Genome-scale phylogeny and the detection of systematic biases

Phylogenetic inference from sequences can be misled by both sampling (stochastic) error and systematic error (nonhistorical signals where reality differs from our simplified models). A recent study of eight yeast species using 106 concatenated genes from complete genomes showed that even small internal edges of a tree received 100% bootstrap support. This effective negation of stochastic error from large data sets is important, but longer sequences exacerbate the potential for biases (systematic error) to be positively misleading. Indeed, when we analyzed the same data set using minimum evolution optimality criteria, an alternative tree received 100% bootstrap support. We identified a compositional bias as responsible for this inconsistency and showed that it is reduced effectively by coding the nucleotides as purines and pyrimidines (RY-coding), reinforcing the original tree. Thus, a comprehensive exploration of potential systematic biases is still required, even though genome-scale data sets greatly reduce sampling error.

Four new avian mitochondrial genomes help get to basic evolutionary questions in the late cretaceous

Good phylogenetic trees are required to test hypotheses about evolutionary processes. We report four new avian mitochondrial genomes, which together with an improved method of phylogenetic analysis for vertebrate mt genomes give results for three questions in avian evolution. The new mt genomes are: magpie goose (Anseranas semipalmata), an owl (morepork, Ninox novaeseelandiae); a basal passerine (rifleman, or New Zealand wren, Acanthisitta chloris); and a parrot (kakapo or owl-parrot, Strigops habroptilus). The magpie goose provides an important new calibration point for avian evolution because the well-studied Presbyornis fossils are on the lineage to ducks and geese, after the separation of the magpie goose. We find, as with other animal mitochondrial genomes, that RY-coding is helpful in adjusting for biases between pyrimidines and between purines. When RY-coding is used at third positions of the codon, the root occurs between paleognath and neognath birds (as expected from morphological and nuclear data). In addition, passerines form a relatively old group in Neoaves, and many modern avian lineages diverged during the Cretaceous. Although many aspects of the avian tree are stable, additional taxon sampling is required.

A novel numerical approximation for the space fractional advection-dispersion equation

In this paper, we consider a space fractional advection–dispersion equation. The equation is obtained from the standard advection–diffusion equation by replacing the first- and second-order space derivatives by the Riesz fractional derivatives of order β1 ∈ (0, 1) and β2 ∈ (1, 2], respectively. The fractional advection and dispersion terms are approximated by using two fractional centred difference schemes. A new weighted Riesz fractional finite-difference approximation scheme is proposed. When the weighting factor θ equals 12, a second-order accuracy scheme is obtained. The stability, consistency and convergence of the numerical approximation scheme are discussed. A numerical example is given to show that the numerical results are in good agreement with our theoretical analysis.

Numerical methods of the variable-order Rayleigh-Stokes problem for a heated generalized second grade fluid with fractional derivative

Rayleigh–Stokes problems have in recent years received much attention due to their importance in physics. In this article, we focus on the variable-order Rayleigh–Stokes problem for a heated generalized second grade fluid with fractional derivative. Implicit and explicit numerical methods are developed to solve the problem. The convergence, stability of the numerical methods and solvability of the implicit numerical method are discussed via Fourier analysis. Moreover, a numerical example is given and the results support the effectiveness of the theoretical analysis.

Anisotropic damage mechanics as a novel approach to improve pre-and post-failure borehole stability analysis

Anisotropic damage distribution and evolution have a profound effect on borehole stress concentrations. Damage evolution is an irreversible process that is not adequately described within classical equilibrium thermodynamics. Therefore, we propose a constitutive model, based on non-equilibrium thermodynamics, that accounts for anisotropic damage distribution, anisotropic damage threshold and anisotropic damage evolution. We implemented this constitutive model numerically, using the finite element method, to calculate stress–strain curves and borehole stresses. The resulting stress–strain curves are distinctively different from linear elastic-brittle and linear elastic-ideal plastic constitutive models and realistically model experimental responses of brittle rocks. We show that the onset of damage evolution leads to an inhomogeneous redistribution of material properties and stresses along the borehole wall. The classical linear elastic-brittle approach to borehole stability analysis systematically overestimates the stress concentrations on the borehole wall, because dissipative strain-softening is underestimated. The proposed damage mechanics approach explicitly models dissipative behaviour and leads to non-conservative mud window estimations. Furthermore, anisotropic rocks with preferential planes of failure, like shales, can be addressed with our model.

Child sexual abuse prevention education : A review of school policy and curriculum provision in Australia

The past four decades have seen increasing public and professional awareness of child sexual abuse. Congruent with public health approaches to prevention, efforts to eliminate child sexual abuse have inspired the emergence of prevention initiatives which can be provided to all children as part of their standard school curriculum. However, relatively little is known about the scope and nature of child sexual abuse prevention efforts in government school systems internationally. This paper assesses and compares the policies and curriculum initiatives for child sexual abuse prevention education in primary (elementary) schools across state and territory Departments of Education in Australia. Using publicly available electronic data, a deductive qualitative content analysis of policy and curriculum documents was undertaken to examine the characteristics of child sexual abuse prevention education in these school systems. It was found that the system-level provision of child sexual abuse prevention education occurs unevenly across state and territory jurisdictions. This results in the potential for substantial inequity in Australian children’s access to learning opportunities in child abuse prevention education as a part of their standard school curriculum. In this research, we have developed a strategy for generating a set of theoretically-sound empirical criteria that may be more extensively applied in comparative research about prevention initiatives internationally.

