Showing papers by "Cooperative Research Centre published in 2013"

Pitfalls of predicting complex traits from SNPs

Abstract: The success of genome-wide association studies (GWASs) has led to increasing interest in making predictions of complex trait phenotypes, including disease, from genotype data. Rigorous assessment of the value of predictors is crucial before implementation. Here we discuss some of the limitations and pitfalls of prediction analysis and show how naive implementations can lead to severe bias and misinterpretation of results.

StAMPP: an R package for calculation of genetic differentiation and structure of mixed-ploidy level populations.

Abstract: Statistical Analysis of Mixed-Ploidy Populations (StAMPP) is a freely available R package for calculation of population structure and differentiation based on single nucleotide polymorphism (SNP) genotype data from populations of any ploidy level, and/or mixed-ploidy levels. StAMPP provides an advance on previous similar software packages, due to an ability to calculate pairwise FST values along with confidence intervals, Nei's genetic distance and genomic relationship matrixes from data sets of mixed-ploidy level. The software code is designed to efficiently handle analysis of large genotypic data sets that are typically generated by high-throughput genotyping platforms. Population differentiation studies using StAMPP are broadly applicable to studies of molecular ecology and conservation genetics, as well as animal and plant breeding.

"Which camera trap type and how many do I need?" A review of camera features and study designs for a range of wildlife research applications

Abstract: Automatically triggered cameras taking photographs or videos of passing animals (camera traps) have emerged over the last decade as one of the most powerful tool for wildlife research. In parallel, a wealth of camera trap systems and models has become commercially available, a phenomenon mainly driven by the increased use of camera traps by sport hunters. This has raised the need for developing criteria to choose the suitable camera trap model in relation to a range of factors, primarily the study aim, but also target species, habitat, trapping site, climate and any other aspect that affects camera performance. There is also fragmented information on the fundamentals of sampling designs that deploy camera trapping, such as number of sampling sites, spatial arrangement and sampling duration. In this review, we describe the relevant technological features of camera traps and propose a set of the key ones to be evaluated when choosing camera models. These features are camera specifications such as trigger speed, sensor sensitivity, detection zone, flash type and flash intensity, power autonomy, and related specifications. We then outline sampling design and camera features for the implementation of major camera trapping applications, specifically: (1) faunal inventories, (2) occupancy studies, (3) density estimation through Capture-Mark-Recapture and (4) density estimation through the Random Encounter Model. We also review a range of currently available models and stress the need for standardized testing of camera models that should be frequently updated and widely distributed. Finally we summarize the "ultimate camera trap", as desired by wildlife biologists, and the current technological limitations of camera traps in relation to their potential for a number of emerging applications. Download the complete issue.

A review of global ocean temperature observations: Implications for ocean heat content estimates and climate change

Abstract: The evolution of ocean temperature measurement systems is presented with a focus on the development and accuracy of two critical devices in use today (expendable bathythermographs and conductivity-temperature-depth instruments used on Argo floats). A detailed discussion of the accuracy of these devices and a projection of the future of ocean temperature measurements are provided. The accuracy of ocean temperature measurements is discussed in detail in the context of ocean heat content, Earth's energy imbalance, and thermosteric sea level rise. Up-to-date estimates are provided for these three important quantities. The total energy imbalance at the top of atmosphere is best assessed by taking an inventory of changes in energy storage. The main storage is in the ocean, the latest values of which are presented. Furthermore, despite differences in measurement methods and analysis techniques, multiple studies show that there has been a multidecadal increase in the heat content of both the upper and deep ocean regions, which reflects the impact of anthropogenic warming. With respect to sea level rise, mutually reinforcing information from tide gauges and radar altimetry shows that presently, sea level is rising at approximately 3 mm yr-1 with contributions from both thermal expansion and mass accumulation from ice melt. The latest data for thermal expansion sea level rise are included here and analyzed. Key Points Oceanographic techniques and analysis have improved over many decadesThese improvements allow more accurate Earth-energy balance estimatesUnderstanding of ocean heat content and sea-level rise has also increased ©2013. American Geophysical Union. All Rights Reserved.

Ice-sheet mass balance and climate change

Abstract: Since the 2007 Intergovernmental Panel on Climate Change Fourth Assessment Report, new observations of ice-sheet mass balance and improved computer simulations of ice-sheet response to continuing climate change have been published. Whereas Greenland is losing ice mass at an increasing pace, current Antarctic ice loss is likely to be less than some recently published estimates. It remains unclear whether East Antarctica has been gaining or losing ice mass over the past 20 years, and uncertainties in ice-mass change for West Antarctica and the Antarctic Peninsula remain large. We discuss the past six years of progress and examine the key problems that remain.

