Castanet: a pipeline for rapid analysis of targeted multi-pathogen genomic data

Motivation: Target enrichment strategies generate genomic data from multiple pathogens in a single process, greatly improving sensitivity over metagenomic sequencing and enabling cost-effective, high-throughput surveillance and clinical applications. However, uptake by research and clinical laboratories is constrained by an absence of computational tools that are specifically designed for the analysis of multi-pathogen enrichment sequence data. Here we present an analysis pipeline, Castanet, for use with multi-pathogen enrichment sequencing data. Castanet is designed to work with short-read data produced by existing targeted enrichment strategies, but can be readily deployed on any BAM file generated by another methodology. Also included are an optional graphical interface and installer script. Results: In addition to genome reconstruction, Castanet reports method-specific metrics that enable quantification of capture efficiency, estimation of pathogen load, differentiation of low-level positives from contamination, and assessment of sequencing quality. Castanet can be used as a traditional end-to-end pipeline for consensus generation, but its strength lies in the ability to process a flexible, pre-defined set of pathogens of interest directly from multi-pathogen enrichment experiments. In our tests, Castanet consensus sequences were accurate reconstructions of reference sequences, including in instances where multiple strains of the same pathogen were present. Castanet performs effectively on standard computers and can process the entire output of a 96-sample enrichment sequencing run (50M reads) using a single batch process command, in

The CUAVA-2 CubeSat: A Second Attempt to Fly the Remote Sensing, Space Weather Study and Earth Observation Instruments

This paper presents the 6U CubeSat mission conducted by the ARC Training Centre for CubeSats, UAVs, and their Applications (CUAVA) at the University of Sydney. CUAVA-2, the second CubeSat project following the CUAVA-1 mission, builds upon lessons learned from its predecessor. CUAVA-1, the first satellite launched by CUAVA, carried first-generation payloads for earth observation goals and technology demonstrations but experienced communication difficulties. A fault root analysis was performed on CUAVA-1 to inform the design of CUAVA-2. The CUAVA-2 satellite incorporates a hyperspectral imager for applications in agriculture, forestry, coastal and marine environments, urban areas, water hazard assessment, and mineral exploration. It also includes a GPS reflectometry payload for remote sea state determination, as well as secondary payloads for technology demonstration and space weather study. This paper discusses the fault analysis findings, lessons learned, and design inputs from CUAVA-1, showcasing their integration into the CUAVA-2 satellite, which is scheduled for launch in February 2024

