A transcriptomic analysis of striped catfish (Pangasianodon hypophthalmus) in response to salinity adaptation: De novo assembly, gene annotation and marker discovery

The striped catfish (Pangasianodon hypophthalmus) culture industry in the Mekong Delta in Vietnam has developed rapidly over the past decade. The culture industry now however, faces some significant challenges, especially related to climate change impacts notably from predicted extensive saltwater intrusion into many low topographical coastal provinces across the Mekong Delta. This problem highlights a need for development of culture stocks that can tolerate more saline culture environments as a response to expansion of saline water-intruded land. While a traditional artificial selection program can potentially address this need, understanding the genomic basis of salinity tolerance can assist development of more productive culture lines. The current study applied a transcriptomic approach using Ion PGM technology to generate expressed sequence tag (EST) resources from the intestine and swim bladder from striped catfish reared at a salinity level of 9 ppt which showed best growth performance. Total sequence data generated was 467.8 Mbp, consisting of 4,116,424 reads with an average length of 112 bp. De novo assembly was employed that generated 51,188 contigs, and allowed identification of 16,116 putative genes based on the GenBank non-redundant database. GO annotation, KEGG pathway mapping, and functional annotation of the EST sequences recovered with a wide diversity of biological functions and processes. In addition, more than 11,600 simple sequence repeats were also detected. This is the first comprehensive analysis of a striped catfish transcriptome, and provides a valuable genomic resource for future selective breeding programs and functional or evolutionary studies of genes that influence salinity tolerance in this important culture species.

Estimating present day extreme total water level exceedance probabilities around the Australian coastline

The occurrence of extreme water level events along low-lying, highly populated and/or developed coastlines can lead to devastating impacts on coastal infrastructure. Therefore it is very important that the probabilities of extreme water levels are accurately evaluated to inform flood and coastal management and for future planning. The aim of this study was to provide estimates of present day extreme total water level exceedance probabilities around the whole coastline of Australia, arising from combinations of mean sea level, astronomical tide and storm surges generated by both extra-tropical and tropical storms, but exclusive of surface gravity waves. The study has been undertaken in two main stages. In the first stage, a high-resolution (~10 km along the coast) hydrodynamic depth averaged model has been configured for the whole coastline of Australia using the Danish Hydraulics Institute’s Mike21 modelling suite of tools. The model has been forced with astronomical tidal levels, derived from the TPX07.2 global tidal model, and meteorological fields, from the US National Center for Environmental Prediction’s global reanalysis, to generate a 61-year (1949 to 2009) hindcast of water levels. This model output has been validated against measurements from 30 tide gauge sites around Australia with long records. At each of the model grid points located around the coast, time series of annual maxima and the several highest water levels for each year were derived from the multi-decadal water level hindcast and have been fitted to extreme value distributions to estimate exceedance probabilities. Stage 1 provided a reliable estimate of the present day total water level exceedance probabilities around southern Australia, which is mainly impacted by extra-tropical storms. However, as the meteorological fields used to force the hydrodynamic model only weakly include the effects of tropical cyclones the resultant water levels exceedance probabilities were underestimated around western, northern and north-eastern Australia at higher return periods. Even if the resolution of the meteorological forcing was adequate to represent tropical cyclone-induced surges, multi-decadal periods yielded insufficient instances of tropical cyclones to enable the use of traditional extreme value extrapolation techniques. Therefore, in the second stage of the study, a statistical model of tropical cyclone tracks and central pressures was developed using histroic observations. This model was then used to generate synthetic events that represented 10,000 years of cyclone activity for the Australia region, with characteristics based on the observed tropical cyclones over the last ~40 years. Wind and pressure fields, derived from these synthetic events using analytical profile models, were used to drive the hydrodynamic model to predict the associated storm surge response. A random time period was chosen, during the tropical cyclone season, and astronomical tidal forcing for this period was included to account for non-linear interactions between the tidal and surge components. For each model grid point around the coast, annual maximum total levels for these synthetic events were calculated and these were used to estimate exceedance probabilities. The exceedance probabilities from stages 1 and 2 were then combined to provide a single estimate of present day extreme water level probabilities around the whole coastline of Australia.

