Sampling phylogenetic tree space with the generalized Gibbs sampler

The generalized Gibbs sampler (GGS) is a recently developed Markov chain Monte Carlo (MCMC) technique that enables Gibbs-like sampling of state spaces that lack a convenient representation in terms of a fixed coordinate system. This paper describes a new sampler, called the tree sampler, which uses the GGS to sample from a state space consisting of phylogenetic trees. The tree sampler is useful for a wide range of phylogenetic applications, including Bayesian, maximum likelihood, and maximum parsimony methods. A fast new algorithm to search for a maximum parsimony phylogeny is presented, using the tree sampler in the context of simulated annealing. The mathematics underlying the algorithm is explained and its time complexity is analyzed. The method is tested on two large data sets consisting of 123 sequences and 500 sequences, respectively. The new algorithm is shown to compare very favorably in terms of speed and accuracy to the program DNAPARS from the PHYLIP package.

Isotopes, wool, and rangeland monitoring: Let the sheep do the sampling

Stable carbon isotope analyses of wool staples provided insight into the vegetation consumed by sheep at a temporal resolution not previously studied. Contemporary Australian and historic South African samples dating back to 1916 were analyzed for their stable carbon isotope ratio, a proxy for the proportion of C-3 and C-4 plant species consumed by animals. Sheep sample vegetation continuously throughout a year, and as their wool grows it integrates and stores information about their diet. In subtropical and tropical rangelands the majority of grass species are C-4. Since sheep prefer to graze, and their wool is an isotopic record of their diet, we now have the potential to develop a high resolution index to the availability of grass from a sheep's perspective. Isotopic analyses of wool suggest a new direction for monitoring grazing and for the reconstruction of past vegetation changes, which will make a significant contribution to traditional rangeland ecology and management. It is recommended that isotopic and other analyses of wool be further developed for use in rangeland monitoring programs to provide valuable feedback for land managers.

Bacteria in shrimp pond sediments: their role in mineralizing nutrients and some suggested sampling strategies

Strategies for sampling sediment bacteria were examined in intensive shrimp, Penaeus monodon (Fabricius), ponds in tropical Australia. Stratified sampling of bacteria at the end of the production season showed that the pond centre, containing flocculated sludge, had significantly higher bacterial counts (15.5 X 10(9) g(-1) dw) than the pond periphery (8.1 X 10(9) g(-1) dw), where the action of aerators had swept the pond floor. The variation in bacterial counts between these two zones within a pond was higher than that between sites within each zone or between ponds. Therefore, sampling effort should be focused within these zones: for example, sampling two ponds at six locations within each of the two zones resulted in a coefficient of variation of approximate to 5%. Bacterial numbers in the sediment were highly correlated with sediment grain size, probably because eroded soil particles and organic waste both accumulated in the centre of the pond. Despite high inputs of organic matter added to the ponds, principally as pelleted feeds, the mean bacterial numbers and nutrient concentrations (i.e. organic carbon, nitrogen and phosphorus) in the sediment were similar to those found in mangrove sediments. This suggests that bacteria are rapidly remineralizing particulates into soluble compounds. Bacterial numbers were highly correlated with organic carbon and total kjeldahl nitrogen in the sediment, suggesting that these were limiting factors to bacterial growth.

Semiochemicals and social signaling in the wild European rabbit in Australia: II. Variations in chemical composition of chin gland secretion across sampling sites

The volatile components of the chin gland secretion of the wild European rabbit, Oryctolagus cuniculus (L.), were investigated with the use of gas chromatography. Studies of the chemical nature of this secretion by previous workers demonstrated that it was important in the maintenance of social structure in this species. This study identified 34 different volatile components that consist primarily of aromatic and aliphatic hydrocarbons. Especially common are a series of alkyl-substituted benzene derivatives that provide most of the compound diversity in the secretion. Samples of chin gland secretion collected from animals at three different geographical locations, separated by more than 100 km, showed significant differences in composition. This work suggests that variation among populations needs to be considered when undertaking semiochemical research. Alternate nonparametric methods are also used for the analysis of chromatographic data.

