Synthesizing and databasing fossil calibrations: divergence dating and beyond

Divergence dating studies, which combine temporal data from the fossil record with branch length data from molecular phylogenetic trees, represent a rapidly expanding approach to understanding the history of life. National Evolutionary Synthesis Center hosted the first Fossil Calibrations Working Group (3–6 March, 2011, Durham, NC, USA), bringing together palaeontologists, molecular evolutionists and bioinformatics experts to present perspectives from disciplines that generate, model and use fossil calibration data. Presentations and discussions focused on channels for interdisciplinary collaboration, best practices for justifying, reporting and using fossil calibrations and roadblocks to synthesis of palaeontological and molecular data. Bioinformatics solutions were proposed, with the primary objective being a new database for vetted fossil calibrations with linkages to existing resources, targeted for a 2012 launch.

Family-level relationships among the Australasian marsupial “herbivores” (Diprotodontia: Koala, wombats, kangaroos and possums)

The marsupial order Diprotodontia includes 10 extant families, which occupy all terrestrial habitats across Australia and New Guinea and have evolved remarkable dietary and locomotory diversity. Despite considerable attention, the interrelations of these families have for the most part remained elusive. In this study, we separately model mitochondrial RNA and protein-coding sequences in addition to nuclear protein-coding sequences to provide near-complete resolution of diprotodontian family-level phylogeny. We show that alternative topologies inferred in some previous studies are likely to be artifactual, resulting from branch-length and compositional biases. Subordinal groupings resolved herein include Vombatiformes (wombats and koala) and Phalangerida, which in turn comprises Petauroidea (petaurid gliders and striped, feathertail, ringtail and honey possums) and a clade whose plesiomorphic members possess blade-like premolars (phalangerid possums, kangaroos and their allies and most likely, pygmy possums). The topology resolved reveals ecological niche structuring among diprotodontians that has likely been maintained for more than 40 million years.

A Bias in ML Estimates of Branch Lengths in the Presence of Multiple Signals

Sequence data often have competing signals that are detected by network programs or Lento plots. Such data can be formed by generating sequences on more than one tree, and combining the results, a mixture model. We report that with such mixture models, the estimates of edge (branch) lengths from maximum likelihood (ML) methods that assume a single tree are biased. Based on the observed number of competing signals in real data, such a bias of ML is expected to occur frequently. Because network methods can recover competing signals more accurately, there is a need for ML methods allowing a network. A fundamental problem is that mixture models can have more parameters than can be recovered from the data, so that some mixtures are not, in principle, identifiable. We recommend that network programs be incorporated into best practice analysis, along with ML and Bayesian trees.

Branch-length estimation bias misleads molecular dating for a vertebrate mitochondrial phylogeny

Despite recent methodological advances in inferring the time-scale of biological evolution from molecular data, the fundamental question of whether our substitution models are sufficiently well specified to accurately estimate branch-lengths has received little attention. I examine this implicit assumption of all molecular dating methods, on a vertebrate mitochondrial protein-coding dataset. Comparison with analyses in which the data are RY-coded (AG → R; CT → Y) suggests that even rates-across-sites maximum likelihood greatly under-compensates for multiple substitutions among the standard (ACGT) NT-coded data, which has been subject to greater phylogenetic signal erosion. Accordingly, the fossil record indicates that branch-lengths inferred from the NT-coded data translate into divergence time overestimates when calibrated from deeper in the tree. Intriguingly, RY-coding led to the opposite result. The underlying NT and RY substitution model misspecifications likely relate respectively to “hidden” rate heterogeneity and changes in substitution processes across the tree, for which I provide simulated examples. Given the magnitude of the inferred molecular dating errors, branch-length estimation biases may partly explain current conflicts with some palaeontological dating estimates.

A Fair Go Beyond the School Gate? Systemic factors affecting participation and attainment in tertiary education by Queensland students from LSES backgrounds