Crop Updates 2005 - Farming Systems

This session covers forty four papers from different authors: PLENARY 1. 2005 Outlook, David Stephens and Nicola Telcik, Department of Agriculture FERTILITY AND NUTRITION 2. The effect of higher nitrogen fertiliser prices on rotation and fertiliser strategies in cropping systems, Ross Kingwell, Department of Agriculture and University of Western Australia 3. Stubble management: The short and long term implications for crop nutrition and soil fertility, Wayne Pluske, Nutrient Management Systems and Bill Bowden, Department of Agriculture 4. Stubble management: The pros and cons of different methods, Bill Bowden, Department of Agriculture, Western Australia and Mike Collins, WANTFA 5. Effect of stubble burning and seasonality on microbial processes and nutrient recycling, Frances Hoyle, The University of Western Australia 6. Soil biology and crop production in Western Australian farming systems, D.V. Murphy, N. Milton, M. Osman, F.C. Hoyle, L.K Abbott, W.R. Cookson and S. Darmawanto, The University of Western Australia 7. Urea is as effective as CAN when no rain for 10 days, Bill Crabtree, Crabtree Agricultural Consulting 8. Fertiliser (N,P,S,K) and lime requirements for wheat production in the Merredin district, Geoff Anderson, Department of Agriculture and Darren Kidson, Summit Fertilizers 9. Trace element applications: Up-front verses foliar? Bill Bowden and Ross Brennan, Department of Agriculture 10. Fertcare®, Environmental Product Stewardship and Advisor Standards for thee Fertiliser Industry, Nick Drew, Fertilizer Industry Federation of Australia (FIFA) SOIL AND LAND MANAGEMENT 11. Species response to row spacing, density and nutrition, Bill Bowden, Craig Scanlan, Lisa Sherriff, Bob French and Reg Lunt, Department of Agriculture 12. Investigation into the influence of row orientation in lupin crops, Jeff Russell, Department of Agriculture and Angie Roe, Farm Focus Consultants 13. Deriving variable rate management zones for crops, Ian Maling, Silverfox Solutions and Matthew Adams, DLI 14. In a world of Precision Agriculture, weigh trailers are not passé, Jeff Russell, Department of Agriculture 15. Cover crop management to combat ryegrass resistance and improve yields, Jeff Russell, Department of Agriculture and Angie Roe, Farm Focus Consultants 16. ARGT home page, the place to find information on annual ryegrass toxicity on the web, Dr George Yan, BART Pty Ltd 17. Shallow leading tine (SLT) ripper significantly reduces draft force, improves soil tilth and allows even distribution of subsoil ameliorants, Mohammad Hamza, Glen Riethmuller and Wal Anderson, Department of Agriculture PASTURE ANS SUMMER CROP SYSTEMS 18. New annual pasture legumes for Mediteranean farming systems, Angelo Loi, Phil Nichols, Clinton Revell and David Ferris, Department of Agriculture 19. How sustainable are phase rotations with Lucerne? Phil Ward, CSIRO Plant Industry 20. Management practicalities of summer cropping, Andrea Hills and Sally-Anne Penny, Department of Agriculture 21. Rainfall zone determines the effect of summer crops on winter yields, Andrea Hills, Sally-Anne Penny and David Hall, Department of Agriculture 22. Summer crops and water use, Andrea Hills, Sally-Anne Penny and David Hall, Department of Agriculture, and Michael Robertson and Don Gaydon, CSIRO Brisbane 23. Risk analysis of sorgum cropping, Andrea Hills and Sally-Anne Penny, Department of Agriculture, and Dr Michael Robertson and Don Gaydon, CSIRO Brisbane FARMER DECISION SUPPORT AND ADOPTION 24. Variety release and End Point Royalties – a new system? Tress Walmsley, Department of Agriculture 25. Farming system analaysis using the STEP Tool, Caroline Peek and Megan Abrahams, Department of Agriculture 26. The Leakage Calculator: A simple tool for groundwater recharge assessment, Paul Raper, Department of Agriculture 27. The cost of Salinity Calculator – your tool to assessing the profitability of salinity management options, Richard O’Donnell and Trevor Lacey, Department of Agriculture 28. Climate decision support tools, Meredith Fairbanks and David Tennant, Department of Agriculture 29. Horses for courses – using the best tools to manage climate risk, Cameron Weeks, Mingenew-Irwin Group/Planfarm and Richard Quinlan, Planfarm Agronomy 30. Use of seasonal outlook for making N decisions in Merredin, Meredith Fairbanks and Alexandra Edward, Department of Agriculture 31. Forecasts and profits, Benefits or bulldust? Chris Carter and Doug Hamilton, Department of Agriculture 32. A tool to estimate fixed and variable header and tractor depreciation costs, Peter Tozer, Department of Agriculture 33. Partners in grain: ‘Putting new faces in new places’, Renaye Horne, Department of Agriculture 34. Results from the Grower group Alliance, Tracey Gianatti, Grower Group Alliance 35. Local Farmer Group Network – farming systems research opportunities through local groups, Paul Carmody, Local Farmer Group Network GREENHOUSE GAS AND CLIMATE CHANGE 36. Changing rainfall patterns in the grainbelt, Ian Foster, Department of Agriculture 37. Vulnerability of broadscale agriculture to the impacts of climate change, Michele John, CSIRO (formerly Department of Agriculture) and Ross George, Department of Agriculture 38. Impacts of climate change on wheat yield at Merredin, Imma Farré and Ian Foster, Department of Agriculture 39. Climate change, land use suitability and water security, Ian Kininmonth, Dennis van Gool and Neil Coles, Department of Agriculture 40. Nitrous oxide emissions from cropping systems, Bill Porter, Department of Agriculture, Louise Barton, University of Western Australia 41. The potential of greenhouse sinks to underwrite improved land management in Western Australia, Richard Harper and Peter Ritson, CRC for Greenhouse Accounting and Forest Products Commission, Tony Beck, Tony Beck Consulting Services, Chris Mitchell and Michael Hill, CRC for Greenhouse Accounting 42. Removing uncertainty from greenhouse emissions, Fiona Barker-Reid, Will Gates, Ken Wilson and Rob Baigent, Department of Primary Industries - Victoria and CRC for Greenhouse Accounting (CRCGA), and Ian Galbally, Mick Meyer and Ian Weeks, CSIRO Atmospheric Research and CRCGA 43. Greenhouse in Agriculture Program (GIA), Traci Griffin, CRC for Greenhouse Accounting 44. Grains Greenhouse Accounting framework, D. Rodriguez, M. Probust, M. Meyers, D. Chen, A. Bennett, W. Strong, R. Nussey, I. Galbally and M. Howden CONTACT DETAILS FOR PRINCIPAL AUTHOR

