A non-hybrid method for the PDF equations of turbulent flows on unstructured grids

In probability density function (PDF) methods of turbulent flows, the joint PDF of several flow variables is computed by numerically integrating a system of stochastic differential equations for Lagrangian particles. A set of parallel algorithms is proposed to provide an efficient solution of the PDF transport equation, modeling the joint PDF of turbulent velocity, frequency and concentration of a passive scalar in geometrically complex configurations. An unstructured Eulerian grid is employed to extract Eulerian statistics, to solve for quantities represented at fixed locations of the domain (e.g. the mean pressure) and to track particles. All three aspects regarding the grid make use of the finite element method (FEM) employing the simplest linear FEM shape functions. To model the small-scale mixing of the transported scalar, the interaction by exchange with the conditional mean model is adopted. An adaptive algorithm that computes the velocity-conditioned scalar mean is proposed that homogenizes the statistical error over the sample space with no assumption on the shape of the underlying velocity PDF. Compared to other hybrid particle-in-cell approaches for the PDF equations, the current methodology is consistent without the need for consistency conditions. The algorithm is tested by computing the dispersion of passive scalars released from concentrated sources in two different turbulent flows: the fully developed turbulent channel flow and a street canyon (or cavity) flow. Algorithmic details on estimating conditional and unconditional statistics, particle tracking and particle-number control are presented in detail. Relevant aspects of performance and parallelism on cache-based shared memory machines are discussed.Comment: Accepted in Journal of Computational Physics, Feb. 20, 200

Joint PDF modelling of turbulent flow and dispersion in an urban street canyon

The joint probability density function (PDF) of turbulent velocity and concentration of a passive scalar in an urban street canyon is computed using a newly developed particle-in-cell Monte Carlo method. Compared to moment closures, the PDF methodology provides the full one-point one-time PDF of the underlying fields containing all higher moments and correlations. The small-scale mixing of the scalar released from a concentrated source at the street level is modelled by the interaction by exchange with the conditional mean (IECM) model, with a micro-mixing time scale designed for geometrically complex settings. The boundary layer along no-slip walls (building sides and tops) is fully resolved using an elliptic relaxation technique, which captures the high anisotropy and inhomogeneity of the Reynolds stress tensor in these regions. A less computationally intensive technique based on wall functions to represent boundary layers and its effect on the solution are also explored. The calculated statistics are compared to experimental data and large-eddy simulation. The present work can be considered as the first example of computation of the full joint PDF of velocity and a transported passive scalar in an urban setting. The methodology proves successful in providing high level statistical information on the turbulence and pollutant concentration fields in complex urban scenarios.Comment: Accepted in Boundary-Layer Meteorology, Feb. 19, 200

Crop Updates 2000 - Cereals part 2

This session covers twenty papers from different authors: DISEASE 1. Forecasting aphid and virus risk in cereals, Debbie Thackray, Jenny Hawkes and Roger Jones, Agriculture Western Australia and Centre for Legumes in Mediterranean Agriculture 2. Cereal Diagnostics, Dominie Wright, Agriculture Western Australia 3. The economic returns from spraying for leaf rust in the central wheatbelt in 1999, Peter Carlton, Trials Coordinator, Elders Limited 4. Impact and Management of Yellow Spot and Leaf Rust in the Northern Agricultural Region, Jat Bhathal and Robert Loughman, Agriculture Western Australia 5. Leaf disease management in wheat and barley in the southern agricultural region, K. Jayasena, R. Loughman and J. Majewski, Agriculture Western Australia 6. Root nematode update, R. Loughman1, S. Kelly1, G. Holloway2, N. Venn1 and D. Diepeveen1 1 Agriculture Western Australia, 2Agriculture Victoria WHEAT AGRONOMY 7. Small Grain Screenings in wheat - the agronomic issues, Brenda Shackley, Agriculture Western Australia, 8. Response of New Wheat Varieties to Seed Rate and applied Nitrogen in the North, Darshan Sharma and Wal Anderson, Agriculture Western Australia 9. Seen vigour in wheat, Darshan Sharma and Wal Anderson, Agriculture Western Australia 10. Influence of the Time of Sowing on New Wheat Varieties in the North, Darshan Sharma and Wal Anderson, Agriculture Western Australia 11, Wheat performance in a high disease season on the South Coast. 1. Disease and grain quality on the Esperance sandplain, Mohammad Amjad, Vanessa Dooley and Wal Anderson, Agriculture Western Australia 12. Wheat performance in a high disease season on the South Coast. 2. Leaf area, disease and yield at Gibson and Salmon Gums, Mohammad Amjad, Vanessa Dooley and Wal Anderson, Agriculture Western Australia 13. Agronomic Evaluation of Wheat in the Central Wheatbelt of Western Australia, Peter Burgess and Ashley Bacon, Agritech Crop Research 14. Mechanisms influencing grain susceptibility to black point in wheat, Frances Hoyle, University of Western Australia and Agriculture Western Australia 15. Improving paddock productivity using renovation cropping techniques on heavier soils, Frances Hoyle, Agriculture Western Australia 16. Improving paddock productivity using renovation cropping techniques on sandplain soils, Frances Hoyle and Keith Devenish, Agriculture Western Australia 17. Increasing profit - Is it possible using high input package approach for cereal production? M. Appelbee, IAMA Agri Services 18. Improving wheat yield, soil physical and chemical fertility by a package of deep ripping, gypsum and complete nutrients, M.A. Hamza and W.K. Anderson, Agriculture Western Australia 19. Organic Wheat - Production System Guidelines, Steven McCoy, Centre for New Industries Development 20. Durum wheat obtains a premium over bread wheat, Steven Penny, Agriculture Western Australi