The purpose of this project was to conduct an empirical study that would result in findings that inform systemic policy development aimed at improving tertiary participation and attainment by students from low socioeconomic status (LSES) backgrounds in Queensland. The project focuses on systemic policy, initiatives and programs that encourage tertiary education participation and attainment by individuals from LSES backgrounds, rather than on institution-specific initiatives or programs. While the broad remit was to consider tertiary education participation, the study particularly highlights issues pertaining to LSES student participation and attainment in the higher education sector, given the notable under representation of this demographic subgroup in Australian universities. This study supports the strategic priority of addressing professional skills shortages and innovations aiming to improve human and social capital in the state of Queensland. The ultimate goal is to contribute to the enhancement of Queensland’s education and training system by maximising participation and attainment by people from LSES backgrounds in higher education, thereby improving their quality of life and future life choices and opportunities. The study addressed the following five research questions: 1. What are the major factors that promote or inhibit participation and attainment in tertiary education by LSES students in Queensland? 2. To what extent do systemic policies or practices(systemic factors) of Queensland’s tertiary education system promote or inhibit participation and attainment by LSES students? That is, what features of Queensland’s tertiary education system have a significant effect on participation and attainment by LSES students? 3. What system policies or practices are found to boost participation and attainment by LSES students in other jurisdictions? 4. What evidence is there to suggest that policies or practices that have boosted participation and attainment by LSES students in other jurisdictions would be successful if implemented in Queensland? 5. What are the implications of the research findings for Queensland’s tertiary education system to improve participation and attainment by LSES students? The project adopted a mixed methods approach to data collection. A comprehensive review of the literature was conducted to identify relevant state, national and international literature. Both qualitative and quantitative methodologies were used to collect data from a range of key stakeholders.

Linear and nonlinear propagation of localised plasmon in metallic nanostructures

A major challenge in modern photonics and nano-optics is the diffraction limit of light which does not allow field localisation into regions with dimensions smaller than half the wavelength. Localisation of light into nanoscale regions (beyond its diffraction limit) has applications ranging from the design of optical sensors and measurement techniques with resolutions as high as a few nanometres, to the effective delivery of optical energy into targeted nanoscale regions such as quantum dots, nano-electronic and nano-optical devices. This field has become a major research direction over the last decade. The use of strongly localised surface plasmons in metallic nanostructures is one of the most promising approaches to overcome this problem. Therefore, the aim of this thesis is to investigate the linear and non-linear propagation of surface plasmons in metallic nanostructures. This thesis will focus on two main areas of plasmonic research –– plasmon nanofocusing and plasmon nanoguiding. Plasmon nanofocusing – The main aim of plasmon nanofocusing research is to focus plasmon energy into nanoscale regions using metallic nanostructures and at the same time achieve strong local field enhancement. Various structures for nanofocusing purposes have been proposed and analysed such as sharp metal wedges, tapered metal films on dielectric substrates, tapered metal rods, and dielectric V-grooves in metals. However, a number of important practical issues related to nanofocusing in these structures still remain unclear. Therefore, one of the main aims of this thesis is to address two of the most important of issues which are the coupling efficiency and heating effects of surface plasmons in metallic nanostructures. The method of analysis developed throughout this thesis is a general treatment that can be applied to a diversity of nanofocusing structures, with results shown here for the specific case of sharp metal wedges. Based on the geometrical optics approximation, it is demonstrated that the coupling efficiency from plasmons generated with a metal grating into the nanofocused symmetric or quasi-symmetric modes may vary between ~50% to ~100% depending on the structural parameters. Optimal conditions for nanofocusing with the view to minimise coupling and dissipative losses are also determined and discussed. It is shown that the temperature near the tip of a metal wedge heated by nanosecond plasmonic pulses can increase by several hundred degrees Celsius. This temperature increase is expected to lead to nonlinear effects, self-influence of the focused plasmon, and ultimately self-destruction of the metal tip. This thesis also investigates a different type of nanofocusing structure which consists of a tapered high-index dielectric layer resting on a metal surface. It is shown that the nanofocusing mechanism that occurs in this structure is somewhat different from other structures that have been considered thus far. For example, the surface plasmon experiences significant backreflection and mode transformation at a cut-off thickness. In addition, the reflected plasmon shows negative refraction properties that have not been observed in other nanofocusing structures considered to date. Plasmon nanoguiding – Guiding surface plasmons using metallic nanostructures is important for the development of highly integrated optical components and circuits which are expected to have a superior performance compared to their electronicbased counterparts. A number of different plasmonic waveguides have been considered over the last decade including the recently considered gap and trench plasmon waveguides. The gap and trench plasmon waveguides have proven to be difficult to fabricate. Therefore, this thesis will propose and analyse four different modified gap and trench plasmon waveguides that are expected to be easier to fabricate, and at the same time acquire improved propagation characteristics of the guided mode. In particular, it is demonstrated that the guided modes are significantly screened by the extended metal at the bottom of the structure. This is important for the design of highly integrated optics as it provides the opportunity to place two waveguides close together without significant cross-talk. This thesis also investigates the use of plasmonic nanowires to construct a Fabry-Pérot resonator/interferometer. It is shown that the resonance effect can be achieved with the appropriate resonator length and gap width. Typical quality factors of the Fabry- Pérot cavity are determined and explained in terms of radiative and dissipative losses. The possibility of using a nanowire resonator for the design of plasmonic filters with close to ~100% transmission is also demonstrated. It is expected that the results obtained in this thesis will play a vital role in the development of high resolution near field microscopy and spectroscopy, new measurement techniques and devices for single molecule detection, highly integrated optical devices, and nanobiotechnology devices for diagnostics of living cells.

