Implications of gain functions in fisheries management

The appealing concept of optimal harvesting is often used in fisheries to obtain new management strategies. However, optimality depends on the objective function, which often varies, reflecting the interests of different groups of people. The aim of maximum sustainable yield is to extract the greatest amount of food from replenishable resources in a sustainable way. Maximum sustainable yield may not be desirable from an economic point of view. Maximum economic yield that maximizes the profit of fishing fleets (harvesting sector) but ignores socio-economic benefits such as employment and other positive externalities. It may be more appropriate to use the maximum economic yield that which is based on the value chain of the overall fishing sector, to reflect better society's interests. How to make more efficient use of a fishery for society rather than fishing operators depends critically on the gain function parameters including multiplier effects and inclusion or exclusion of certain costs. In particular, the optimal effort level based on the overall value chain moves closer to the optimal effort for the maximum sustainable yield because of the multiplier effect. These issues are illustrated using the Australian Northern Prawn Fishery.

Robust estimating functions and bias correction for longitudinal data analysis

Robust methods are useful in making reliable statistical inferences when there are small deviations from the model assumptions. The widely used method of the generalized estimating equations can be "robustified" by replacing the standardized residuals with the M-residuals. If the Pearson residuals are assumed to be unbiased from zero, parameter estimators from the robust approach are asymptotically biased when error distributions are not symmetric. We propose a distribution-free method for correcting this bias. Our extensive numerical studies show that the proposed method can reduce the bias substantially. Examples are given for illustration.

Groucho homologue Grg5 interacts with the transcription factor Runx2-Cbfa1 and modulates its activity during postnatal growth in mice

Runx2-Cbfal, a Runt transcription factor, plays important roles during skeletal development. It is required for differentiation and function of osteoblasts. In its absence, chondrocyte hypertrophy is severely impaired and there is no vascularization of cartilage templates during skeletal development. These tissue-specific functions of Runx2 are likely to be dependent on its interaction with other proteins. We have therefore searched for proteins that may modulate the activity of Runx2. The yeast two-hybrid system was used to identify a groucho homologue, Grg5, as a Runx2-interacting protein. Grg5 enhances Runx2 activity in a cell culture-based assay and by analyses of postnatal growth in mice we demonstrate that Grg5 and Runx2 interact genetically. We also show that Runx2 haploinsufficiency in the absence of Grg5 results in a more severe delay in ossification of cranial sutures and fontanels than occurs with Runx2 haploinsufficiency on a wild-type background. Finally, we find shortening of the proliferative and hypertrophic zones, and expansion of the resting zone in the growth plates of Runx2(+/-)Grg5(-/-) mice that are associated with reduced Ihh expression and Indian hedgehog (Ihh) signaling. We therefore conclude that Grg5 enhances Runx2 activity in vivo.

Overfitting Bayesian mixture models with an unknown number of components

This paper proposes solutions to three issues pertaining to the estimation of finite mixture models with an unknown number of components: the non-identifiability induced by overfitting the number of components, the mixing limitations of standard Markov Chain Monte Carlo (MCMC) sampling techniques, and the related label switching problem. An overfitting approach is used to estimate the number of components in a finite mixture model via a Zmix algorithm. Zmix provides a bridge between multidimensional samplers and test based estimation methods, whereby priors are chosen to encourage extra groups to have weights approaching zero. MCMC sampling is made possible by the implementation of prior parallel tempering, an extension of parallel tempering. Zmix can accurately estimate the number of components, posterior parameter estimates and allocation probabilities given a sufficiently large sample size. The results will reflect uncertainty in the final model and will report the range of possible candidate models and their respective estimated probabilities from a single run. Label switching is resolved with a computationally light-weight method, Zswitch, developed for overfitted mixtures by exploiting the intuitiveness of allocation-based relabelling algorithms and the precision of label-invariant loss functions. Four simulation studies are included to illustrate Zmix and Zswitch, as well as three case studies from the literature. All methods are available as part of the R package Zmix, which can currently be applied to univariate Gaussian mixture models.