Antarctic Bottom Water production by intense sea-ice formation in the Cape Darnley polynya

Abstract: Antarctic Bottom Water fills much of the global abyssal ocean, and is known to form in three main sites in the Southern Ocean. Data from instrumented elephant seals and moorings suggest an additional source of bottom-water formation in the Cape Darnley polynya that is driven by sea-ice production.

Outcomes of early- and late-identified children at 3 years of age: findings from a prospective population-based study.

Abstract: Objective:To address the question of whether, on a population level, early detection and amplification improve outcomes of children with hearing impairment.Design:All families of children who were born between 2002 and 2007, and who presented for hearing services below 3 years of age at Australian H

Widespread inundation of Pacific islands triggered by distant-source wind-waves

Abstract: It is essential to understand the causes of sea level extremes in order to anticipate and respond to coastal flooding (inundation), and to adapt to sea level rise. We investigate a series of inundation events which occurred across the western Pacific over several consecutive days during December 2008, causing severe impacts to five Pacific Island nations. These events were not associated with commonly identified causes: tropical cyclones or unusually large astronomical tides. Instead, the dissipation of wind-waves generated by distant extra-tropical cyclones (swell) was the main cause, although regional sea level variability, including recent accelerated rise, significantly contributed to the severity of impact experienced at many locations. The implication of recent sea level rise in the severity of these events suggests that episodic swell will increasingly cause major impacts of the nature described herein, although such impacts will continue to be modulated by El Nino/Southern Oscillation (ENSO) variability in the region. Significantly, tide gauges recorded little evidence of extreme sea levels during the event, implying that causes of extreme sea levels inferred from tide gauge analysis are unlikely to include this important cause of inundation. Therefore, any assessment of inundation risk predicated on tide gauge information (as well as larger scale sea level information such as satellite altimetry) may fail at many locations in the Pacific. To be accurate, such efforts must include information on the relationship between wave climate, wave forecasts and local extreme water levels. Further development of related early warning systems will become more pertinent as modern SLR continues to add to the magnitude of extremes.

Characterizing soil salinity in irrigated agriculture using a remote sensing approach

Abstract: Managing salinity in irrigated agriculture is crucial for minimising its negative environmental impacts and for ensuring the long-term sustainability of irrigated agriculture. It demands establishing rapid monitoring systems that help develop sustainable management plans. Remote sensing offers several advantages over the conventional proximal methods to map and predict areas at salinity risk. This paper presents an integrated approach to characterize soil salinity using remotely-sensed data in the District Faisalabad, Punjab, Pakistan. The IRS-1B LISS-II digital data was acquired and analysed in combination with field data and topographical maps. Remotely-sensed data based salinity indices or band combinations were developed to monitor the occurrence pattern of salt-affected soils. Using supervised maximum likelihood classification, the images were classified into eight land use classes with an overall accuracy of around 90%. The classified images showed that 22.2% of the total area was under salt-affected soils in 1992. The occurrence pattern of salt-affected soils varied with positive and negative trends during 1992–1995 to a minimum of 10.6%. The delineation analysis into levels of saline soils revealed three types based on USDA classification ( USDA, 1954 ). The slightly saline, moderately saline and strongly saline soils during 1992 were in the order of 15%, 3%, and 1% respectively. The interactive behaviour of salinity and sodicity and their combinations showed that saline-sodic soils occurred predominantly ranging from 6.9% to 17.3% of the salt-affected soils. The shallow watertable was found to be of hazardous quality in 28% of the study area. The relationship between salt-affected soils, waterlogged soils and groundwater quality revealed that 60–70% of the salt-affected soils occurred in shallow watertable areas during 1992–1995. The reuse of poor quality groundwater for irrigation and the failure of tile drainage system in the area are likely to further increase the risk of salinisation in the Indus Basin of Pakistan.

A uniform, quality controlled Surface Ocean CO2 Atlas (SOCAT)

Abstract: A well-documented, publicly available, global data set of surface ocean carbon dioxide (CO2) parameters has been called for by international groups for nearly two decades. The Surface Ocean CO2 Atlas (SOCAT) project was initiated by the international marine carbon science community in 2007 with the aim of providing a comprehensive, publicly available, regularly updated, global data set of marine surface CO2, which had been subject to quality control (QC). Many additional CO2 data, not yet made public via the Carbon Dioxide Information Analysis Center (CDIAC), were retrieved from data originators, public websites and other data centres. All data were put in a uniform format following a strict protocol. Quality control was carried out according to clearly defined criteria. Regional specialists performed the quality control, using state-of-the-art web-based tools, specially developed for accomplishing this global team effort. SOCAT version 1.5 was made public in September 2011 and holds 6.3 million quality controlled surface CO2 data points from the global oceans and coastal seas, spanning four decades (1968–2007). Three types of data products are available: individual cruise files, a merged complete data set and gridded products. With the rapid expansion of marine CO2 data collection and the importance of quantifying net global oceanic CO2 uptake and its changes, sustained data synthesis and data access are priorities.

