Characterisation of full-length cDNA sequences provides insights into the Eimeria tenellatranscriptome

<p>Abstract</p> <p>Background</p> <p><it>Eimeria tenella </it>is an apicomplexan parasite that causes coccidiosis in the domestic fowl. Infection with this parasite is diagnosed frequently in intensively reared poultry and its control is usually accorded a high priority, especially in chickens raised for meat. Prophylactic chemotherapy has been the primary method used for the control of coccidiosis. However, drug efficacy can be compromised by drug-resistant parasites and the lack of new drugs highlights demands for alternative control strategies including vaccination. In the long term, sustainable control of coccidiosis will most likely be achieved through integrated drug and vaccination programmes. Characterisation of the <it>E. tenella </it>transcriptome may provide a better understanding of the biology of the parasite and aid in the development of a more effective control for coccidiosis.</p> <p>Results</p> <p>More than 15,000 partial sequences were generated from the 5' and 3' ends of clones randomly selected from an <it>E. tenella </it>second generation merozoite full-length cDNA library. Clustering of these sequences produced 1,529 unique transcripts (UTs). Based on the transcript assembly and subsequently primer walking, 433 full-length cDNA sequences were successfully generated. These sequences varied in length, ranging from 441 bp to 3,083 bp, with an average size of 1,647 bp. Simple sequence repeat (SSR) analysis identified CAG as the most abundant trinucleotide motif, while codon usage analysis revealed that the ten most infrequently used codons in <it>E. tenella </it>are UAU, UGU, GUA, CAU, AUA, CGA, UUA, CUA, CGU and AGU. Subsequent analysis of the <it>E. tenella </it>complete coding sequences identified 25 putative secretory and 60 putative surface proteins, all of which are now rational candidates for development as recombinant vaccines or drug targets in the effort to control avian coccidiosis.</p> <p>Conclusions</p> <p>This paper describes the generation and characterisation of full-length cDNA sequences from <it>E. tenella </it>second generation merozoites and provides new insights into the <it>E. tenella </it>transcriptome. The data generated will be useful for the development and validation of diagnostic and control strategies for coccidiosis and will be of value in annotation of the <it>E. tenella </it>genome sequence.</p

Core concepts for zero-sodium-void-worth core'' in metal fuelled fast reactor

Core design options to reduce the sodium void worth in metal fueled LMRs are investigated. Two core designs which achieve a zero sodium void worth are analyzed in detail. The first design is a pancaked'' and annular core with enhanced transuranic burning capabilities; the high leakage in this design yields a low breeding ratio and small void worth. The second design is an axially multilayered annular core which is fissile self-sufficient; in this design, the upper and lower core regions are neutronically decoupled for reduced void worth while fissile self-sufficiency is achieved using internal axial blankets plus external radial and axial blanket zones. The neutronic performance characteristics of these low void worth designs are assessed here; their passive safety properties are discussed in a companion paper. 16 refs., 2 figs., 3 tabs

A Full-Depth Amalgamated Parallel 3D Geometric Multigrid Solver for GPU Clusters

Numerical computations of incompressible flow equations with pressure-based algorithms necessitate the solution of an elliptic Poisson equation, for which multigrid methods are known to be very efficient. In our previous work we presented a dual-level (MPI-CUDA) parallel implementation of the Navier-Stokes equations to simulate buoyancy-driven incompressible fluid flows on GPU clusters with simple iterative methods while focusing on the scalability of the overall solver. In the present study we describe the implementation and performance of a multigrid method to solve the pressure Poisson equation within our MPI-CUDA parallel incompressible flow solver. Various design decisions and algorithmic choices for multigrid methods are explored in light of NVIDIA’s recent Fermi architecture. We discuss how unique aspects of an MPI-CUDA implementation for GPU clusters is related to the software choices made to implement the multigrid method. We propose a new coarse grid solution method of embedded multigrid with amalgamation and show that the parallel implementation retains the numerical efficiency of the multigrid method. Performance measurements on the NCSA Lincoln and TACC Longhorn clusters are presented for up to 64 GPUs

Nothing New in the (North) East? Interpreting the Rhetoric and Reality of Japanese Corporate Governance