Identifying and addressing psychosocial determinants of adherence to physical distancing guidance during the COVID-19 pandemic – project protocol

Optimising public health physical distancing measures has been a critical part of the global response to the spread of COVID-19. Evidence collected during the current pandemic shows that the transmission rate of the virus is significantly reduced following implementation of intensive physical distancing measures. Adherence to these recommendations has been poorer than adherence to other key transmission reduction behaviours such as handwashing. There are a complex range of reasons that are likely to predict why people do not or only partially adhere to physical distancing recommendations. In the current project we aim to address the following research questions: (1) What are the psychosocial determinants of physical distancing for the general public and for key socio-demographic sub-groups (e.g., young adults, older adults, etc.)?; (2) Do current Government of Ireland COVID-19 physical distancing communications address the determinants of physical distancing?; and (3) How can communications be optimised and tailored to sub-groups to ensure maximum adherence to guidelines? These will be addressed by conducting three work packages (WPs). In WP1, we will work closely with the iCARE international study, which includes a large online survey of public responses to measures established to reduce and slow the spread of COVID-19, including physical distancing. We will analyse Irish data, comparing it to data from other countries, to identify the key psychosocial determinants of physical distancing behaviour. This will be followed by a qualitative study to explore in depth the barriers and facilitators of physical distancing behaviour among the Irish public (WP2). In WP3, we will conduct a content analysis and evidence mapping of current government messaging around physical distancing, to ensure the findings from this research feed into the development of ongoing communication and future messaging about physical distancing

