, different methods now operational may lead to different outcomes. These latter differences may be alleviated more easily than those related to paradigmatic choices, as they are partly a matter of refinement, and they partly result from legitimate differences in subjective priorities. The more basic paradigmatic differences can hardly be bridged. The practical relevancy of the subject is proven by applying different operational methods to one case, showing widely differing outcomes. The paradigm behind evaluating environmental effects is either values based, directly or through policy decisions, or economics based, as individual preferences measured in the monetary terms of willingness-to-pay. Accordingly, the different methods are “policy-oriented” or “monetary”. It may be doubted if the differences between these can be overcome in standardisation.     

区域农业综合生产力的AHP-Fuzzy综合评判

根据系统分析原理,在确定区域农业综合生产力系统的层次结构基础上,用层次分析法确定各因素的权重,用模糊多级综合评判法对各区域综合生产力进行综合的评价．具有一定的科学性和实用价格．