ATM is required for the cellular response to thymidine induced replication fork stress

Genetically distinct checkpoints, activated as a consequence of either DNA replication arrest or ionizing radiation-induced DNA damage, integrate DNA repair responses into the cell cycle programme. The ataxia-telangiectasia mutated (ATM) protein kinase blocks cell cycle progression in response to DNA double strand breaks, whereas the related ATR is important in maintaining the integrity of the DNA replication apparatus. Here, we show that thymidine, which slows the progression of replication forks by depleting cellular pools of dCTP, induces a novel DNA damage response that, uniquely, depends on both ATM and ATR. Thymidine induces ATM-mediated phosphorylation of Chk2 and NBS1 and an ATM-independent phosphorylation of Chk1 and SMC1. AT cells exposed to thymidine showed decreased viability and failed to induce homologous recombination repair (HRR). Taken together, our results implicate ATM in the HRR-mediated rescue of replication forks impaired by thymidine treatment.

A tumour-derived mutant allele of XRCC2 preferentially suppresses homologous recombination at DNA replication forks

Homologous recombination repair (HRR) is required for both the repair of DNA double strand breaks (DSBs) and the maintenance of the integrity of DNA replication forks. To determine the effect of a mutant allele of the RAD51 paralog XRCC2 (342delT) found in an HRR-defective tumour cell line, 342delT was introduced into HRR proficient cells containing a recombination reporter substrate. In one set of transfectants, expression of 342delT conferred sensitivity to thymidine and mitomycin C and suppressed HRR induced at the recombination reporter by thymidine but not by DSBs. In a second set of transfectants, the expression of 342delT was accompanied by a decreased level of the full-length XRCC2. These cells were defective in the induction of HRR by either thymidine or DSBs. Thus 342delT suppresses recombination induced by thymidine in a dominant negative manner while recombination induced by DSBs appears to depend upon the level of XRCC2 as well as the expression of the mutant XRCC2 allele. These results suggest that HRR pathways responding to stalled replication forks or DSBs are genetically distinguishable. They further suggest a critical role for XRCC2 in HRR at replication forks, possibly in the loading of RAD51 onto gapped DNA.

Evaluation in health outcomes research : linking theories, methodologies and practice in health promotion.

Health outcomes research has developed as a means of evaluating the effectiveness of health care interventions and as an approach to informing resource allocation. The use of a health outcomes approach in health promotion has made increasing demands on evaluation methodologies to demonstrate program effectiveness. However, criticism of the contribution of health promotion to outcomes research has made several assumptions about the use of qualitative methodologies and the content of program objectives largely derived from a biomedical approach. In contrast to the measurement of biomedical interventions in clinical health care, health promotion practice involves social phenomena, wide-reaching cultural, psychological, political and ideological problems and issues. The integration of methodologies of health promotion evaluation will inform further conceptualisation of the health outcomes approach with the differentiation of three types of outcomes: health development outcomes; social health outcomes; and biomedical health outcomes. It is concluded that this differentiation moves away from dualist concepts that advocate the replacement of goals and targets with regional and locally based approaches. Rather, the future direction for health promotion evaluation needs to employ a framework that elaborates multiple methodologies and approaches necessary for establishing what relationships exist between morbidity, mortality, health advancement and equity.

Mechanical properties of mussel byssus threads

The byssus threads of the common mussel, Mytilus edulis L., have been tested mechanically and the results from the tests related to the ecology of the animal. The threads are mechanically similar to other crystalline polymers such as polyethylene having a modulus of about 108N m−2 and a long relaxation time. Resilience of 60% is similar to tendon; ultimate strain is about five times that of tendon at 0.44. The thread is laid down with a prestrain of 10% and so guys the mussel in position. Calculation shows that a mussel with 50 byssus threads would be able to resist all but severe winter storms.

Social enterprises in rural community development

Social enterprises are hybrid organizational forms that combine characteristics of for-profit businesses and community sector organizations. This article explores how rural communities may use social enterprises to progress local development agendas across both economic and social domains. Drawing on qualitative case studies of three social enterprises in rural North West Tasmania, this article explores the role of social enterprises in local development processes. The case study social enterprises, despite differences in size, structure, mission and age, are strongly embedded in their local places and local communities. As deeply contextualized development actors, these social enterprises mobilize multiple resources and assets to achieve a range of local development outcomes, including but not limited to social capital

The knock-on from the knock-off : recent shifts within Australian mass market fashion design practice

Australia's mass market fashion labels have traditionally benefitted from their peripheral location to the world's fashion centres. Operating a season behind, Australian mass market designers and buyers were well-placed to watch trends play out overseas before testing them in the Australian marketplace. For this reason, often a designer's role was to source and oversee the manufacture of 'knock-offs', or close copies of northern hemisphere mass market garments. Both Weller and Walsh have commented on this practice.12 The knock-on effect from this continues to be a cautious, derivative fashion sensibility within Australian mass market fashion design, where any new trend or product is first tested and proved overseas months earlier. However, there is evidence that this is changing. The rapid online dissemination of global fashion trends, coupled with the Australian consumer’s willingness to shop online, has meant that the ‘knock-off’ is less viable. For this reason, a number of mass market companies are moving away from the practice of direct sourcing and are developing product in-house under a northern hemisphere model. This shift is also witnessed in the trend for mass market companies to develop collections in partnership with independent Australian designers. This paper explores the current and potential effects of these shifts within Australian mass market design practice, and discusses how they may impact on both consumers and on the wider culture of Australian fashion.