Robust estimation using the Huber function with a data-dependent tuning constant

Robust estimation often relies on a dispersion function that is more slowly varying at large values than the square function. However, the choice of tuning constant in dispersion functions may impact the estimation efficiency to a great extent. For a given family of dispersion functions such as the Huber family, we suggest obtaining the "best" tuning constant from the data so that the asymptotic efficiency is maximized. This data-driven approach can automatically adjust the value of the tuning constant to provide the necessary resistance against outliers. Simulation studies show that substantial efficiency can be gained by this data-dependent approach compared with the traditional approach in which the tuning constant is fixed. We briefly illustrate the proposed method using two datasets.

Effects of variance-function misspecification in analysis of longitudinal data

The approach of generalized estimating equations (GEE) is based on the framework of generalized linear models but allows for specification of a working matrix for modeling within-subject correlations. The variance is often assumed to be a known function of the mean. This article investigates the impacts of misspecifying the variance function on estimators of the mean parameters for quantitative responses. Our numerical studies indicate that (1) correct specification of the variance function can improve the estimation efficiency even if the correlation structure is misspecified; (2) misspecification of the variance function impacts much more on estimators for within-cluster covariates than for cluster-level covariates; and (3) if the variance function is misspecified, correct choice of the correlation structure may not necessarily improve estimation efficiency. We illustrate impacts of different variance functions using a real data set from cow growth.

Kallikrein-related peptidases in prostate cancer: From molecular function to clinical application

Prostate cancer is a leading contributor to male cancer-related deaths worldwide. Kallikrein-related peptidases (KLKs) are serine proteases that exhibit deregulated expression in prostate cancer, with KLK3, or prostate specific antigen (PSA), being the widely-employed clinical biomarker for prostate cancer. Other KLKs, such as KLK2, show promise as prostate cancer biomarkers and, additionally, their altered expression has been utilised for the design of KLK-targeted therapies. There is also a large body of in vitro and in vivo evidence supporting their role in cancer-related processes. Here, we review the literature on studies to date investigating the potential of other KLKs, in addition to PSA, as biomarkers and in therapeutic options, as well as their current known functional roles in cancer progression. Increased knowledge of these KLK-mediated functions, including degradation of the extracellular matrix, local invasion, cancer cell proliferation, interactions with fibroblasts, angiogenesis, migration, bone metastasis and tumour growth in vivo, may help define new roles as prognostic biomarkers and novel therapeutic targets for this cancer.

Effects of the sensorimotor training volume on sensorimotor function in patients following lower limb arthroplasty

Background Sensorimotor function is degraded in patients after lower limb arthroplasty. Sensorimotor training is thought to improve sensorimotor skills, however, the optimal training stimulus with regard to volume, frequency, duration, and intensity is still unknown. The aim of this study, therefore, was to firstly quantify the progression of sensorimotor function after total hip (THA) or knee (TKA) arthroplasty and, as second step, to evaluate effects of different sensorimotor training volumes. Methods 58 in-patients during their rehabilitation after THA or TKA participated in this prospective cohort study. Sensorimotor function was assessed using a test battery including measures of stabilization capacity, static balance, proprioception, and gait, along with a self-reported pain and function. All participants were randomly assigned to one of three intervention groups performing sensorimotor training two, four, or six times per week. Outcome measures were taken at three instances, at baseline (pre), after 1.5 weeks (mid) and at the conclusion of the 3 week program (post). Results All measurements showed significant improvements over time, with the exception of proprioception and static balance during quiet bipedal stance which showed no significant main effects for time or intervention. There was no significant effect of sensorimotor training volume on any of the outcome measures. Conclusion We were able to quantify improvements in measures of dynamic, but not static, sensorimotor function during the initial three weeks of rehabilitation following TKA/THA. Although sensorimotor improvements were independent of the training volume applied in the current study, long-term effects of sensorimotor training volume need to be investigated to optimize training stimulus recommendations.

An improved Fabens method for estimation of growth parameters in the vonBertalanffy model with individual asymptotes

In the analysis of tagging data, it has been found that the least-squares method, based on the increment function known as the Fabens method, produces biased estimates because individual variability in growth is not allowed for. This paper modifies the Fabens method to account for individual variability in the length asymptote. Significance tests using t-statistics or log-likelihood ratio statistics may be applied to show the level of individual variability. Simulation results indicate that the modified method reduces the biases in the estimates to negligible proportions. Tagging data from tiger prawns (Penaeus esculentus and Penaeus semisulcatus) and rock lobster (Panulirus ornatus) are analysed as an illustration.