Degradation of phenanthrene and pyrene in soil slurry reactors with immobilized bacteria Zoogloea sp.

The environmental fate of polycyclic aromatic hydrocarbons (PAHs) in soils is motivated by their wide distribution, high persistence, and potentially deleterious effect on human health. Polycyclic aromatic hydrocarbons constitute the largest group of environmental contaminants released in the environment. Therefore, the potential biodegradation of these compounds is of vital importance. A biocarrier suitable for the colonization by micro-organisms for the purpose of purifying soil contaminated by polycyclic aromatic hydrocarbons was developed. The optimized composition of the biocarrier was polyvinyl alcohol (PVA) 10%, sodium alginate (SA) 0.5%, and powdered activated carbon (PAC) 5%. There was no observable cytotoxicity of biocarriers on immobilized cells and a viable cell population of 1.86 x 10(10) g(-1) was maintained for immobilized bacterium. Biocarriers made from chemical methods had a higher biodegradation but lower mechanical strengths. Immobilized bacterium Zoogloea sp. had an ideal capability of biodegradation for phenanthrene and pyrene over a relative wide concentration range. The study results showed that the biodegradation of phenanthrene and pyrene reached 87.0 and 75.4%, respectively, by using the optimal immobilized method of Zoogloea sp. cultivated in a sterilized soil. Immobilized Zoogloea sp. was found to be effective for biodegrading the soil contaminated with phenanthrene and pyrene. Even in natural (unsterilized) soil, the biodegradation of phenanthrene and pyrene using immobilized Zoogloea sp. reached 85.0 and 67.1%, respectively, after 168 h of cultivation, more than twice that achieved if the cells were not immobilized on the biocarrier. Therefore, the immobilization technology enhanced the competitive ability of introduced micro-organisms and represents an effective method for the biotreatment of soil contaminated with phenanthrene and pyrene.

A Comparison of Bayesian and Sampling Theory Inferences in a Probit Model

HE PROBIT MODEL IS A POPULAR DEVICE for explaining binary choice decisions in econometrics. It has been used to describe choices such as labor force participation, travel mode, home ownership, and type of education. These and many more examples can be found in papers by Amemiya (1981) and Maddala (1983). Given the contribution of economics towards explaining such choices, and given the nature of data that are collected, prior information on the relationship between a choice probability and several explanatory variables frequently exists. Bayesian inference is a convenient vehicle for including such prior information. Given the increasing popularity of Bayesian inference it is useful to ask whether inferences from a probit model are sensitive to a choice between Bayesian and sampling theory techniques. Of interest is the sensitivity of inference on coefficients, probabilities, and elasticities. We consider these issues in a model designed to explain choice between fixed and variable interest rate mortgages. Two Bayesian priors are employed: a uniform prior on the coefficients, designed to be noninformative for the coefficients, and an inequality restricted prior on the signs of the coefficients. We often know, a priori, whether increasing the value of a particular explanatory variable will have a positive or negative effect on a choice probability. This knowledge can be captured by using a prior probability density function (pdf) that is truncated to be positive or negative. Thus, three sets of results are compared:those from maximum likelihood (ML) estimation, those from Bayesian estimation with an unrestricted uniform prior on the coefficients, and those from Bayesian estimation with a uniform prior truncated to accommodate inequality restrictions on the coefficients.

Effects of sampling opportunities on preference for adults with severe disabilities

A variable that appears to affect preference development is the exposure to a variety of options. Providing opportunities for systematically sampling different options is one procedure that can facilitate the development of preference, which is indicated by the consistency of selections. The purpose of this study was to evaluate the effects of providing sampling opportunities on the preference development for two adults with severe disabilities. Opportunities for sampling a variety of drink items were presented, followed by choice opportunities for selections at the site where sampling occurred and at a non-sampling site (a grocery store). Results show that the participants developed a definite response consistency in selections at both sites. Implications for sampling practices are discussed.