Japan finally seems to be pulling itself out of its lost decade (and a half) of economic stagnation. Some grudgingly or triumphantly attribute this to micro-economic reforms, freeing up arthritic markets, although there is also evidence that macro-economic policy failures have been a major cause of poor performance since the 1990s. Many point to overlapping transformations in corporate governance, broadly defined to cover relationships among managers and employees as well as between firms and outside shareholders, creditors, and other stakeholders. These relationships are in flux, with moves arguably favouring shareholders and more market-driven control mechanisms. It has certainly been a found decade for law reform in Japan, particularly in corporate law, with a plethora of legislative amendments commencing around 1993 and culminating in the enactment of a consolidated Company Law in 2005. This modernisation project, particularly since 2001, is reportedly aimed at (i) securing better corporate governance, (ii) bringing the law into line with a highly-developed information society, (iii) liberalising fundraising measures, (iv) bringing corporate law into line with the internationalization of corporate activity, and (v) modernizing terms and consolidating corporate law. Because the suite of revisions has moved away from strict mandatory rules set out originally in Japan\u27s Commercial Code of 1899, modeled primarily on German law, another growing perception is that Japanese corporate law and practice is or will soon be converging significantly on US models. However, assessments remain divided as to whether these moves in corporate governance and capitalism more generally in Japan amount to a new paradigm or regime shift . Focusing primarily on quite influential commentary in English, Part I of this paper outlines two pairs of views. It concludes that the most plausible assessment is of significant but gradual transformation towards a more market-driven approach, evident also in other advanced political economies. Drawing more generally from these often virulently divided views, Part II sets out five ways forward through the proliferating literature and source material on corporate governance in Japan. Particular care must be taken in: (i) selecting the temporal timeframe, (ii) selecting countries to compare, (iii) balancing black-letter law and broader socio-economic context, (iv) reflecting on and disclosing normative preferences, and (v) giving weight to processes as well as outcomes, when assessing change in Japan - and any other country\u27s governance system. Part III ends with a call for further research particularly on law- and policy-producing processes, rather than mainly outcomes. It also outlines the usefulness of this analytical framework for analysing the broader field of Corporate Social Responsibility, now emerging as the next major area of debate and transformation in Japan - as elsewhere

Sushi in the United States, 1945-1970

Sushi first achieved widespread popularity in the United States in the mid-1960s. Many accounts of sushi’s US establishment foreground the role of a small number of key actors, yet underplay the role of a complex web of large-scale factors that provided the context in which sushi was able to flourish. This article critically reviews existing literature, arguing that sushi’s US popularity arose from contingent, long-term, and gradual processes. It examines US newspaper accounts of sushi during 1945–1970, which suggest the discursive context for US acceptance of sushi was considerably more propitious than generally acknowledged. Using California as a case study, the analysis also explains conducive social and material factors, and directs attention to the interplay of supply- and demand-side forces in the favorable positioning of this “new” food. The article argues that the US establishment of sushi can be understood as part of broader public acceptance of Japanese cuisine

Regionally aggregated, stitched and de‐drifted CMIP‐climate data, processed with netCDF‐SCM v2.0.0

The world's most complex climate models are currently running a range of experiments as part of the Sixth Coupled Model Intercomparison Project (CMIP6). Added to the output from the Fifth Coupled Model Intercomparison Project (CMIP5), the total data volume will be in the order of 20PB. Here, we present a dataset of annual, monthly, global, hemispheric and land/ocean means derived from a selection of experiments of key interest to climate data analysts and reduced complexity climate modellers. The derived dataset is a key part of validating, calibrating and developing reduced complexity climate models against the behaviour of more physically complete models. In addition to its use for reduced complexity climate modellers, we aim to make our data accessible to other research communities. We facilitate this in a number of ways. Firstly, given the focus on annual, monthly, global, hemispheric and land/ocean mean quantities, our dataset is orders of magnitude smaller than the source data and hence does not require specialized ‘big data’ expertise. Secondly, again because of its smaller size, we are able to offer our dataset in a text-based format, greatly reducing the computational expertise required to work with CMIP output. Thirdly, we enable data provenance and integrity control by tracking all source metadata and providing tools which check whether a dataset has been retracted, that is identified as erroneous. The resulting dataset is updated as new CMIP6 results become available and we provide a stable access point to allow automated downloads. Along with our accompanying website (cmip6.science.unimelb.edu.au), we believe this dataset provides a unique community resource, as well as allowing non-specialists to access CMIP data in a new, user-friendly way