Application of commercially available, low-cost, miniaturised NIR spectrometers to the assessment of the sugar content of intact fruit

Recent decreases in costs, and improvements in performance, of silicon array detectors open a range of potential applications of relevance to plant physiologists, associated with spectral analysis in the visible and short-wave near infra-red (far-red) spectrum. The performance characteristics of three commercially available ‘miniature’ spectrometers based on silicon array detectors operating in the 650–1050-nm spectral region (MMS1 from Zeiss, S2000 from Ocean Optics, and FICS from Oriel, operated with a Larry detector) were compared with respect to the application of non-invasive prediction of sugar content of fruit using near infra-red spectroscopy (NIRS). The FICS–Larry gave the best wavelength resolution; however, the narrow slit and small pixel size of the charge-coupled device detector resulted in a very low sensitivity, and this instrumentation was not considered further. Wavelength resolution was poor with the MMS1 relative to the S2000 (e.g. full width at half maximum of the 912 nm Hg peak, 13 and 2 nm for the MMS1 and S2000, respectively), but the large pixel height of the array used in the MMS1 gave it sensitivity comparable to the S2000. The signal-to-signal standard error ratio of spectra was greater by an order of magnitude with the MMS1, relative to the S2000, at both near saturation and low light levels. Calibrations were developed using reflectance spectra of filter paper soaked in range of concentrations (0–20% w/v) of sucrose, using a modified partial least squares procedure. Calibrations developed with the MMS1 were superior to those developed using the S2000 (e.g. coefficient of correlation of 0.90 and 0.62, and standard error of cross-validation of 1.9 and 5.4%, respectively), indicating the importance of high signal to noise ratio over wavelength resolution to calibration accuracy. The design of a bench top assembly using the MMS1 for the non-invasive assessment of mesocarp sugar content of (intact) melon fruit is reported in terms of light source and angle between detector and light source, and optimisation of math treatment (derivative condition and smoothing function).

A towed instrument package for fisheries research in great barrier reef waters

A tethered remote instrument package (TRIP) has been developed for biological surveys over Queensland's continental shelf and slope. The present system, evolved from an earlier sled configuration, is suspended above the sea bed and towed at low speeds. Survey information is collected through video and film cameras while instrument and environmental variables are handled by a minicomputer. The operator was able to "fly" the instrument package above the substrate by using an altitude echosounder, forward-looking sonar and real-time television viewing. Unwanted movements of the viewing system were stabilized through a gyro-controlled camera-head panning system. the hydrodynamic drag of the umbilical presented a major control problem which could be overcome only by a reduction in towing speed. Despite the constraints of towing a device such as this through the coral reef environment, the package performed well during a recent biological survey where it was worked at 50% of its 350 m design depth.

Morphological Characteristics of Genetically-Modified Pineapple Fruit

Genetic engineering is an attractive method for changing a single characteristic of ‘Smooth Cayenne’ pineapple, without altering its other desirable attributes. Techniques used in pineapple transformation, however, such as tissue culture and biolistic-mediated or Agrobacterium-mediated gene insertion are prone to somaclonal variation, resulting in the production of several morphological mutations (Smith et al., 2002). Fruit mutations can include distortion in fruit shape (round ball, conical, fan-shaped), reduced fruit size, multiple crowns, crownless fruit, fruitless crowns, and spiny crown leaves (Dalldorf, 1975; Sanewski et al., 1992). The present paper describes the variability in fruit-shape mutations between transgenic and non-transgenic fruit, and its subsequent impact on organoleptic characteristics.

Molecular tools for studying puberty in the grey mullet, Mugil cephalus: cloning of cDNAs that regulate reproductive function

The cDNAs coding for the brain GnRHs (AY373449-51), pituitary GH, SL and PRL, and liver IGFs (AY427954-5) were isolated. Partial cDNA sequences of the brain (Cyp19b) and gonadal (Cyp19a) aromatases have also been obtained. These tools would be utilized to study the endocrine regulation of puberty in the grey mullet.

A spatially explicit multi-competitor coexistence model of penaeid (shrimp) distribution on the Australian Great Barrier Reef

A spatially explicit multi-competitor coexistence model was developed for meta-populations of prawns (shrimp) occupying habitat patches across the Great Barrier Reef, where dispersal was localised and dispersal rates varied between species. Prawns were modelled as individuals moving to and from patches or cells according to pre-set decision rules. The landscape was simulated as a matrix of cells with each cell having a spatially explicit survival index for each species. Mixed species prawn assemblages moved over this simplified spatially explicit landscape. A low level of chronic random environmental disturbance was assumed (cyclone and tropical storm damage) with additional acute spatially confined disturbance due to commercial trawling, modelled as an increase in mortality affecting inter-specific competition. The general form of the results was for increased disturbance to favour good-colonising "generalist" species at the expense of good-competitor "specialists". Increasing fishing mortality (local patch extinctions) combined with poor colonising ability resulted in low equilibrium abundance for even the best competitor, while in the same circumstances the poorest competitor but best coloniser could have the highest equilibrium abundance. This mimics the switch from high-value prawn species to lower-value prawn species as trawl effort increases, reflected in historic catch and effort logbook data and reported anecdotaly from the north Queensland trawl fleet. To match the observed distribution and behaviour of prawn assemblages, a combination inter-species competition, a spatially explicit landscape, and a defined pattern of disturbance (trawling) was required. Modelling this combination could simulate not only general trends in spatial distribution of each of prawn species but also localised concentrations observed in the survey data

