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.

Bifurcation in growth patterns for arrays of parallel Griffith, edge and sliding cracks

This paper presents the recent finding by Muhlhaus et al [1] that bifurcation of crack growth patterns exists for arrays of two-dimensional cracks. This bifurcation is a result of the nonlinear effect due to crack interaction, which is, in the present analysis, approximated by the dipole asymptotic or pseudo-traction method. The nonlinear parameter for the problem is the crack length/ spacing ratio lambda = a/h. For parallel and edge crack arrays under far field tension, uniform crack growth patterns (all cracks having same size) yield to nonuniform crack growth patterns (i.e. bifurcation) if lambda is larger than a critical value lambda(cr) (note that such bifurcation is not found for collinear crack arrays). For parallel and edge crack arrays respectively, the value of lambda(cr) decreases monotonically from (2/9)(1/2) and (2/15.096)(1/2) for arrays of 2 cracks, to (2/3)(1/2)/pi and (2/5.032)(1/2)/pi for infinite arrays of cracks. The critical parameter lambda(cr) is calculated numerically for arrays of up to 100 cracks, whilst discrete Fourier transform is used to obtain the exact solution of lambda(cr) for infinite crack arrays. For geomaterials, bifurcation can also occurs when array of sliding cracks are under compression.

Morphology of the thyroid in coastal and noncoastal populations of the koala (Phascolarctos cinereus) in Queensland

The gross morphology, histology, and ultrastructure of the thyroid gland of the koala, Phascolarctos cinereus, is described. Generally, the glands were found to contain large-diameter follicles in association with an epithelium of low height. Morphometric analysis demonstrated a high relative thyroid weight (0.3 +/- 0.2 g/kg) for koalas compared with the 0.07-0.24 g/kg typical of eutherian mammals and 0.03-0.1 g/kg found in other marsupials. The relative thyroid weight of glands (0.33 +/- 0.21 g/kg) from the coastal population (less than 28 km from the coastline) was found to be significantly higher (ANOVA: P = 0.007, significant at the 1% level) than that for glands (0.21 +/- 0.11 g/kg) of noncoastal koalas (greater than 28 km from the coastline). Follicle size was positively correlated (at the 0.1% level) with relative thyroid weight in the overall koala sample. The presence of C cells, occurring singly in the epithelial layer, was demonstrated in electron micrographs. Structural features such as low epithelial height, large follicle length and width, and large intercellular spaces in association with low concentrations of free TS (3.3 +/- 2.1 pM) and free T-3 (1.4 +/- 0.9 pM) as reported previously (Lawson et al., 1996) are consistent with an unusually low level of glandular activity in the koala thyroid even though iodine concentrations in the thyroid gland [4.7 +/- 1.6 mg/g (dry weight)] as well as leaf [0.8 +/- 0.3 mu g (dry weight)] and soil samples [3.8 mu g/g (dry weight)] from the koalas' habitat appear unremarkable. (C) 1998 Academic Press.

Strain-dependent fluid flow defined through rock mass classification schemes

Strain-dependent hydraulic conductivities are uniquely defined by an environmental factor, representing applied normal and shear strains, combined with intrinsic material parameters representing mass and component deformation moduli, initial conductivities, and mass structure. The components representing mass moduli and structure are defined in terms of RQD (rock quality designation) and RMR (rock mass rating) to represent the response of a whole spectrum of rock masses, varying from highly fractured (crushed) rock to intact rock. These two empirical parameters determine the hydraulic response of a fractured medium to the induced-deformations The constitutive relations are verified against available published data and applied to study one-dimensional, strain-dependent fluid flow. Analytical results indicate that both normal and shear strains exert a significant influence on the processes of fluid flow and that the magnitude of this influence is regulated by the values of RQD and RMR.