Atmospheric visibility and PM10 as indicators of new particle formation in an urban environment

It is well-known that new particle formation (NPF) in the atmosphere is inhibited by pre-existing particles in the air that act as condensation sinks to decrease the concentration and, thus, the supersaturation of precursor gases. In this study, we investigate the effects of two parameters - atmospheric visibility, expressed as the particle back-scatter coefficient (BSP), and PM10 particulate mass concentration, on the occurrences of NPF events in an urban environment where the majority of precursor gases originate from motor vehicle and industrial sources. This is the first attempt to derive direct relationships between each of these two parameters and the occurrence of NPF. NPF events were identified from data obtained with a neutral cluster and air ion spectrometer over 245 days within a calendar year. Bayesian logistic regression was used to determine the probability of observing NPF as functions of BSP and PM10. We show that the BSP at 08 h on a given day is a reliable indicator of an NPF event later that day. The posterior median probability of observing an NPF event was greater than 0.5 (95%) when the BSP at 08 h was less than 6.8 Mm-1.

Book Review "Selling sex: a hidden history of prostitution", R. Frances, UNSW Press, Sydney, 2007

In the opening pages of Selling Sex we are introduced to 'Joy', a statue of a young female sex worker which stood in East Sydney for eighteen months during 1995- 1997. Following complaints by local residents, the statue was removed from public view and returned to its owner. Evidently, Joy was considered a reminder of the community's 'bad old days', when it was better known for prostitution than restaurants. In a nation in which almost every sizable community has proudly erected monuments to military men, the removal of Joy reveals much about labour and gender relations in Australia. For Frances, the removal of Joy is symbolic, our historical treatment of sex workers having parallels with our treatment of the convicts. This work sets out to give these women (male prostitutes do not figure in this history) a voice and break with the stereotypes of 'abandoned whores' or 'sad victims'. It also sets out to place the sex industry in the broader national and international context in which it has historically operated...

Gene-based pleiotropy across migraine with aura and migraine without aura patient groups

Introduction: It is unclear whether patients diagnosed according to International Classification of Headache Disorders criteria for migraine with aura (MA) and migraine without aura (MO) experience distinct disorders or whether their migraine subtypes are genetically related. Aim: Using a novel gene-based (statistical) approach, we aimed to identify individual genes and pathways associated both with MA and MO. Methods: Gene-based tests were performed using genome-wide association summary statistic results from the most recent International Headache Genetics Consortium study comparing 4505 MA cases with 34,813 controls and 4038 MO cases with 40,294 controls. After accounting for non-independence of gene-based test results, we examined the significance of the proportion of shared genes associated with MA and MO. Results: We found a significant overlap in genes associated with MA and MO. Of the total 1514 genes with a nominally significant gene-based p value (pgene-based ≤ 0.05) in the MA subgroup, 107 also produced pgene-based ≤ 0.05 in the MO subgroup. The proportion of overlapping genes is almost double the empirically derived null expectation, producing significant evidence of gene-based overlap (pleiotropy) (pbinomial-test = 1.5 × 10–4). Combining results across MA and MO, six genes produced genome-wide significant gene-based p values. Four of these genes (TRPM8, UFL1, FHL5 and LRP1) were located in close proximity to previously reported genome-wide significant SNPs for migraine, while two genes, TARBP2 and NPFF separated by just 259 bp on chromosome 12q13.13, represent a novel risk locus. The genes overlapping in both migraine types were enriched for functions related to inflammation, the cardiovascular system and connective tissue. Conclusions: Our results provide novel insight into the likely genes and biological mechanisms that underlie both MA and MO, and when combined with previous data, highlight the neuropeptide FF-amide peptide encoding gene (NPFF) as a novel candidate risk gene for both types of migraine.