Review : "A criminological imagination : essays on justice, punishment and discourse by Part Carlen"

There are four contributors to this review symposium. David Brown's review focuses on the questions of abolitionism that cut across much of Carlen's scholarship on punishment and prisons. Kerry Carrington's review attempts to articulate Pat Carlen's contributions to feminism, critque and crimnology, a selection of which is republished in the third scetion 'A criminological imgination'. Kelly Hannah-Moffat's review provides a succint but broad ranging analysis of Carlen's contributions to knowledge, politics and penal reform. Jo Phoenix takes Carlen's contributions to women, crim and scoial control as her main source of inspiration from this large body of work to review.

The grow-shrink-and-turncoat

This reversible garment, the grow-shrink-and-turncoat, is constructed in modules which allow it to be extended or tightened depending on the wearer. Later, it can be disassembled and then reassembled to form a new garment. The laser-cut holes allow for layers of cloth to be added or removed. The design was developed in part from a brainstorming activity with first and second year QUT students – their ideas included a garment which can be taken apart, a garment to fit many people, and most intriguingly, a garment that can open and ‘grow’ like a flower, swelling up in cold weather to warm the body. Taking these ideas, I developed a garment which can be disassembled, with layers added or subtracted by the wearer according to aesthetics and / or comfort. The shell is constructed from six squares of laser cut cloth, draped together with six smaller laser-cut rectangles, held in place with removable stitching. Additional squares and rectangles of cloth can be added / subtracted with ties knotted through the laser-cut holes. The laser cutting becomes a patterning device as well as integral to the construction of the garment. Conceptually, the garment is grounded in the notion of fabric as a precious resource – the pieces are designed to be disassembled at end-of-life, and then reconfigured into a fresh design.

Safety impacts of alcohol and other drugs in construction : development of an industry policy and cultural change management program

There is increasing concern about the impact of employees‟ alcohol and other drug (AOD) consumption on workplace safety and performance, particularly within the construction industry. While most Australian jurisdictions have identified this as a critical safety issue, information is limited regarding the prevalence of AODs in the workplace and there is limited evidential guidance regarding how to effectively and efficiently address such an issue. The current research aims to scientifically evaluate the use of AODs within the Australian construction industry in order to reduce the potential resulting safety and performance impacts and engender a cultural change in the workforce - to render it unacceptable to arrive at a construction workplace with impaired judgement from AODs. The study will adopt qualitative and quantitative methods to firstly evaluate the extent of general AOD use in the industry. Secondly, the development of an appropriate industry policy will adopt a non-punitive and rehabilitative approach developed in consultation with employers and employees across the infrastructure and building sectors, with the aim it be adopted nationally for adoption at the construction workplace. Finally, an industry specific cultural change management program and implementation plan will be developed through a nationally collaborative approach. Final results indicate that a proportion of those sampled in the construction sector may be at risk of hazardous alcohol consumption. A total of 286 respondents (58%) scored above the cut-off cumulative score for risky or hazardous alcohol. Other drug use was also identified as a major issue. Results support the need for evidence-based, preventative educational initiatives that are tailored to the industry. This paper will discuss the final survey and interview results.

Associations between socioeconomic position, food insecurity and BMI

Introduction: Food insecurity is a social determinant of health and is defined as limited ability to access sufficient amounts of nutritionally adequate or safe food for a healthy and active life. Food insecurity is associated with poor health status and the exacerbation of other health inequalities. This study examined whether an association existed between 1) socioeconomic position (SEP) and food insecurity and 2) food insecurity and weight status. Methods: Data from the 1995 National Nutrition Survey was analysed. A random sample of households (n = 13 858) were asked about dietary habits and food choices. Information about gender, age, BMI, waist circumference, household income and whether the household had run out of money to purchase food in the previous 12 months was obtained and analysed using chi-square and logistic regression. Results: Income was significantly associated with food insecurity; households with lower income were at higher risk of food insecurity. Lower income males were nine times more likely to experience food insecurity and lower income females were three times more likely to experience food insecurity than their higher income counterparts. Food insecurity was significantly associated with body mass index (BMI) among women but not men. Women experiencing food insecurity were at higher risk of overweight/obesity according to BMI and waist circumference measures. Conclusion: Evidence suggests that low income households are at higher risk of food insecurity and women who are food insecure are at higher risk of being overweight or obese. Food insecurity may mediate the association between SEP and BMI.