Management of a high grade pan stage schedule to reduce the steam consumption

MOST PAN stages in Australian factories use only five or six batch pans for the high grade massecuite production and operate these in a fairly rigid repeating production schedule. It is common that some of the pans are of large dropping capacity e.g. 150 to 240 t. Because of the relatively small number and large sizes of the pans, steam consumption varies widely through the schedule, often by ±30% about the mean value. Large fluctuations in steam consumption have implications for the steam generation/condensate management of the factory and the evaporators when bleed vapour is used. One of the objectives of a project to develop a supervisory control system for a pan stage is to (a) reduce the average steam consumption and (b) reduce the variation in the steam consumption. The operation of each of the high grade pans within the schedule at Macknade Mill was analysed to determine the idle (or buffer) time, time allocations for essential but unproductive operations (e.g. pan turn round, charging, slow ramping up of steam rates on pan start etc.), and productive time i.e. the time during boil-on of liquor and molasses feed. Empirical models were developed for each high grade pan on the stage to define the interdependence of the production rate and the evaporation rate for the different phases of each pan’s cycle. The data were analysed in a spreadsheet model to try to reduce and smooth the total steam consumption. This paper reports on the methodology developed in the model and the results of the investigations for the pan stage at Macknade Mill. It was found that the operation of the schedule severely restricted the ability to reduce the average steam consumption and smooth the steam flows. While longer cycle times provide increased flexibility the steam consumption profile was changed only slightly. The ability to cut massecuite on the run among pans, or the use of a high grade seed vessel, would assist in reducing the average steam consumption and the magnitude of the variations in steam flow.

The cost-effectiveness of total laparoscopic hysterectomy compared to total abdominal hysterectomy for the treatment of early stage endometrial cancer

Objective To summarise how costs and health benefits will change with the adoption of total laparoscopic hysterectomy compared to total abdominal hysterectomy for the treatment of early stage endometrial cancer. Design Cost-effectiveness modelling using the information from a randomised controlled trial. Participants Two hypothetical modelled cohorts of 1000 individuals undergoing total laparoscopic hysterectomy and total abdominal hysterectomy. Outcome measures Surgery costs; hospital bed days used; total healthcare costs; quality-adjusted life years; and net monetary benefits. Results For 1000 individuals receiving total laparoscopic hysterectomy surgery, the costs were $509 575 higher, 3548 hospital fewer bed days were used and total health services costs were reduced by $3 746 221. There were 39.13 more quality-adjusted life years for a 5 year period following surgery. Conclusions The adoption of total laparoscopic hysterectomy is almost certainly a good decision for health services policy makers. There is 100% probability that it will be cost saving to health services, a 86.8% probability that it will increase health benefits and a 99.5% chance that it returns net monetary benefits greater than zero.

Using the Alliance Form for Operation and Maintenance of Privatized Infrastructures

A significant number of privatizations utilized to operate and maintain critical networked infrastructures have failed to meet contractual expectations and the expectations of the community. The author carried out empirical research ex-ploring four urban water systems. This research revealed that of the four forms of privatization the alliance form was particularly suited to the stewardship of an ur-ban water system. The question then is whether these findings from urban water can be generalised to O&M of infrastructure generally. The answer is increasingly important as governments seek financial sustainability through reapplying the contestability strategy and outsource and privatise further services and activities. This paper first examines the issues encountered with O & M privatisations. Second the findings as to the stewardship achieved by the four case study water systems are unpacked with particular focus upon the alliance form. Third the key variables which were found to have distinct causal links to the stewardship-like behaviour of the private participants in the Alliance case study are described. Fourth the variables which may be crucial to the successful application of the alliance form to the broader range of infrastructures are separated out. Fifth this paper then sets the path for research into these crucial features of the alliance form.

