Clusterings should not be compared by visual inspection: response to Gagné & Proulx

In Heikinheimo et al . ( Journal of Biogeography , 2007, 34 , 1053–1064) we used clustering to analyse European land mammal fauna. Gagné & Proulx criticized our choice of the Euclidean distance measure in the analysis, and advocated the use of the Hellinger distance measure, claiming that this leads to very different clustering results. The criticism fails to take into account the probabilistic nature of the methods used and the fact that in this case the similarity measures correlate strongly. Gagné & Proulx used subjective inspection as the criterion of similarity between clusterings. We show that this is insufficient and misleading. Namely, owing to the local minimum problem, two clustering runs rarely give identical results. In the case of our study, the measured similarity (using the kappa statistic) between the Euclidean- and Hellinger-based clusterings is roughly equal to the similarity between two clusterings that both use the Hellinger distance but different random initialization points.     

On Analysis of Proportions in Tables with Spoiled Data

This paper discusses analysis of dispersion tests in tables with spoiled data, that is, where some cells are missing. BENNETT (1987) gave a method for estimating the missing cells in a two-way table and illustrated it with a simple example. This paper uses GLIM to estimate the models and indicates that the General Linear Model performs the computations without need to estimate the missing values. The binomial error model also may be used for this problem, and is the more natural approach to the problem.     

Enantiopurity and absolute configuration determination of arene cis‐dihydrodiol metabolites and derivatives using chiral boronic acids

The relative merits of the methods employed to determine enantiomeric excess (ee) values and absolute configurations of chiral arene and alkene cis‐1,2‐diol metabolites, including boronate formation, using racemic or enantiopure (+) and (?)‐2‐(1‐methoxyethyl)phenylboronic acid (MEPBA), are discussed. Further applications of: 1) MEPBA derived boronates of chiral mono‐ and poly‐cyclic arene cis‐dihydrodiol, cyclohex‐2‐en‐1‐one cis‐diol, heteroarene cis/trans‐2,3‐diol, and catechol metabolites in estimating their ee values, and 2) new chiral phenylboronic acids, 2‐[1‐methoxy‐2,2‐dimethylpropyl]phenyl boronic acid (MDPBA) and 2‐[1‐methoxy‐1‐phenylmethyl]phenyl boronic acid (MPPBA) and their advantages over MEPBA, as reagents for stereochemical analysis of arene and alkene cis‐diol metabolites, are presented.     

Use and non-use values as motivational construct dimensions for farm animal welfare: impacts on the economic outcome for the farm

This study explored how farmers’ motivation in terms of use values and/or non-use values to work with farm animal welfare are associated with the economic outcome for the farm. Use values in farm animal welfare refer to economic value derived from productivity and profitability considerations. Non-use values in farm animal welfare refer to economic value derived from good animal welfare, irrespective of the use the farmer derives from the animal, currently or in the future. The analysis was based on detailed information about the income statements of a sample of Swedish dairy farmers, obtained from the Swedish Farm Economic Survey, complemented with survey information about their perceived use and non-use values in farm animal welfare. The findings suggest that farm economic outcome is significantly associated with motivation in terms of use values, but not so much with motivation in terms of non-use values. This is interesting from a policy point of view, because it indicates that farmers with different approaches to farm animal welfare may experience different economic outcomes for their farms. Findings can, for instance, be used to strengthen farmers’ engagement in various private quality assurance standards, which generally focus on values of non-use type, by pointing to that realisation of such values will not impair the economic outcome of the farms. Moreover, findings also suggest that farmers’ economic incentives for engagement in such standards may need to be further strengthened in order to become more attractive, as findings point to that a focus on non-use values generally is not associated with more favourable economic outcomes.     

Role of AP‐endonuclease (Ape1) active site residues in stabilization of the reactant enzyme‐DNA complex

Apurinic/apyrimidinic endonuclease 1 (Ape1) is an important metal‐dependent enzyme in the base excision repair mechanism, responsible for the backbone cleavage of abasic DNA through a phosphate hydrolysis reaction. Molecular dynamics simulations of Ape1 complexed to its substrate DNA performed for models containing 1 or 2 Mg²⁺‐ions as cofactor located at different positions show a complex with 1 metal ion bound on the leaving group site of the scissile phosphate to be the most likely reaction‐competent conformation. Active‐site residue His309 is found to be protonated based on pKa calculations and the higher conformational stability of the Ape1‐DNA substrate complex compared to scenarios with neutral His309. Simulations of the D210N mutant further support the prevalence of protonated His309 and strongly suggest Asp210 as the general base for proton acceptance by a nucleophilic water molecule.     

Valuation study of urban bushland at Hartfield Park, Forrestfield, Western Australia

Summary Hartfield Park bushland represents a typical area of Perth urban bushland, and is identified as one site worthy of protection in the Western Australian Government's Bush Forever Plan. Two thirds of the Reserve is developed and parts of the remaining bushland are under threat of future development for parking and playing fields. This paper reports a study undertaken to estimate the economic value placed by the community on a specified urban bushland site using the contingent valuation method, a stated preference, non‐market valuation technique which captures both use and non‐use values. Because environmental goods such as urban bushland exist without organized markets, they are often omitted from the decision‐making process regarding the socially optimal management of resources. In estimating a valuation for Hartfield Park, it may be included in any cost–benefit analysis conducted for the site in future. A survey was conducted across the Perth metropolitan area during April 2001 that involved the mail out of 1000 questionnaires to names and addresses obtained at random from the Western Australia Electoral Roll. A 54% response rate was obtained. Regression analysis was used to predict the probability of people being willing to pay for the preservation of this urban bushland and the significant predictors of willingness to pay related to income and educational levels rather than proximity to or knowledge of the site. Willingness to pay was also estimated and the results indicate a conservative mean willingness to pay for the preservation of the bushland of $A21.60 per person per annum. Extrapolation of this figure across the total adult metropolitan community resulted in an estimated valuation of $A16.6 million. Median willingness to pay was also estimated and equalled $A4.35 per person per annum with a valuation for the total adult metropolitan community equal to $A3.3 million. Extrapolation of these mean and median figures across Perth households rather than adult individuals resulted in an estimated valuation of $A9.6 million and $A1.9 million, respectively. These figures indicate that the community value for this environmental amenity may exceed the costs of providing alternative facilities elsewhere.