The mechanical properties of Saccharomyces cerevisiae

Cell-wall mechanical properties play an integral part in the growth and form of Saccharomyces cerevisiae, In contrast to the tremendous knowledge on the genetics of S. cerevisiae, almost nothing is known about its mechanical properties. We have developed a micromanipulation technique to measure the force required to burst single cells and have recently established a mathematical model to extract the mechanical properties of the cell wall from such data, Here we determine the average surface modulus of the S, cerevisiae cell wall to be 11.1 +/- 0.6 N/m and 12.9 +/- 0.7 N/m in exponential and stationary phases, respectively, giving corresponding Young's moduli of 112 +/- 6 MPa and 107 +/- 6 MPa, This result demonstrates that yeast cell populations strengthen as they enter stationary phase by increasing wall thickness and hence the surface modulus, without altering the average elastic properties of the cell-wall material. We also determined the average breaking strain of the cell wall to be 82% +/- 3% in exponential phase and 80% +/- 3% in stationary phase, This finding provides a failure criterion that can be used to predict when applied stresses (e,g,, because of fluid flow) will lead to wall rupture, This work analyzes yeast compression experiments in different growth phases by using engineering methodology.

Numerical modelling of single-layer folding: clarification of an issue regarding the possible effect of computer codes and the influence of initial irregularities

The influence of initial perturbation geometry and material propel-ties on final fold geometry has been investigated using finite-difference (FLAC) and finite-element (MARC) numerical models. Previous studies using these two different codes reported very different folding behaviour although the material properties, boundary conditions and initial perturbation geometries were similar. The current results establish that the discrepancy was not due to the different computer codes but due to the different strain rates employed in the two previous studies (i.e. 10(-6) s(-1) in the FLAC models and 10(-14) s(-1) in the MARC models). As a result, different parts of the elasto-viscous rheological field were bring investigated. For the same material properties, strain rate and boundary conditions, the present results using the two different codes are consistent. A transition in Folding behaviour, from a situation where the geometry of initial perturbation determines final fold shape to a situation where material properties control the final geometry, is produced using both models. This transition takes place with increasing strain rate, decreasing elastic moduli or increasing viscosity (reflecting in each case the increasing influence of the elastic component in the Maxwell elastoviscous rheology). The transition described here is mechanically feasible but is associated with very high stresses in the competent layer (on the order of GPa), which is improbable under natural conditions. (C) 2000 Elsevier Science Ltd. All rights reserved.

Developing a reliable audit instrument to measure the physical environment for physical activity

Background: The physical environment plays an important role in influencing participation in physical activity, although which factors of the physical environment have the greatest effect on patterns of activity remain to be determined. We describe the development of a comprehensive instrument to measure the physical environmental factors that may influence walking and cycling in local neighborhoods and report on its reliability. Methods: Following consultation with experts from a variety of fields and a literature search, we developed a Systematic Pedestrian and Cycling Environmental Scan (SPACES) instrument and used it to collect data over a total of 1987 kilometers of roads in metropolitan Perth, Western Australia. The audit instrument is available from the first author on request. Additional environmental information was collected using desktop methods and geographic information systems (GIS) technology. We assessed inter- and intra-rater reliability of the instrument among the 16 observers who collected the data. Results: The observers reported that the audit instrument was easy to use. Both inter- and intra-rater reliability of the environmental scan instrument were generally high. Conclusions: Our instrument provides a reliable, practical, and easy to-use method for collecting detailed street-level data on physical environmental factors that are potential influences on walking in local neighborhoods.

Apparent strain localization and shear wave dispersion in elastic fault gouge with microrotations

Shear deformation of fault gouge or other particulate materials often results in observed strain localization, or more precisely, the localization of measured deformation gradients. In conventional elastic materials the strain localization cannot take place therefore this phenomenon is attributed to special types of non-elastic constitutive behaviour. For particulate materials however the Cosserat continuum which takes care of microrotations independent of displacements is a more appropriate model. In elastic Cosserat continuum the localization in displacement gradients is possible under some combinations of the generalized Cosserat elastic moduli. The same combinations of parameters also correspond to a considerable dispersion in shear wave propagation which can be used for independent experimental verification of the proposed mechanism of apparent strain localization in fault gouge.

Characterization of optically driven fluid stress fields with optical tweezers

We present a controlled stress microviscometer with applications to complex fluids. It generates and measures microscopic fluid velocity fields, based on dual beam optical tweezers. This allows an investigation of bulk viscous properties and local inhomogeneities at the probe particle surface. The accuracy of the method is demonstrated in water. In a complex fluid model (hyaluronic acid), we observe a strong deviation of the flow field from classical behavior. Knowledge of the deviation together with an optical torque measurement is used to determine the bulk viscosity. Furthermore, we model the observed deviation and derive microscopic parameters.