A test rig for the condition-based maintenance application on the traction chain of very high speed trains

The preventive maintenance of traction equipment for Very High Speed Trains (VHST) nowadays is becoming very expensive owing to the high complexity and quality of these components that require high reliability. An efficient maintenance approach like the Condition-Based Maintenance (CBM) should be implemented to reduce the costs. For this purpose, an experimental full-scale test rig for the CBM of VHST traction equipment has been designed to investigate in detail failures in the main mechanical components of system, i.e. motor, bearings and gearbox. The paper describes the main characteristics of this unique test rig, able to reproduce accurately the train operating conditions, including the relative movements of the motor, the gearbox and the wheel axle. Gearbox, bearing seats and motor are equipped by accelerometers, thermocouples, torque meter and other sensors in different positions. The testing results give important information about the most suitable sensor position and type to be installed for each component and show the effectiveness of the techniques used for the signal analysis in order to identify faults of the gearbox and motor bearings.

Modelling total duration of traffic incidents including incident detection and recovery time

Traffic incidents are key contributors to non-recurrent congestion, potentially generating significant delay. Factors that influence the duration of incidents are important to understand so that effective mitigation strategies can be implemented. To identify and quantify the effects of influential factors, a methodology for studying total incident duration based on historical data from an ‘integrated database’ is proposed. Incident duration models are developed using a selected freeway segment in the Southeast Queensland, Australia network. The models include incident detection and recovery time as components of incident duration. A hazard-based duration modelling approach is applied to model incident duration as a function of a variety of factors that influence traffic incident duration. Parametric accelerated failure time survival models are developed to capture heterogeneity as a function of explanatory variables, with both fixed and random parameters specifications. The analysis reveals that factors affecting incident duration include incident characteristics (severity, type, injury, medical requirements, etc.), infrastructure characteristics (roadway shoulder availability), time of day, and traffic characteristics. The results indicate that event type durations are uniquely different, thus requiring different responses to effectively clear them. Furthermore, the results highlight the presence of unobserved incident duration heterogeneity as captured by the random parameter models, suggesting that additional factors need to be considered in future modelling efforts.

A review of the potential role of greenhouse gas abatement in native vegetation management in Queensland's rangelands

Concern about the risk of harmful human-induced climate change has resulted in international efforts to reduce greenhouse gas emissions to the atmosphere. We review the international and national context for consideration of greenhouse abatement in native vegetation management and discuss potential options in Queensland. Queensland has large areas of productive or potentially productive land with native woody vegetation cover with approximately 76 million ha with woody cover remaining in 1991. High rates of tree clearing, predominantly to increase pasture productivity, continued throughout the 1990s with an average 345,000 ha/a estimated to have been cleared, including non-remnant (woody regrowth) as well as remnant vegetation. Estimates of greenhouse gas emissions associated with land clearing currently have a high uncertainty but clearing was reported to contribute a significant proportion of Australia's total greenhouse gas emissions from 1990 (21%) to 1999 (13%). In Queensland, greenhouse emissions from land clearing were estimated to have been 54.5 Mt CO(2)-e in 1999. Management of native vegetation for timber harvesting and the proliferation of woody vegetation (vegetation thickening) in the grazed woodlands also represent large carbon fluxes. Forestry (plantations and native forests) in Queensland was reported to be a 4.4 Mt CO(2)-e sink in 1999 but there are a lack of comprehensive data on timber harvesting in private hardwood forests. Vegetation thickening is reported for large areas of the c. 60 million ha grazed woodlands in Queensland. The magnitude of the carbon sink in 27 million ha grazed eucalypt woodlands has been estimated to be 66 Mt CO(2)-e/a but this sink is not currently included in Australia's inventory of anthropogenic greenhouse emissions. Improved understanding of the function and dynamics of natural and managed ecosystems is required to support management of native vegetation to preserve and enhance carbon stocks for greenhouse benefits while meeting objectives of sustainable and productive management and biodiversity protection.

Productive inefficiency analysis and toxic chemical substances in US and Japanese manufacturing sectors

Corporate social responsibility is imperative for manufacturing companies to achieve sustainable development. Under a strong environmental information disclosure system, polluting companies are disadvantaged in terms of market competitiveness, because they lack an environmentally friendly image. The objective of this study is to analyze productive inefficiency change in relation to toxic chemical substance emissions for the United States and Japan and their corresponding policies. We apply the weighted Russell directional distance model to measure companies productive inefficiency, which represents their production technology. The data encompass 330 US manufacturing firms observed from 1999 to 2007, and 466 Japanese manufacturing firms observed from 2001 to 2008. The article focuses on nine high-pollution industries (rubber and plastics; chemicals and allied products; paper and pulp; steel and non-ferrous metal; fabricated metal; industrial machinery; electrical products; transportation equipment; precision instruments) categorized into two industry groups: basic materials industries and processing and assembly industries. The results show that productive inefficiency decreased in all industrial sectors in the United States and Japan from 2001 to 2007. In particular, that of the electrical products industry decreased rapidly after 2002 for both countries, possibly because of the enforcement of strict environmental regulations for electrical products exported to European markets.