An Experimental Study of Gridded and Virtual Cathode Inertial Electrostatic Confinement Fusion Systems

Inertial electrostatic confinement (IEC) fusion is a technique by which electric fields confine and heat ions. The concept uses concentric electrodes to accelerate and focus ions thereby creating the conditions necessary for nuclear fusion. IEC cathodes may be mechanical, in the form of metallic grids or virtual, formed through trapping a net negative space charge. An experimental study was carried out into the operation of IEC devices of both types. The phenomenon of surface fusion in a gridded IEC was examined and the total fusion rate found to be dominated by atomic interactions on the cathode surface. The material and temperature of the IEC cathode were found to have a profound influence on the observed fusion rate, with graphite seen to perform exceptionally well when compared to transition metal cathodes. The research indicates that great improvements in the fusion efficiency of gridded IEC machines are possible through careful choice of grid material and the implementation of active cathode cooling. Also described is the design and construction, as well as initial operation of MCVC-0, a successor to previous Polywell style devices constructed at The University of Sydney. The device makes use of a biconic cusp magnetic field to confine electrons in space, thereby generating a virtual cathode. Biased and floating Langmuir probe measurements were used to examine potential well formation in the new machine, as well as diagnose the fundamental plasma parameters of temperature and density. Preliminary experimental work indicates poor performance of MCVC-0 with respect to virtual cathode formation and these shortcomings are addressed in terms of non-isotropic electrical conductivity in magnetised plasmas. The plasma conductivity model is extended to previously published virtual cathode machines and is shown to adequately describe the observed device behaviour, providing a possible alternate physical explanation for virtual cathode formation

Langmuir probe measurements of the secondary electron population across the cathodic pre-sheath of a DC argon discharge

International audienceCylindrical Langmuir probe measurements in a low-pressure DC argon discharge are used to obtain the spatial evolution of ion, cold and hot electron parameters across the cathodic pre-sheath. The cathodic pre-sheath is formed by a stainless steel plate allowed to float negatively with respect to the plasma. The velocity distribution function of the hot electron population in the pre-sheath is shown to be matched by a drifting Maxwellian that thermalizes across it. The source of the hot electron population is hypothesized to arise from secondary electron emission from the plate. A Bayesian estimation routine is proposed to compare and validate different Langmuir probe models as well as calculating the relative uncertainty between models. The results are analyzed using existing pre-sheath theory for which experimental evidence of the spatial influence of energetic electrons is lacking. The data are shown to follow Riemann's pre-sheath model that the ion-neutral mean free path λ i is proportional to the pre-sheath characteristic length l, and that the potential drop ϕ ( x ) with distance x from the sheath/pre-sheath boundary x0 follows ϕ ( x ) ∝ ( x 0 − x ) / l