Analyzing the researcher's work in generating data: The case of complaints

This article investigates the researcher's work in the coproduction (or not) of complaint sequences in research interviews. Using a conversation analytic approach, we show how the interviewer's management of complaint sequences in a research setting is consequential for subsequent talk and thus directly affects the data generated. In the examples shown here, researchers sharing cocategorial incumbency with respondents may well provide spaces for research participants to formulate complaints. This article examines sequences of talk surrounding complaints to show how researchers generate complaints (or not) and handle unsafe complaints. Researchers are able to provoke specific types of accounts from respondents, whereas their respondents may actively resist the researchers' direction. For researchers using the interview as a method of data generation, examination of complaint sequences and how these appear in interview data provides insight into how interview talk is coproduced and managed within a socially situated setting.

Language and disability in Japan

Language relating to disability in the public arena has been a sensitive issue in Japan as elsewhere. Since the 1970s and 80s, major media organisations have replaced words considered derogatory with more acceptable equivalents; laws, statutes and other legal documents have likewise been revised. This article examines how the language used to portray people with disabilities has changed, how the changes came about and how they were received. The debate has largely been played out in four public spaces, which to some extent intersect and overlap: the media (both print and visual), the laws, literature and, increasingly now, the Internet. I argue that while the laws were rewritten primarily as the result of external international trends, such as the International Year of Disabled Persons, disability groups achieved media compliance mainly by exploiting the keen desire of Japanese media organisations to avoid public embarrassment resulting from vocal protests over infractions.

Relations between coal petrology and gas content in the Upper Newlands Seam, central Queensland, Australia

The Upper Newlands Seam in the northern Bowen Basin, Queensland, Australia consists of six benches (A-F) that have different petrographic assemblages. Benches C and E contain relatively abundant inertodetrinite and mineral matter, as well as anomalously high reflectance values; these characteristics support a largely allochthonous, detrital origin for the C and E benches. Fractures and cleats in the seam show a consistent orientation of northeast- southwest for face cleats, and a wide range of orientations for fractures. Cleat systems are well developed in bright bands, with poor continuity in the dull coal. Both maceral content and cleat character are suggested to influence gas drainage in the Upper Newlands Seam. A pronounced positive correlation between vitrinite abundance and gas desorption data suggests more efficient drainage from benches with abundant vitrinite. Conversely, inertinite-rich benches are suggested to have less efficient drainage, and possibly retain gas within pore spaces, which could increase the outburst potential of the coal. (C) 2001 Elsevier Science BN. All rights reserved.

Space: Irrealis objects in technology policy and their role in a new political economy

In this article, I show how new spaces are being prefigured for colonization in new economy policy discourses. Drawing on a corpus of 1.3 million words collected from legislatures throughout the world, I show the role of policy language in creating the foundations of an emergent form of political economy: The analysis is informed by principles from critical discourse analysis (CDA), classical political economy and critical media studies. It foregrounds a functional aspect of language called process metaphor to show how aspects of human activity are prefigured for mass commodification by the manipulation of realis and irrealis spaces. I also show how the fundamental element of any new political economy, the property element, is being largely ignored. Current moves to create a privately owned global space, which is as concrete as landed property - namely, the electromagnetic spectrum - has significant ramifications for the future of social relations in any global knowledge economy.

The endgame for national girls' schooling policies in Australia?

Gender equity: A framework for Australian schools is the most recent policy dealing with gender in schools at the national level in Australia. This paper provides a critical discourse analysis of the policy document, tracking two themes: 'the construction of gender', and 'equity: a discourse of education for all boys and girls'. Through this analysis the authors argue that the policy signals a substantial shift in focus-from girls and boys in relation to girls, to both girls and boys-within a framework of presumptive equality. It is also argued that the policy shuts down federal involvement in policy for girls' schooling. In the process, responsibility is devolved to the states and territories where, in many cases, gender equity programs will be struggled over at a local, school-based level. At the same time, however, spaces have been created which potentially enable new strategies for gender equity policies in Australian schools.