Risk maps for Antarctic krill under projected Southern Ocean acidification

Abstract: Little is known about the sensitivity of Antarctic krill, a key part of the food chain, to ocean acidification. A circumpolar risk map of krill hatching success is presented for projected ocean acidification levels. Important krill recruitment habitats are likely to become high-risk this century, with the possibility of collapse of the krill population by 2300 without mitigation of CO2 emissions.

Carbohydrate diet and reproductive performance of a fruit fly parasitoid, Diachasmimorpha tryoni

Abstract: Augmentative releases of parasitoid wasps are often used successfully for biological control of fruit flies in programs worldwide. The development of cheaper and more effective augmentative releases of the parasitoid wasp Diachasmimorpha tryoni (Cameron) (Hymenoptera: Braconidae) may allow its use to be expanded to cover Queensland fruit fly, Bactrocera tryoni (Froggatt) (Diptera: Tephritidae), a serious pest of many vegetables and most fruit production in Australia. This demands a fuller understanding of the parasitoid's reproductive biology. In this study, mating status, fecundity, and size of female D. tryoni were determined under laboratory conditions. A range of pre-release diets, 10% concentrations of honey, white sugar, and golden syrup, were also assessed in the laboratory. Mature egg loads and progeny yields of mated and unmated parasitoid females were statistically similar, demonstrating that mating status was not a determinant of parasitoid performance. Female lifespan was not negatively impacted by the act of oviposition, though larger females carried more eggs than smaller individuals, indicating a need to produce large females in mass-rearing facilities to maintain this trait. White sugar gave the highest adult female lifespan, while honey and golden syrup shared similar survivorship curves, all significantly greater compared with water control females. Pre-release feeding of D. tryoni, particularly with white sugar, may enhance the impact of released parasitoids on B. tryoni. These findings are important because honey is currently the standard diet for mass-reared braconids, but white sugar is less than one-third the cost of other foods; however further work is required to assess postrelease performance of the parasitoid.

An integrated modelling framework for regulated river systems

Abstract: Management of regulated water systems has become increasingly complex due to rapid socio-economic growth and environmental changes in river basins over recent decades. This paper introduces the Source Integrated Modelling System (IMS), and describes the individual modelling components and how they are integrated within it. It also describes the methods employed for tracking and assessment of uncertainties, as well as presenting outcomes of two case study applications. Traditionally, the mathematical tools for water resources planning and management were generally designed for sectoral applications with, for example, groundwater being modelled separately from surface water. With the increasing complexity of water resources management in the 21st century those tools are becoming outmoded. Water management organisations are increasingly looking for new generation tools that allow integration across domains to assist their decision making processes for short-term operations and long-term planning; not only to meet current needs, but those of the future as well. In response to the need for an integrated tool in the water industry in Australia, the eWater Cooperative Research Centre (CRC) has developed a new generation software package called the Source IMS. The Source IMS is an integrated modelling environment containing algorithms and approaches that allow defensible predictions of water flow and constituents from catchment sources to river outlets at the sea. It is designed and developed to provide a transparent, robust and repeatable approach to underpin a wide range of water planning and management purposes. It can be used to develop water sharing plans and underpin daily river operations, as well as be used for assessments on water quantity and quality due to changes in: i) land-use and climate; ii) demands (irrigation, urban, ecological); iii) infrastructure, such as weirs and reservoirs; iv) management rules that might be associated with these; and v) the impacts of all of the above on various ecological indices. The Source IMS integrates the existing knowledge and modelling capabilities used by different state and federal water agencies across Australia and has additional functionality required for the river system models that will underpin the next round of water sharing plans in the country. It is built in a flexible modelling environment to allow stakeholders to incorporate new scientific knowledge and modelling methods as they evolve, and is designed as a generic tool suitable for use across different jurisdictions. Due to its structure, the platform can be extended/customised for use in other countries and basins, particularly where there are boundary issues.

Leveraging Big Data Analytics to Reduce Healthcare Costs

Abstract: The healthcare sector deals with large volumes of electronic data related to patient services. This article describes two novel applications that leverage big data to detect fraud, abuse, waste, and errors in health insurance claims, thus reducing recurrent losses and facilitating enhanced patient care. The results indicate that claim anomalies detected using these applications help private health insurance funds recover hidden cost overruns that aren't detectable using transaction processing systems. This article is part of a special issue on leveraging big data and business analytics.