Crop Updates 2001 - Cereals

This session covers forty two papers from different authors: PLENARY 1. Planning your cropping program in season 2001, Dr Ross Kingwell, Agriculture Western Australia and University of Western Australia WORKSHOP 2. Can we produce high yields without high inputs? Wal Anderson, Centre for Cropping Systems, Agriculture Western Australia VARIETIES 3. Local and interstate wheat variety performance and $ return to WA growers, Eddy Pol, Peter Burgess and Ashley Bacon, Agritech Crop Research CROP ESTABLISHMENT 4 Soil management of waterlogged soils, D.M. Bakker, G.J. Hamilton, D. Houlbrooke and C. Spann, Agriculture Western Australia 5. Effect of soil amelioration on wheat yield in a very dry season, M.A Hamza and W.K. Anderson, Agriculture Western Australia 6. Fuzzy tramlines for more yield and less weed, Paul Blackwell1 and Maurice Black2 1Agriculture Western Australia, 2Harbour Lights Estate, Geraldton 7. Tramline farming for dollar benefits, Paul Blackwell, Agriculture Western Australia NUTRITION 8. Soil immobile nutrients for no-till crops, M.D.A. Bolland1, R.F. Brennan1,and W.L. Crabtree2, 1Agriculture Western Australia, 2Western Australian No-Tillage Farmers Association 9. Burn stubble windrows: to diagnose soil fertility problems, Bill Bowden, Chris Gazey and Ross Brennan, Agriculture Western Australia 10. Calcium: magnesium ratios; are they important? Bill Bowden1, Rochelle Strahan2, Bob Gilkes2 and Zed Rengel2 1Agriculture Western Australia, 2Department of Soil Science and Plant Nutrition, UWA 11. Responses to late foliar applications of Flexi-N, Stephen Loss, Tim O’Dea, Patrick Gethin, Ryan Guthrie, Lisa Leaver, CSBP futurefarm 12. A comparison of Flexi-N placements, Stephen Loss, Tim O’Dea, Patrick Gethin, Ryan Guthrie, Lisa Leaver, CSBP futurefarm 13. What is the best way to apply potassium? Stephen Loss, Tim O’Dea, Patrick Gethin, Ryan Guthrie, CSBP futurefarm 14. Claying affects potassium nutrition in barley, Stephen Loss, David Phelps, Tim O’Dea, Patrick Gethin, Ryan Guthrie, Lisa Leaver, CSBP futurefarm 15. Nitrogen and potassium improve oaten hay quality, Stephen Loss, Tim O’Dea, Patrick Gethin, Ryan Guthrie, Lisa Leaver, CSBP futurefarm AGRONOMY 16. Agronomic responses of new wheat varieties in the northern wheatbelt, Darshan Sharma and Wal Anderson, Agriculture Western Australia 17. Wheat agronomy research on the south coast, Mohammad Amjad and Wal Anderson, Agriculture Western Australia 18. Influence of sowing date on wheat yield and quality in the south coast environment, Mohammad Amjadand Wal Anderson, Agriculture Western Australia 19. More profit from durum, Md.Shahajahan Miyan and Wal Anderson, Agriculture Western Australia 20. Enhancing recommendations of flowering and yield in wheat, JamesFisher1, Senthold Asseng2, Bill Bowden1 and Michael Robertson3 ,1AgricultureWestern Australia, 2CSIRO Plant Industry, 3CSIRO Sustainable Ecosystems 21. When and where to grow oats, Glenn McDonald, Agriculture Western Australia 22. Managing Gaidner barley for quality, Kevin Young and Blakely Paynter, Agriculture Western Australia PESTS AND DISEASES 23. Strategies for leaf disease management in wheat, Jatinderpal Bhathal1, Cameron Weeks2, Kith Jayasena1 and Robert Loughman1 ,1Agriculture Western Australia. 2Mingenew-Irwin Group Inc 24. Strategies for leaf disease management in malting barley, K. Jayasena1, Q. Knight2 and R. Loughman1, 1Agriculture Western Australia, 2IAMA Agribusiness 25. Cereal disease diagnostics, Dominie Wright and Nichole Burges, Agriculture Western Australia 26. The big rust: Did you get your money back!! Peter Burgess, Agritech Crop Research 27. Jockey – winning the race against disease in wheat, Lisa-Jane Blacklow, Rob Hulme and Rob Giffith, Aventis CropScience 28. Distribution and incidence of aphids and barley yellow dwarf virus in over-summering grasses in WA wheatbelt, Jenny Hawkes and Roger Jones, CLIMA and Agriculture Western Australia 29. Further developments in forecasting aphid and virus risk in cereals, Debbie Thackray, Jenny Hawkes and Roger Jones, Agriculture Western Australia and Centre for Legumes in Mediterranean Agriculture 30. Effect of root lesion nematodes on wheat yields in Western Australia, S. B. Sharma, S. Kelly and R. Loughman, Crop Improvement Institute, Agriculture Western Australia 31. Rotational crops and varieties for management of root lesion nematodes in Western Australia, S.B. Sharma, S. Kelly and R. Loughman, Crop Improvement Institute, Agriculture Western Australia WEEDS 32. Phenoxy herbicide tolerance of wheat, Peter Newman and Dave Nicholson, Agriculture Western Australia 33. Tolerance of wheat to phenoxy herbicides,Harmohinder S. Dhammu, Terry Piper and Mario F. D\u27Antuono, Agriculture Western Australia 34. Herbicide tolerance of durum wheats, Harmohinder S. Dhammu, Terry Piper and David Nicholson, Agriculture Western Australia 35. Herbicide tolerance of new wheats, Harmohinder S. Dhammu, Terry Piper and David F. Nicholson, Agriculture Western Australia BREEDING 36. Towards molecular breeding of barley: construction of a molecular genetic map, Mehmet Cakir1, Nick Galwey1, David Poulsen2, Garry Ablett3, Reg Lance4, Rob Potter5 and Peter Langridge6,1Plant Sciences, Faculty of Agriculture, UWA, 2Queensland Department of Primary Industries, Qld, 3Centre for Plant Conservation Genetics Southern Cross University, Lismore NSW, 5SABC Murdoch University, WA, 6Department of Plant Science University of Adelaide, Glen Osmond SA 37. Toward molecular breeding of barley: Identifying markers linked to genes for quantitative traits, Mehmet Cakir1, Nick Galwey1, David Poulsen2, Reg Lance3, Garry Ablett4, Greg Platz2, Joe Panozzo5, Barbara Read6, David Moody5, Andy Barr7 and Peter Langridge7 , 1Plant Sciences, Faculty of Agriculture, UWA, 2Queensland Department of Primary Industries, Warwick, QLD,3Agriculture Western Australia, 4Centre for Plant Conservation Genetics, Southern Cross University, Lismore NSW, 5VIDA Private Bag 260, Horsham VIC, 6NSW Dept. of Agriculture, Wagga Wagga NSW, 7Department of Plant Science, University of Adelaide, Glen Osmond SA 38. Can we improve grain yield by breeding for greater early vigour in wheat? Tina Botwright1, Tony Condon1, Robin Wilson2 and Iain Barclay2, 1CSIRO Plant Industry, 2Agriculture Western Australia MARKETING AND QUALITY 39. The Crop Improvement Royalty, Howard Carr, Agriculture Western Australia 40. GrainGuardÔ - The development of a protection plan for the wheat industry, Greg Shea, Agriculture Western Australia CLIMATE 41. Rainfall – what happened in 2000 and the prospects for 2001, Ian Foster, Agriculture Western Australia 42. Software for climate management issues, David Tennant,Agriculture Western Australia CONTRIBUTING AUTHOR CONTACT DETAIL