Effects of slurry rheology on industrial grinding performance

To determine the effect of slurry rheology on industrial grinding performance, 45 surveys were conducted on 16 full-scale grinding mills in five sites. Four operating variables - mill throughput, slurry density, slurry viscosity and feed fines content-were investigated. The rheology of the mill discharge slurries was measured either on-line or off-line, and the data were processed using a standard procedure to obtain a full range of flow curves. Multi-linear regression was employed as a statistical analysis tool to determine whether or not rheological effects exert an influence on industrial grinding, and to assess the influence of the four mill operating conditions on mill performance in terms of the Grinding Index, a criterion describing the overall breakage of particles across the mill. The results show that slurry rheology does influence industrial grinding. The trends of these effects on Grinding Index depend upon the rheological nature of the slurry-whether the slurries are dilatant or pseudoplastic, and whether they exhibit a high or low yield stress. The interpretation of the regression results is discussed, the observed effects are summarised, and the potential for incorporating rheological principles into process control is considered, Guidelines are established to improve industrial grinding operations based on knowledge of the rheological effects. This study confirms some trends in the effect of slurry rheology on grinding reported in the literature, and extends these to a broader understanding of the relationship between slurry properties and rheology, and their effects on industrial milling performance. (C) 2002 Elsevier Science B.V. All rights reserved.

Low-density koala (Phascolarctos cinereus) populations in the mulgalands of south-west Queensland. I. Faecal pellet sampling protocol

Koala (Phascolarctos cinereus) populations in eastern Australia are threatened by land clearing for agricultural and urban development. At the same time, conservation efforts are hindered by a dearth of information about inland populations. Faecal deposits offer a source of information that is readily available and easily collected non-invasively. We detail a faecal pellet sampling protocol that was developed for use in a large rangeland biogeographic region. The method samples trees in belt transects, uses a thorough search at the tree base to quickly identify trees with koala pellets under them, then estimates the abundance of faecal pellets under those trees using 1-m(2) quadrats. There was a strong linear relationship between these estimates and a complete enumeration of pellet abundance under the same trees. We evaluated the accuracy of our method in detecting trees where pellets were present by means of a misclassification index that was weighed more heavily for missed trees that had high numbers of pellets under them. This showed acceptable accuracy in all landforms except riverine, where some trees with large numbers of pellets were missed. Here, accuracy in detecting pellet presence was improved by sampling with quadrats, rather than basal searches. Finally, we developed a method to reliably age pellets and demonstrate how this protocol could be used with the faecal-standing-crop method to derive a regional estimate of absolute koala abundance.

Investigation of the effects of chrome ball charge on slurry rheology and milling performance

Ten surveys of the ball milling circuit at the Mt Isa Mines (MIM) Copper Concentrator were conducted aiming to identify any changes in slurry theology caused by the use of chrome balls charge, and the associated effect on grinding performance. Slurry theology was measured using an on-line viscometer. The data were mass balanced and analysed with statistical tools. Comparison of the rheogram demonstrated that slurry density and fines content affected slurry rheology significantly, while the effect of the chrome ball charge being negligible. Statistical analysis showed the effects of mill throughput and cyclone efficiency on the Grinding Index (a term describing the overall breakage). There was no difference in the Grinding Index between using the chrome ball charge and the ordinary steel ball charge. (C) 2002 Elsevier Science Ltd. All rights reserved.

Two-dimensional balanced sampling plans excluding contiguous units

A balanced sampling plan excluding contiguous units (or BSEC for short) was first introduced by Hedayat, Rao and Stufken in 1988. These designs can be used for survey sampling when the units are arranged in one-dimensional ordering and the contiguous units in this ordering provide similar information. In this paper, we generalize the concept of a BSEC to the two-dimensional situation and give constructions of two-dimensional BSECs with block size 3. The existence problem is completely solved in the case where lambda = 1.