Self-assembled hyperbranched polymer - gold nanoparticle hybrids : understanding the effect of polymer coverage on assembly size and SERS performance

In the past few years, remarkable progress has been made in unveiling novel and unique optical properties of strongly coupled plasmonic nanostructures. However, application of such plasmonic nanostructures in biomedicine remains challenging due to the lack of facile and robust assembly methods for producing stable nanostructures. Previous attempts to achieve plasmonic nano-assemblies using molecular ligands were limited due to the lack of flexibility that could be exercised in forming them. Here, we report the utilization of tailor-made hyperbranched polymers (HBP) as linkers to assemble gold nanoparticles (NPs) into nano-assemblies. The ease and flexibility in tuning the particle size and number of branch ends of a HBP makes it an ideal candidate as a linker, as opposed to DNA, small organic molecules and linear or dendrimeric polymers. We report a strong correlation of polymer (HBP) concentration with the size of the hybrid nano-assemblies and “hot-spot” density. We have shown that such solutions of stable HBP-gold nano-assemblies can be barcoded with various Raman tags to provide improved surface-enhanced Raman scattering (SERS) compared with non-aggregated NP systems. These Raman barcoded hybrid nano-assemblies, with further optimization of NP shape, size and “hot-spot” density, may find application as diagnostic tools in nanomedicine.

Comparison of antigen detection and quantitative PCR in the detection of chlamydial infection in koalas (Phascolarctos cinereus)

The gold standard method for detecting chlamydial infection in domestic and wild animals is PCR, but the technique is not suited to testing animals in the field when a rapid diagnosis is frequently required. The objective of this study was to compare the results of a commercially available enzyme immunoassay test for Chlamydia against a quantitative Chlamydia pecorum-specific PCR performed on swabs collected from the conjunctival sac, nasal cavity and urogenital sinuses of naturally infected koalas (Phascolarctos cinereus). The level of agreement for positive results between the two assays was low (43.2%). The immunoassay detection cut-off was determined as approximately 400 C. pecorum copies, indicating that the test was sufficiently sensitive to be used for the rapid diagnosis of active chlamydial infections.

University Student Depression Inventory (USDI) : confirmatory factor analysis and review of psychometric properties

Background: The 30-item USDI is a self-report measure that assesses depressive symptoms among university students. It consists of three correlated three factors: Lethargy, Cognitive-Emotional and Academic motivation. The current research used confirmatory factor analysis to asses construct validity and determine whether the original factor structure would be replicated in a different sample. Psychometric properties were also examined. Method: Participants were 1148 students (mean age 22.84 years, SD = 6.85) across all faculties from a large Australian metropolitan university. Students completed a questionnaire comprising of the USDI, the Depression Anxiety Stress Scale (DASS) and Life Satisfaction Scale (LSS). Results: The three correlated factor model was shown to be an acceptable fit to the data, indicating sound construct validity. Internal consistency of the scale was also demonstrated to be sound, with high Cronbach Alpha values. Temporal stability of the scale was also shown to be strong through test-retest analysis. Finally, concurrent and discriminant validity was examined with correlations between the USDI and DASS subscales as well as the LSS, with sound results contributing to further support the construct validity of the scale. Cut-off points were also developed to aid total score interpretation. Limitations: Response rates are unclear. In addition, the representativeness of the sample could be improved potentially through targeted recruitment (i.e. reviewing the online sample statistics during data collection, examining the representativeness trends and addressing particular faculties within the university that were underrepresented). Conclusions: The USDI provides a valid and reliable method of assessing depressive symptoms found among university students.

Taxonomic revision of Ustilago, Sporisorium and Macalpinomyces

The three genera of smut fungi, Ustilago, Sporisorium and Macalpinomyces, form a complex that has eluded resolution by morphology (Langdon & Fullerton 1975, Vánky 1991, Piepenbring et al. 1998) and molecular phylogenetic analysis (Stoll et al. 2003, 2005). Two suggestions to reconcile the taxonomy of the complex have been proposed. The first was to break up the current taxa into several smaller genera and subgenera, and the second to unify the three genera into a single genus, Ustilago (Vánky 2002, Piepenbring 2004). The former solution is dependent on finding morphological synapomorphies that can delimit the genera, and the latter solution dismisses the wide morphological diversity within the group (McTaggart et al. 2012b). Synapomorphic morphological characters and host plant classification delimited clades in the Ustilago-Sporisorium-Macalpinomyces complex (McTaggart et al. 2012a). The current study defines these synapomorphic characters and proposes a new classification for many species currently placed in Ustilago, Sporisorium and Macalpinomyces. This approach preserves the well-known genera Ustilago, Sporisorium and Macalpinomyces, and enables the classification to reflect morphological diversity in the complex.