Madagascar’s extraordinary biodiversity: Evolution, distribution, and use

Madagascar's biota is hyperdiverse and includes exceptional levels of endemicity. We review the current state of knowledge on Madagascar's past and current terrestrial and freshwater biodiversity by compiling and presenting comprehensive data on species diversity, endemism, and rates of species description and human uses, in addition to presenting an updated and simplified map of vegetation types. We report a substantial increase of records and species new to science in recent years; however, the diversity and evolution of many groups remain practically unknown (e.g., fungi and most invertebrates). Digitization efforts are increasing the resolution of species richness patterns and we highlight the crucial role of field- and collections-based research for advancing biodiversity knowledge and identifying gaps in our understanding, particularly as species richness corresponds closely to collection effort. Phylogenetic diversity patterns mirror that of species richness and endemism in most of the analyzed groups. We highlight humid forests as centers of diversity and endemism because of their role as refugia and centers of recent and rapid radiations. However, the distinct endemism of other areas, such as the grassland-woodland mosaic of the Central Highlands and the spiny forest of the southwest, is also biologically important despite lower species richness. The documented uses of Malagasy biodiversity are manifold, with much potential for the uncovering of new useful traits for food, medicine, and climate mitigation. The data presented here showcase Madagascar as a unique living laboratory for our understanding of evolution and the complex interactions between people and nature. The gathering and analysis of biodiversity data must continue and accelerate if we are to fully understand and safeguard this unique subset of Earth's biodiversity

Madagascar’s extraordinary biodiversity: Threats and opportunities

Madagascar's unique biota is heavily affected by human activity and is under intense threat. Here, we review the current state of knowledge on the conservation status of Madagascar's terrestrial and freshwater biodiversity by presenting data and analyses on documented and predicted species-level conservation statuses, the most prevalent and relevant threats, ex situ collections and programs, and the coverage and comprehensiveness of protected areas. The existing terrestrial protected area network in Madagascar covers 10.4% of its land area and includes at least part of the range of the majority of described native species of vertebrates with known distributions (97.1% of freshwater fishes, amphibians, reptiles, birds, and mammals combined) and plants (67.7%). The overall figures are higher for threatened species (97.7% of threatened vertebrates and 79.6% of threatened plants occurring within at least one protected area). International Union for Conservation of Nature (IUCN) Red List assessments and Bayesian neural network analyses for plants identify overexploitation of biological resources and unsustainable agriculture as themost prominent threats to biodiversity. We highlight five opportunities for action at multiple levels to ensure that conservation and ecological restoration objectives, programs, and activities take account of complex underlying and interacting factors and produce tangible benefits for the biodiversity and people of Madagascar

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead