Assistive classification for improving the efficiency of avian species richness surveys

Avian species richness surveys, which measure the total number of unique avian species, can be conducted via remote acoustic sensors. An immense quantity of data can be collected, which, although rich in useful information, places a great workload on the scientists who manually inspect the audio. To deal with this big data problem, we calculated acoustic indices from audio data at a one-minute resolution and used them to classify one-minute recordings into five classes. By filtering out the non-avian minutes, we can reduce the amount of data by about 50% and improve the efficiency of determining avian species richness. The experimental results show that, given 60 one-minute samples, our approach enables to direct ecologists to find about 10% more avian species.

Computer-assisted sampling of acoustic data for more efficient determination of bird species richness

Bird species richness survey is one of the most intriguing ecological topics for evaluating environmental health. Here, bird species richness denotes the number of unique bird species in a particular area. Factors affecting the investigation of bird species richness include weather, observation bias, and most importantly, the prohibitive costs of conducting surveys at large spatiotemporal scales. Thanks to advances in recording techniques, these problems have been alleviated by deploying sensors for acoustic data collection. Although automated detection techniques have been introduced to identify various bird species, the innate complexity of bird vocalizations, the background noise present in the recording and the escalating volumes of acoustic data pose a challenging task on determination of bird species richness. In this paper we proposed a two-step computer-assisted sampling approach for determining bird species richness in one-day acoustic data. First, a classification model is built based on acoustic indices for filtering out minutes that contain few bird species. Then the classified bird minutes are ordered by an acoustic index and the redundant temporal minutes are removed from the ranked minute sequence. The experimental results show that our method is more efficient in directing experts for determination of bird species compared with the previous methods.

Growth hormone resistance and somatomedins in children with end-stage liver disease awaiting transplantation

Background: The success of orthotopic liver transplantation as treatment for end-stage liver disease has prompted investigation of strategies to maintain or improve nutrition and growth in children awaiting transplantation, because malnutrition is an adverse prognostic factor. The purpose of this study was to evaluate the effect of recombinant human growth hormone therapy on body composition and indices of liver function in patients awaiting transplant. Methods: The study was designed as a placebo- controlled, double-blind, crossover trial. Patients received 0.2 U/kg growth hormone, subcutaneously, or placebo daily for 28 days during two treatment periods, separated by a 2-week washout period. Ten patients (mean age, 3.06 ± 1.15 years; range, 0.51-11.65 years, five men), with extrahepatic biliary atresia (n = 8) or two with Alagille's syndrome (n = 2), with end-stage liver disease, completed the trial while awaiting orthotopic liver transplantation. Height, weight, total body potassium, total body fat, resting energy expenditure, respiratory quotient, hematologic and multiple biochemical profile, number of albumin infusions, insulin-like growth factor-1 and 1, growth hormone binding protein (GHBP), and insulin-like growth factor binding protein-1 (IGFBP-1) and insulin-like growth factor binding protein (IGFBP-3) were measured at the beginning and end of each treatment period. Results: Growth hormone treatment was associated with a significant decline in serum bilirubin (-34.6 ± 16.5 μmol/l vs. 18.2 ± 11.59 μmol/l; p < 0.02) but there was no significant effect on any anthropometric or body composition measurements, or on any biochemical or hematologic parameters. Conclusions: These children with end-stage liver disease displayed growth hormone resistance, particularly in relation to the somatomedin axis. Exogenous growth hormone administration may be of limited value in these patients

Malnutrition, gastroenteritis and trypsinogen concentration in hospitalised aboriginal children