Genetic influences on handedness: data from 25,732 Australian and Dutch twin families

Handedness refers to a consistent asymmetry in skill or preferential use between the hands and is related to lateralization within the brain of other functions such as language. Previous twin studies of handedness have yielded inconsistent results resulting from a general lack of statistical power to find significant effects. Here we present analyses from a large international collaborative study of handedness (assessed by writing/drawing or self report) in Australian and Dutch twins and their siblings (54,270 individuals from 25,732 families). Maximum likelihood analyses incorporating the effects of known covariates (sex, year of birth and birth weight) revealed no evidence of hormonal transfer, mirror imaging or twin specific effects. There were also no differences in prevalence between zygosity groups or between twins and their singleton siblings. Consistent with previous meta-analyses, additive genetic effects accounted for about a quarter (23.64%) of the variance (95%CI 20.17, 27.09%) with the remainder accounted for by non-shared environmental influences. The implications of these findings for handedness both as a primary phenotype and as a covariate in linkage and association analyses are discussed.

Replication of the association of common rs9939609 variant of FTO with increased BMI in an Australian adult twin population but no evidence for gene by environment (G x E) interaction

OBJECTIVE: To further investigate a common variant (rs9939609) in the fat mass- and obesity-associated gene (FTO), which recent genome-wide association studies have shown to be associated with body mass index (BMI) and obesity. DESIGN: We examined the effect of this FTO variant on BMI in 3353 Australian adult male and female twins. RESULTS: The minor A allele of rs9939609 was associated with an increased BMI (P=0.0007). Each additional copy of the A allele was associated with a mean BMI increase of approximately 1.04 kg/m(2) (approximately 3.71 kg). Using variance components decomposition, we estimate that this single-nucleotide polymorphism accounts for approximately 3% of the genetic variance in BMI in our sample (approximately 2% of the total variance). By comparing intrapair variances of monozygotic twins of different genotypes we were able to perform a direct test of gene by environment (G x E) interaction in both sexes and gene by parity (G x P) interaction in women, but no evidence was found for either. CONCLUSIONS: In addition to supporting earlier findings that the rs9939609 variant in the FTO gene is associated with an increased BMI, our results indicate that the associated genetic effect does not interact with environment or parity.

Ion irradiation as a tool for modifying the surface and optical properties of plasma polymerised thin films

Radio frequency (R.F.) glow discharge polyterpenol thin films were prepared on silicon wafers and irradiated with I10+ ions to fluences of 1 × 1010 and 1 × 1012 ions/cm2. Post-irradiation characterisation of these films indicated the development of well-defined nano-scale ion entry tracks, highlighting prospective applications for ion irradiated polyterpenol thin films in a variety of membrane and nanotube-fabrication functions. Optical characterisation showed the films to be optically transparent within the visible spectrum and revealed an ability to selectively control the thin film refractive index as a function of fluence. This indicates that ion irradiation processing may be employed to produce plasma-polymer waveguides to accommodate a variety of wavelengths. XRR probing of the substrate-thin film interface revealed interfacial roughness values comparable to those obtained for the uncoated substrate's surface (i.e., both on the order of 5 Å), indicating minimal substrate etching during the plasma deposition process.

R U there yet? using virtual classrooms to transform teaching practice

Access to quality higher education is challenging for many Western Australians that live outside the metropolitan area. In 2010, the School of Education moved to flexible delivery of a fully online Bachelor of Education degree for their non -metropolitan students. The new model of delivery allows access for students from any location provided they have a computer and an internet connection. A number of academic staff had previously used an asynchronous environment to deliver learning modules housed within a learning management system (LMS) but had not used synchronous software with their students. To enhance the learning environment and to provide high quality learning experiences to students learning at a distance, the adoption of synchronous software (Elluminate Live) was introduced. This software is a real-time virtual classroom environment that allows for communication through Voice over Internet Protocol (VoIP) and videoconferencing, along with a large number of collaboration tools to engage learners. This research paper reports on the integration of a live e-learning solution into the current LMS environment. Qualitative data were collected from academic staff through informal interviews and participant observation. The findings discuss (i) perceived level of support; (ii) identification of strategies used to create an effective online teacher presence; (iii) the perceived impact on the students' learning outcomes; and (iv) guidelines for professional development to enhance pedagogy within the live e-learning environment.