Reproductive biology of the red throat emperor Lethrinus miniatus (Pisces : Lethrinidae) from the southern Great Barrier Reef, Australia

The reproductive biology of the red throat emperor, Lethrinus miniatus (Schneider, 1801) was examined in the southern Great Barrier Reef (GBR), Australia. The species was found to display the characteristics of an incomplete metagynous hermaphrodite based on histological evidence and size frequency information. Over 95% of functional males possessed a remnant lumen, but there was no evidence of oocytes in the testes of males. A single transitional fish was sampled which had both ovarian and testicular tissue present in its gonad. Size frequency data showed that females dominated the smaller size classes with the majority of fish < 40 cm being females. Lethrinus miniatus had an extended spawning season from July-November, although spawning was more pronounced during the spring. Spawning was initiated earlier at lower latitudes. There was no particular size or age when sex change occurred since females older than 20 and males as young as 2-yrs old were sampled.

Tree species diversity and ecosystem function: Can tropical multi-species plantations generate greater productivity?

Results from the humid tropics of Australia demonstrate that diverse plantations can achieve greater productivity than monocultures. We found that increases in both the observed species number and the effective species richness were significantly related to increased levels of productivity as measured by stand basal area or mean individual tree basal area. Four of five plantation species were more productive in mixtures with other species than in monocultures, offering on average, a 55% increase in mean tree basal area. A general linear model suggests that species richness had a significant effect on mean individual tree basal area when environmental variables were included in the model. As monoculture plantations are currently the preferred reforestation method throughout the tropics these results suggest that significant productivity and ecological gains could be made if multi-species plantations are more broadly pursued.

Serum immunoreactive pancreatic lipase and cationic trypsinogen for the assessment of exocrine pancreatic function in older patients with cystic fibrosis

Indirect and qualitative tests of pancreatic function are commonly used to screen patients with cystic fibrosis for pancreatic insufficiency. In an attempt to develop a more quantitative assessment, we compared the usefulness of measuring serum pancreatic lipase using a newly developed enzyme-linked immunosorbent immunoassay with that of cationic trypsinogen using a radioimmunoassay in the assessment of exocrine pancreatic function in patients with cystic fibrosis. Previously, we have shown neither lipase nor trypsinogen to be of use in assessing pancreatic function prior to 5 years of age because the majority of patients with cystic fibrosis in early infancy have elevated serum levels regardless of pancreatic function. Therefore, we studied 77 patients with cystic fibrosis older than 5 years of age, 41 with steatorrhea and 36 without steatorrhea. In addition, 28 of 77 patients consented to undergo a quantitative pancreatic stimulation test. There was a significant difference between the steatorrheic and nonsteatorrheic patients with the steatorrheic group having lower lipase and trypsinogen values than the nonsteatorrheic group (P < .001). Sensitivities and specificities in detecting steatorrhea were 95% and 86%, respectively, for lipase and 93% and 92%, respectively, for trypsinogen. No correlations were found between the serum levels of lipase and trypsinogen and their respective duodenal concentrations because of abnormally high serum levels of both enzymes found in some nonsteatorrheic patients. We conclude from this study that both serum lipase and trypsinogen levels accurately detect steatorrhea in patients with cystic fibrosis who are older than 5 years but are imprecise indicators of specific pancreatic exocrine function above the level needed for normal fat absorption.

Incorporating dugong habitats into the marine protected area design for the Great Barrier Reef Marine Park, Queensland, Australia.

Dugong habitats were considered in the design for the new zoning network for the Great Barrier Reef Marine Park as part of the Representative Areas Program. One of the specific design guidelines developed as part of the biophysical operational principles recommended that 50% of all high priority dugong habitats should be incorporated in the network of no-take areas. The high priority dugong habitat incorporated in no-take protection increased from 1396 to 3476 km2 (or 16.9-42.0% of all identified sites). Although this increase in protection fell short of the recommended 50%, overall the level of protection afforded by the Great Barrier Reef Marine Park Zoning Plan 2003 increased for all the locations identified.