Objective: To explore relationships between malnutrition and pancreatic damage in hospitalised aboriginal children. Methods: Immunoreactive trypsinogen (IRT) concentrations were measured in two populations of hospitalised aboriginal children in Australia; 472 children aged 0-3 years, in Alice Springs (Northern Territory); and 187 children aged 0-16 years in Mount Isa (Queensland). Correlation of whole blood IRT with height and weight z-scores, four-site skinfold thickness and upper arm circumference was sought. Results: In Mount Isa, the geometric mean IRT concentration rose with decreasing weight z-score. The IRT concentration was otherwise unrelated to nutritional indices. Sixty percent of the 39 Mount Isa patients with gastroenteritis and 24.5% of the 358 Alice Springs patients with gastroenteritis had an IRT concentration in the upper quartile for their population, compared with 16% for patients with other diagnoses in both populations. Conclusions: A high IRT concentration in patients with low weight z-scores is a confounding effect of gastroenteritis, and may result from subclinical pancreatic disease in gastroenteritis.

Predictors of clinical improvement in children with recurrent abdominal pain

Forty-three children with recurrent abdominal pain who had received treatment from a paediatric gastroenterology clinic were reassessed 6 and 12 months after initial presentation. Measures of children's pain included a pain diary (PD) which measured pain intensity, a parent observation record (POR) which assessed pain behaviour and a structured interview to assess the degree to which pain interferes with the child's activities. Pretreatment measures of the child's history of pain, coping strategies in dealing with pain, and their mother's caregiving strategies were examined as predictors of two indices of clinical improvement: the extent of change in pain on the child's pain diary from pre-test to 6 months follow-up, and the degree of interference to the child's activities. All children had shown significant improvement in the level of pain at follow up, with 74.4% being pain free at 12 month follow-up on the PD and 83.7% being pain free on the POR. The amount of change they showed varied, with some showing residual impairment even though they were significantly improved. Regression analyses showed that children with greatest reductions on the child's pain diary at the 6 month follow-up were those with a stress-related mode of onset, whose mothers used more adaptive caregiving strategies, and who received cognitive behavioural family intervention. There was also a non significant trend for younger children to fare better. These data suggest the importance of early diagnosis and routinely assessing parental caregiving behaviour and beliefs about the origins of pain in planning treatment for children with RAP.

Detection of anuran calling activity in long field recordings for bio-acoustic monitoring

This paper presents a system to analyze long field recordings with low signal-to-noise ratio (SNR) for bio-acoustic monitoring. A method based on spectral peak track, Shannon entropy, harmonic structure and oscillation structure is proposed to automatically detect anuran (frog) calling activity. Gaussian mixture model (GMM) is introduced for modelling those features. Four anuran species widespread in Queensland, Australia, are selected to evaluate the proposed system. A visualization method based on extracted indices is employed for detection of anuran calling activity which achieves high accuracy.

Load estimation with uncertainties from opportunistic sampling data: A semiparametric approach

We consider estimating the total load from frequent flow data but less frequent concentration data. There are numerous load estimation methods available, some of which are captured in various online tools. However, most estimators are subject to large biases statistically, and their associated uncertainties are often not reported. This makes interpretation difficult and the estimation of trends or determination of optimal sampling regimes impossible to assess. In this paper, we first propose two indices for measuring the extent of sampling bias, and then provide steps for obtaining reliable load estimates that minimizes the biases and makes use of informative predictive variables. The key step to this approach is in the development of an appropriate predictive model for concentration. This is achieved using a generalized rating-curve approach with additional predictors that capture unique features in the flow data, such as the concept of the first flush, the location of the event on the hydrograph (e.g. rise or fall) and the discounted flow. The latter may be thought of as a measure of constituent exhaustion occurring during flood events. Forming this additional information can significantly improve the predictability of concentration, and ultimately the precision with which the pollutant load is estimated. We also provide a measure of the standard error of the load estimate which incorporates model, spatial and/or temporal errors. This method also has the capacity to incorporate measurement error incurred through the sampling of flow. We illustrate this approach for two rivers delivering to the Great Barrier Reef, Queensland, Australia. One is a data set from the Burdekin River, and consists of the total suspended sediment (TSS) and nitrogen oxide (NO(x)) and gauged flow for 1997. The other dataset is from the Tully River, for the period of July 2000 to June 2008. For NO(x) Burdekin, the new estimates are very similar to the ratio estimates even when there is no relationship between the concentration and the flow. However, for the Tully dataset, by incorporating the additional predictive variables namely the discounted flow and flow phases (rising or recessing), we substantially improved the model fit, and thus the certainty with which the load is estimated.

An extended regression approach to estimating loads and their uncertainties in Great Barrier Reef catchments

There are numerous load estimation methods available, some of which are captured in various online tools. However, most estimators are subject to large biases statistically, and their associated uncertainties are often not reported. This makes interpretation difficult and the estimation of trends or determination of optimal sampling regimes impossible to assess. In this paper, we first propose two indices for measuring the extent of sampling bias, and then provide steps for obtaining reliable load estimates by minimizing the biases and making use of possible predictive variables. The load estimation procedure can be summarized by the following four steps: - (i) output the flow rates at regular time intervals (e.g. 10 minutes) using a time series model that captures all the peak flows; - (ii) output the predicted flow rates as in (i) at the concentration sampling times, if the corresponding flow rates are not collected; - (iii) establish a predictive model for the concentration data, which incorporates all possible predictor variables and output the predicted concentrations at the regular time intervals as in (i), and; - (iv) obtain the sum of all the products of the predicted flow and the predicted concentration over the regular time intervals to represent an estimate of the load. The key step to this approach is in the development of an appropriate predictive model for concentration. This is achieved using a generalized regression (rating-curve) approach with additional predictors that capture unique features in the flow data, namely the concept of the first flush, the location of the event on the hydrograph (e.g. rise or fall) and cumulative discounted flow. The latter may be thought of as a measure of constituent exhaustion occurring during flood events. The model also has the capacity to accommodate autocorrelation in model errors which are the result of intensive sampling during floods. Incorporating this additional information can significantly improve the predictability of concentration, and ultimately the precision with which the pollutant load is estimated. We also provide a measure of the standard error of the load estimate which incorporates model, spatial and/or temporal errors. This method also has the capacity to incorporate measurement error incurred through the sampling of flow. We illustrate this approach using the concentrations of total suspended sediment (TSS) and nitrogen oxide (NOx) and gauged flow data from the Burdekin River, a catchment delivering to the Great Barrier Reef. The sampling biases for NOx concentrations range from 2 to 10 times indicating severe biases. As we expect, the traditional average and extrapolation methods produce much higher estimates than those when bias in sampling is taken into account.

A note on Gittins indexes for pharmaceutical research

The Bernoulli/exponential target process is considered. Such processes have been found useful in modelling the search for active compounds in pharmaceutical research. An inequality is presented which improves a result of Gittins (1989), thus providing a better approximation to the Gittins indices which define the optimal search policy.

Effects of fish density distribution and effort distribution on catchability

The effects of fish density distribution and effort distribution on the overall catchability coefficient are examined. Emphasis is also on how aggregation and effort distribution interact to affect overall catch rate [catch per unit effort (cpue)]. In particular, it is proposed to evaluate three indices, the catchability index, the knowledge parameter, and the aggregation index, to describe the effectiveness of targeting and the effects on overall catchability in the stock area. Analytical expressions are provided so that these indices can easily be calculated. The average of the cpue calculated from small units where fishing is random is a better index for measuring the stock abundance. The overall cpue, the ratio of lumped catch and effort, together with the average cpue, can be used to assess the effectiveness of targeting. The proposed methods are applied to the commercial catch and effort data from the Australian northern prawn fishery. The indices are obtained assuming a power law for the effort distribution as an approximation of targeting during the fishing operation. Targeting increased catchability in some areas by 10%, which may have important implications on management advice.

Analysing commercial catch and effort data from a penaeid trawl fishery: A comparison of linear models, mixed models, and generalised estimating equations approaches

Statistical methods are often used to analyse commercial catch and effort data to provide standardised fishing effort and/or a relative index of fish abundance for input into stock assessment models. Achieving reliable results has proved difficult in Australia's Northern Prawn Fishery (NPF), due to a combination of such factors as the biological characteristics of the animals, some aspects of the fleet dynamics, and the changes in fishing technology. For this set of data, we compared four modelling approaches (linear models, mixed models, generalised estimating equations, and generalised linear models) with respect to the outcomes of the standardised fishing effort or the relative index of abundance. We also varied the number and form of vessel covariates in the models. Within a subset of data from this fishery, modelling correlation structures did not alter the conclusions from simpler statistical models. The random-effects models also yielded similar results. This is because the estimators are all consistent even if the correlation structure is mis-specified, and the data set is very large. However, the standard errors from different models differed, suggesting that different methods have different statistical efficiency. We suggest that there is value in modelling the variance function and the correlation structure, to make valid and efficient statistical inferences and gain insight into the data. We found that fishing power was separable from the indices of prawn abundance only when we offset the impact of vessel characteristics at assumed values from external sources. This may be due to the large degree of confounding within the data, and the extreme temporal changes in certain aspects of individual vessels, the fleet and the fleet dynamics.

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.

Sequential allocation in clinical trials

Suppose two treatments with binary responses are available for patients with some disease and that each patient will receive one of the two treatments. In this paper we consider the interests of patients both within and outside a trial using a Bayesian bandit approach and conclude that equal allocation is not appropriate for either group of patients. It is suggested that Gittins indices should be used (using an approach called dynamic discounting by choosing the discount rate based on the number of future patients in the trial) if the disease is rare, and the least failures rule if the disease is common. Some analytical and simulation results are provided.

Parental divorce and adjustment in adulthood: Findings from a community sample

The current study examines the link between the experience of divorce in childhood and several indices of adjustment in adulthood in a large community sample of women. Results replicated previous research on the long-term correlation between parental divorce and depression and divorce in adulthood. Results further suggested that parental divorce was associated with a wide range of early risk factors, life course patterns, and several indices of adult adjustment. Regression analyses indicated that the long-term correlation between parental divorce and depression in adulthood is explained by quality of parent-child and parental marital relations (in childhood), concurrent levels of stressful life events and social support, and cohabitation. The long-term association between parental divorce and experiencing a divorce in adulthood was partly mediated through quality of parent-child relations, teenage pregnancy, leaving home before 18 years, and educational attainment.

CBCT-guided radiotherapy for locally advanced head and cancer: dosimetric impact of weight loss on VMAT and IMRT plans for selected organs at risk structures (OARs)

Purpose: It is common for head and neck patients to be affected by time trend errors as a result of weight loss during a course of radiation treatment. The objective of this planning study was to investigate the impact of weight loss on Volumetric Modulated Arc Therapy (VMAT) as well as Intensity modulated radiation therapy (IMRT) for locally advanced head and neck cancer using automatic co-registration of the CBCT. Methods and Materials: A retrospective analysis of previously treated IMRT plans for 10 patients with locally advanced head and neck cancer patients was done. A VMAT plan was also produced for all patients. We calculated the dose–volume histograms (DVH) indices for spinal cord planning at risk volumes (PRVs), the brainstem PRVs (SC+0.5cm and BS+0.5cm, respectively) as well as mean dose to the parotid glands. Results: The results show that the mean difference in dose to the SC+0.5cm was 1.03% and 1.27% for the IMRT and VMAT plans, respectively. As for dose to the BS+0.5, the percentage difference was 0.63% for the IMRT plans and 0.61% for the VMAT plans. The analysis of the parotid gland doses shows that the percentage change in mean dose to left parotid was -8.0% whereas that of the right parotid was -6.4% for the IMRT treatment plans. In the VMAT plans, the percentages change for the left and the right parotid glands were -6.6% and -6.7% respectively. Conclusions: This study shows a clinically significant impact of weight loss on DVH indices analysed in head and neck organs at risk. It highlights the importance of adaptive radiotherapy in head and neck patients if organ at risk sparing is to be maintained.