PolyPatEx : an R package for paternity exclusion in autopolyploids

Microsatellite markers have demonstrated their value for performing paternity exclusion and hence exploring mating patterns in plants and animals. Methodology is well established for diploid species, and several software packages exist for elucidating paternity in diploids; however, these issues are not so readily addressed in polyploids due to the increased complexity of the exclusion problem and a lack of available software. We introduce polypatex, an r package for paternity exclusion analysis using microsatellite data in autopolyploid, monoecious or dioecious/bisexual species with a ploidy of 4n, 6n or 8n. Given marker data for a set of offspring, their mothers and a set of candidate fathers, polypatex uses allele matching to exclude candidates whose marker alleles are incompatible with the alleles in each offspring–mother pair. polypatex can analyse marker data sets in which allele copy numbers are known (genotype data) or unknown (allelic phenotype data) – for data sets in which allele copy numbers are unknown, comparisons are made taking into account all possible genotypes that could arise from the compared allele sets. polypatex is a software tool that provides population geneticists with the ability to investigate the mating patterns of autopolyploids using paternity exclusion analysis on data from codominant markers having multiple alleles per locus.

Platelet endothelial cell adhesion molecule 1 (PECAM-1) and its interactions with glycosaminoglycans: 2. Biochemical analyses

Platelet endothelial cell adhesion molecule 1 (PECAM-1) (CD31), a member of the immunoglobulin (Ig) superfamily of cell adhesion molecules with six Ig-like domains, has a range of functions, notably its contributions to leukocyte extravasation during inflammation and in maintaining vascular endothelial integrity. Although PECAM-1 is known to mediate cell adhesion by homophilic binding via domain 1, a number of PECAM-1 heterophilic ligands have been proposed. Here, the possibility that heparin and heparan sulfate (HS) are ligands for PECAM-1 was reinvestigated. The extracellular domain of PECAM-1 was expressed first as a fusion protein with the Fc region of human IgG1 fused to domain 6 and second with an N-terminal Flag tag on domain 1 (Flag-PECAM-1). Both proteins bound heparin immobilized on a biosensor chip in surface plasmon resonance (SPR) binding experiments. Binding was pH-sensitive but is easily measured at slightly acidic pH. A series of PECAM-1 domain deletions, prepared in both expression systems, were tested for heparin binding. This revealed that the main heparin-binding site required both domains 2 and 3. Flag-PECAM-1 and a Flag protein containing domains 1-3 bound HS on melanoma cell surfaces, but a Flag protein containing domains 1-2 did not. Heparin oligosaccharides inhibited Flag-PECAM-1 from binding immobilized heparin, with certain structures having greater inhibitory activity than others. Molecular modeling similarly identified the junction of domains 2 and 3 as the heparin-binding site and further revealed the importance of the iduronic acid conformation for binding. PECAM-1 does bind heparin/HS but by a site that is distinct from that required for homophilic binding.

Platelet endothelial cell adhesion molecule 1 (PECAM-1) and its interactions with glycosaminoglycans: 1. Molecular modeling studies

Platelet endothelial cell adhesion molecule 1 (PECAM-1) has many functions, including its roles in leukocyte extravasation as part of the inflammatory response and in the maintenance of vascular integrity through its contribution to endothelial cell−cell adhesion. PECAM-1 has been shown to mediate cell−cell adhesion through homophilic binding events that involve interactions between domain 1 of PECAM-1 molecules on adjacent cells. However, various heterophilic ligands of PECAM-1 have also been proposed. The possible interaction of PECAM-1 with glycosaminoglycans (GAGs) is the focus of this study. The three-dimensional structure of the extracellular immunoglobulin (Ig) domains of PECAM-1 were constructed using homology modeling and threading methods. Potential heparin/heparan sulfate-binding sites were predicted on the basis of their amino acid consensus sequences and a comparison with known structures of sulfate-binding proteins. Heparin and other GAG fragments have been docked to investigate the structural determinants of their protein-binding specificity and selectivity. The modeling has predicted two regions in PECAM-1 that appear to bind heparin oligosaccharides. A high-affinity binding site was located in Ig domains 2 and 3, and evidence for a low-affinity site in Ig domains 5 and 6 was obtained. These GAG-binding regions were distinct from regions involved in PECAM-1 homophilic interactions.