Total factor productivity growth and convergence in the petroleum industry : empirical analysis testing for convexity

While economic theory acknowledges that some features of technology (e.g., indivisibilities, economies of scale and specialization) can fundamentally violate the traditional convexity assumption, almost all empirical studies accept the convexity property on faith. In this contribution, we apply two alternative flexible production technologies to measure total factor productivity growth and test the significance of the convexity axiom using a nonparametric test of closeness between unknown distributions. Based on unique field level data on the petroleum industry, the empirical results reveal significant differences, indicating that this production technology is most likely non-convex. Furthermore, we also show the impact of convexity on answers to traditional convergence questions in the productivity growth literature.

A random key genetic algorithm for live migration of multiple virtual machines in data centers

Live migration of multiple Virtual Machines (VMs) has become an integral management activity in data centers for power saving, load balancing and system maintenance. While state-of-the-art live migration techniques focus on the improvement of migration performance of an independent single VM, only a little has been investigated to the case of live migration of multiple interacting VMs. Live migration is mostly influenced by the network bandwidth and arbitrarily migrating a VM which has data inter-dependencies with other VMs may increase the bandwidth consumption and adversely affect the performances of subsequent migrations. In this paper, we propose a Random Key Genetic Algorithm (RKGA) that efficiently schedules the migration of a given set of VMs accounting both inter-VM dependency and data center communication network. The experimental results show that the RKGA can schedule the migration of multiple VMs with significantly shorter total migration time and total downtime compared to a heuristic algorithm.

Prevalence of asymptomatic malaria and bed net ownership and use in Bhutan, 2013 : a country earmarked for malaria elimination

Background With dwindling malaria cases in Bhutan in recent years, the government of Bhutan has made plans for malaria elimination by 2016. This study aimed to determine coverage, use and ownership of LLINs, as well as the prevalence of asymptomatic malaria at a single time-point, in four sub-districts of Bhutan. Methods A cross-sectional study was carried out in August 2013. Structured questionnaires were administered to a single respondent in each household (HH) in four sub-districts. Four members from 25 HH, randomly selected from each sub-district, were tested using rapid diagnostic tests (RDT) for asymptomatic Plasmodium falciparum and Plasmodium vivax infection. Multivariable logistic regression models were used to identify factors associated with LLIN use and maintenance. Results All blood samples from 380 participants tested negative for Plasmodium infections. A total of 1,223 HH (92.5% of total HH) were surveyed for LLIN coverage and use. Coverage of LLINs was 99.0% (1,203/1,223 HH). Factors associated with decreased odds of sleeping under a LLIN included: washing LLINs nine months compared to washing LLINs every six months; HH in the least poor compared to the most poor socio-economic quintile; a HH income of Nu 5,001-10,000 (US$1 = Nu 59.55), and Nu >10,000, compared to HH with income of

Making optimal and justifiable asset maintenance decisions

Maintenance decisions for large-scale asset systems are often beyond an asset manager's capacity to handle. The presence of a number of possibly conflicting decision criteria, the large number of possible maintenance policies, and the reality of budget constraints often produce complex problems, where the underlying trade-offs are not apparent to the asset manager. This paper presents the decision support tool "JOB" (Justification and Optimisation of Budgets), which has been designed to help asset managers of large systems assess, select, interpret and optimise the effects of their maintenance policies in the presence of limited budgets. This decision support capability is realized through an efficient, scalable backtracking- based algorithm for the optimisation of maintenance policies, while enabling the user to view a number of solutions near this optimum and explore tradeoffs with other decision criteria. To assist the asset manager in selecting between various policies, JOB also provides the capability of Multiple Criteria Decision Making. In this paper, the JOB tool is presented and its applicability for the maintenance of a complex power plant system.