Suggestive linkage of 2p22-25 and 11q12-13 with low bone mineral density at the lumbar spine in the Irish population

Osteoporosis is a disease characterized by low bone mineral density (BMD) and poor bone quality. Peak bone density is achieved by the third decade of life, after which bone is maintained by a balanced cycle of bone resorption and synthesis. Age-related bone loss occurs as the bone resorption phase outweighs the bone synthesis phase of bone metabolism. Heritability accounts for up to 90% of the variability in BMD. Chromosomal loci including 1p36, 2p22-25, 11q12-13, parathyroid hormone receptor type 1 (PTHR1), interleukin-6 (IL-6), interleukin 1 alpha (IL-1α) and type II collagen A1/vitamin D receptor (COL11A1/VDR) have been linked or shown suggestive linkage with BMD in other populations. To determine whether these loci predispose to low BMD in the Irish population, we investigated 24 microsatellite markers at 7 chromosomal loci by linkage studies in 175 Irish families of probands with primary low BMD (T-score ≤ -1.5). Nonparametric analysis was performed using the maximum likelihood variance estimation and traditional Haseman-Elston tests on the Mapmaker/Sibs program. Suggestive evidence of linkage was observed with lumbar spine BMD at 2p22-25 (maximum LOD score 2.76) and 11q12-13 (MLS 2.55). One region, 1p36, approached suggestive linkage with femoral neck BMD (MLS 2.17). In addition, seven markers achieved LOD scores > 1.0, D2S149, D11S1313, D11S987, D11S1314 including those encompassing the PTHR1 (D3S3559, D3S1289) for lumbar spine BMD and D2S149 for femoral neck BMD. Our data suggest that genes within a these chromosomal regions are contributing to a predisposition to low BMD in the Irish population.

Centile reference charts for total energy expenditure in infants from 1 to 12 months

Background: A knowledge of energy expenditure in infancy is required for the estimation of recommended daily amounts of food energy, for designing artificial infant feeds, and as a reference standard for studies of energy metabolism in disease states. Objectives: The objectives of this study were to construct centile reference charts for total energy expenditure (TEE) in infants across the first year of life. Methods: Repeated measures of TEE using the doubly labeled water technique were made in 162 infants at 1.5, 3, 6, 9 and 12 months. In total, 322 TEE measurements were obtained. The LMS method with maximum penalized likelihood was used to construct the centile reference charts. Centiles were constructed for TEE expressed as MJ/day and also expressed relative to body weight (BW) and fat-free mass (FFM). Results: TEE increased with age and was 1.40,1.86, 2.64, 3.07 and 3.65 MJ/day at 1.5, 3, 6, 9 and 12 months, respectively. The standard deviations were 0.43, 0.47, 0.52,0.66 and 0.88, respectively. TEE in MJ/kg increased from 0.29 to 0.36 and in MJ/day/kg FFM from 0.36 to 0.48. Conclusions: We have presented centile reference charts for TEE expressed as MJ/day and expressed relative to BW and FFM in infants across the first year of life. There was a wide variation or biological scatter in TEE values seen at all ages. We suggest that these centile charts may be used to assess and possibly quantify abnormal energy metabolism in disease states in infants.

Estimating the parameters of stochastic volatility models using option price data

This article describes a maximum likelihood method for estimating the parameters of the standard square-root stochastic volatility model and a variant of the model that includes jumps in equity prices. The model is fitted to data on the S&P 500 Index and the prices of vanilla options written on the index, for the period 1990 to 2011. The method is able to estimate both the parameters of the physical measure (associated with the index) and the parameters of the risk-neutral measure (associated with the options), including the volatility and jump risk premia. The estimation is implemented using a particle filter whose efficacy is demonstrated under simulation. The computational load of this estimation method, which previously has been prohibitive, is managed by the effective use of parallel computing using graphics processing units (GPUs). The empirical results indicate that the parameters of the models are reliably estimated and consistent with values reported in previous work. In particular, both the volatility risk premium and the jump risk premium are found to be significant.

Generalised growth models for aquatic species with an application to blacklip abalone (Haliotis rubra)

This paper presents a maximum likelihood method for estimating growth parameters for an aquatic species that incorporates growth covariates, and takes into consideration multiple tag-recapture data. Individual variability in asymptotic length, age-at-tagging, and measurement error are also considered in the model structure. Using distribution theory, the log-likelihood function is derived under a generalised framework for the von Bertalanffy and Gompertz growth models. Due to the generality of the derivation, covariate effects can be included for both models with seasonality and tagging effects investigated. Method robustness is established via comparison with the Fabens, improved Fabens, James and a non-linear mixed-effects growth models, with the maximum likelihood method performing the best. The method is illustrated further with an application to blacklip abalone (Haliotis rubra) for which a strong growth-retarding tagging effect that persisted for several months was detected

Improved estimation of size-transition matrices using tag-recapture data

We derive a new method for determining size-transition matrices (STMs) that eliminates probabilities of negative growth and accounts for individual variability. STMs are an important part of size-structured models, which are used in the stock assessment of aquatic species. The elements of STMs represent the probability of growth from one size class to another, given a time step. The growth increment over this time step can be modelled with a variety of methods, but when a population construct is assumed for the underlying growth model, the resulting STM may contain entries that predict negative growth. To solve this problem, we use a maximum likelihood method that incorporates individual variability in the asymptotic length, relative age at tagging, and measurement error to obtain von Bertalanffy growth model parameter estimates. The statistical moments for the future length given an individual's previous length measurement and time at liberty are then derived. We moment match the true conditional distributions with skewed-normal distributions and use these to accurately estimate the elements of the STMs. The method is investigated with simulated tag-recapture data and tag-recapture data gathered from the Australian eastern king prawn (Melicertus plebejus).

An extravariation model for improving confidence intervals of population size estimates from removal data

We propose a new model for estimating the size of a population from successive catches taken during a removal experiment. The data from these experiments often have excessive variation, known as overdispersion, as compared with that predicted by the multinomial model. The new model allows catchability to vary randomly among samplings, which accounts for overdispersion. When the catchability is assumed to have a beta distribution, the likelihood function, which is refered to as beta-multinomial, is derived, and hence the maximum likelihood estimates can be evaluated. Simulations show that in the presence of extravariation in the data, the confidence intervals have been substantially underestimated in previous models (Leslie-DeLury, Moran) and that the new model provides more reliable confidence intervals. The performance of these methods was also demonstrated using two real data sets: one with overdispersion, from smallmouth bass (Micropterus dolomieu), and the other without overdispersion, from rat (Rattus rattus).

Iterative estimating equations: Linear convergence and asymptotic properties

We propose an iterative estimating equations procedure for analysis of longitudinal data. We show that, under very mild conditions, the probability that the procedure converges at an exponential rate tends to one as the sample size increases to infinity. Furthermore, we show that the limiting estimator is consistent and asymptotically efficient, as expected. The method applies to semiparametric regression models with unspecified covariances among the observations. In the special case of linear models, the procedure reduces to iterative reweighted least squares. Finite sample performance of the procedure is studied by simulations, and compared with other methods. A numerical example from a medical study is considered to illustrate the application of the method.

Stock-recruitment relationships of the tiger prawns (Penaeus esculentus and Penaeus semisulcatus) in the Australian Northern Prawn Fishery

This paper investigates the stock-recruitment and equilibrium yield dynamics for the two species of tiger prawns (Penaeus esculentus and Penaeus semisulcatus) in Australia's most productive prawn fishery: the Northern Prawn Fishery. Commercial trawl logbooks for 1970-93 and research surveys are used to develop population models for these prawns. A population model that incorporates continuous recruitment is developed. Annual spawning stock and recruitment indices are then estimated from the population model. Spawning stock indices represent the abundance of female prawns that are likely to spawn; recruitment indices represent the abundance of all prawns less than a certain size. The relationships between spawning stock and subsequent recruitment (SRR), between recruitment and subsequent spawning stock (RSR), and between recruitment and commercial catch were estimated through maximum-likelihood models that incorporated autoregressive terms. Yield as a function of fishing effort was estimated by constraining to equilibrium the SRR and RSR. The resulting production model was then used to determine maximum sustainable yield (MSY) and its corresponding fishing effort (f(MSY)). Long-term yield estimates for the two tiger prawn species range between 3700 and 5300 t. The fishing effort at present is close to the level that should produce MSY for both species of tiger prawns. However, current landings, recruitment and spawning stock are below the equilibrium values predicted by the models. This may be because of uncertainty in the spawning stock-recruitment relationships, a change in carrying capacity, biased estimates of fishing effort, unreliable catch statistics, or simplistic assumptions about stock structure. Although our predictions of tiger prawn yields are uncertain, management will soon have to consider new measures to counteract the effects of future increases in fishing effort.

Estimating the efficiency of a small beam trawl for sampling tiger prawns Penaeus esculentus and P. semisulcatus in seagrass by removal experiments

The efficiency with which a small beam trawl (1 x 0.5 m mouth) sampled postlarvae and juveniles of tiger prawns Penaeus esculentus and P, semisulcatus at night was estimated in 3 tropical seagrass communities (dominated by Thalassia hemprichii, Syringodium isoetifolium and Enhalus acoroides, respectively) in the shallow waters of the Gulf of Carpentaria in northern Australia. An area of seagrass (40 x 3 m) was enclosed by a net and the beam trawl was repeatedly hand-hauled over the substrate. Net efficiency (q) was calculated using 4 methods: the unweighted Leslie, weighted Leslie, DeLury and Maximum-likelihood (ML) methods. The Maximum-likelihood is the preferred method for estimating efficiency because it makes the fewest assumptions and is not affected by zero catches. The major difference in net efficiencies was between postlarvae (mean ML q +/- 95% confidence limits = 0.66 +/- 0.16) and juveniles of both species (mean q for juveniles in water less than or equal to 1.0 m deep = 0.47 +/- 0.05), i.e. the beam trawl was more efficient at capturing postlarvae than juveniles. There was little difference in net efficiency for P, esculentus between seagrass types (T, hemprichii versus S. isoetifolium), even though the biomass and morphologies of seagrass in these communities differed greatly (biomasses were 54 and 204 g m(-2), respectively). The efficiency of the net appeared to be the same for juveniles of the 2 species in shallow water, but was lower for juvenile P, semisulcatus at high tide when the water was deeper (1.6 to 1.9 m) (0.35 +/- 0.08). The lower efficiency near the time of high tide is possibly because the prawns are more active at high than low tide, and can also escape above the net. Factors affecting net efficiency and alternative methods of estimating net efficiency are discussed.

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.

Autonomous UAVs wildlife detection using thermal imaging, predictive navigation and computer vision

There is an increased interest on the use of Unmanned Aerial Vehicles (UAVs) for wildlife and feral animal monitoring around the world. This paper describes a novel system which uses a predictive dynamic application that places the UAV ahead of a user, with a low cost thermal camera, a small onboard computer that identifies heat signatures of a target animal from a predetermined altitude and transmits that target’s GPS coordinates. A map is generated and various data sets and graphs are displayed using a GUI designed for easy use. The paper describes the hardware and software architecture and the probabilistic model for downward facing camera for the detection of an animal. Behavioral dynamics of target movement for the design of a Kalman filter and Markov model based prediction algorithm are used to place the UAV ahead of the user. Geometrical concepts and Haversine formula are applied to the maximum likelihood case in order to make a prediction regarding a future state of the user, thus delivering a new way point for autonomous navigation. Results show that the system is capable of autonomously locating animals from a predetermined height and generate a map showing the location of the animals ahead of the user.

A new family of multivariate heavy-tailed distributions with variable marginal amounts of tailweight: Application to robust clustering

We propose a family of multivariate heavy-tailed distributions that allow variable marginal amounts of tailweight. The originality comes from introducing multidimensional instead of univariate scale variables for the mixture of scaled Gaussian family of distributions. In contrast to most existing approaches, the derived distributions can account for a variety of shapes and have a simple tractable form with a closed-form probability density function whatever the dimension. We examine a number of properties of these distributions and illustrate them in the particular case of Pearson type VII and t tails. For these latter cases, we provide maximum likelihood estimation of the parameters and illustrate their modelling flexibility on simulated and real data clustering examples.

Co2 emissions and income trajectory in Australia: The role of technological change

This study investigates the relationship between per capita carbon dioxide (CO2) emissions and per capita GDP in Australia, while controlling for technological state as measured by multifactor productivity and export of black coal. Although technological progress seems to play a critical role in achieving long term goals of CO2 reduction and economic growth, empirical studies have often considered time trend to proxy technological change. However, as discoveries and diffusion of new technologies may not progress smoothly with time, the assumption of a deterministic technological progress may be incorrect in the long run. The use of multifactor productivity as a measure of technological state, therefore, overcomes the limitations and provides practical policy directions. This study uses recently developed bound-testing approach, which is complemented by Johansen- Juselius maximum likelihood approach and a reasonably large sample size to investigate the cointegration relationship. Both of the techniques suggest that cointegration relationship exists among the variables. The long-run and short-run coefficients of CO2 emissions function is estimated using ARDL approach. The empirical findings in the study show evidence of the existence of Environmental Kuznets Curve type relationship for per capita CO2 emissions in the Australian context. The technology as measured by the multifactor productivity, however, is not found as an influencing variable in emissionsincome trajectory.

The complete mitochondrial genome of the eastern grey kangaroo (Macropus giganteus)

We present the complete mitochondrial genome (accession number: LK995454) of an iconic Australian species, the eastern grey kangaroo (Macropus giganteus). The mitogenomic organization is consistent with other marsupials, encoding 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, an origin of light strand replication and a control region or Dloop. No repetitive sequences were detected in the control region. The M. giganteus mitogenome exemplifies a combination of tRNA gene order and structural peculiarities that appear to be unique to marsupials. We present a maximum likelihood phylogeny based on complete mitochondrial protein and RNA coding sequences that confirms the phylogenetic position of the grey kangaroo among macropodids.

The phylogeny and evolutionary timescale of muscoide (Diptera: Brachycera: Calyptratae) inferred from mitochondrial genomes

Muscoidea is a significant dipteran clade that includes house flies (Family Muscidae), latrine flies (F. Fannidae), dung flies (F. Scathophagidae) and root maggot flies (F. Anthomyiidae). It is comprised of approximately 7000 described species. The monophyly of the Muscoidea and the precise relationships of muscoids to the closest superfamily the Oestroidea (blow flies, flesh flies etc) are both unresolved. Until now mitochondrial (mt) genomes were available for only two of the four muscoid families precluding a thorough test of phylogenetic relationships using this data source. Here we present the first two mt genomes for the families Fanniidae (Euryomma sp.) (family Fanniidae) and Anthomyiidae (Delia platura (Meigen, 1826)). We also conducted phylogenetic analyses containing of these newly sequenced mt genomes plus 15 other species representative of dipteran diversity to address the internal relationship of Muscoidea and its systematic position. Both maximum-likelihood and Bayesian analyses suggested that Muscoidea was not a monophyletic group with the relationship: (Fanniidae + Muscidae) + ((Anthomyiidae + Scathophagidae) + (Calliphoridae + Sarcophagidae)), supported by the majority of analysed datasets. This also infers that Oestroidea was paraphyletic in the majority of analyses. Divergence time estimation suggested that the earliest split within the Calyptratae, separating (Tachinidae + Oestridae) from the remaining families, occurred in the Early Eocene. The main divergence within the paraphyletic muscoidea grade was between Fanniidae + Muscidae and the lineage ((Anthomyiidae + Scathophagidae) + (Calliphoridae + Sarcophagidae)) which occurred in the Late Eocene