48 research outputs found
Guide to growing summer grain & forages in the south coast region, Western Australia
Growing summer grain and forages in the south coast region of Western Australia. Information is included for sorghum, millet family, sunflowers, and safflower
Preferred reporting items for journal and conference abstracts of systematic reviews and meta-analyses of diagnostic test accuracy studies (PRISMA-DTA for Abstracts):checklist, explanation, and elaboration
For many users of the biomedical literature, abstracts may be the only source of information about a study. Hence, abstracts should allow readers to evaluate the objectives, key design features, and main results of the study. Several evaluations have shown deficiencies in the reporting of journal and conference abstracts across study designs and research fields, including systematic reviews of diagnostic test accuracy studies. Incomplete reporting compromises the value of research to key stakeholders. The authors of this article have developed a 12 item checklist of preferred reporting items for journal and conference abstracts of systematic reviews and meta-analyses of diagnostic test accuracy studies (PRISMA-DTA for Abstracts). This article presents the checklist, examples of complete reporting, and explanations for each item of PRISMA-DTA for Abstracts
Crop Updates 2008 - Cereals
This session covers twenty four papers from different authors:
WHEAT AGRONOMY
1. Wheat variety performance in the Northern Agricultural Region in 2007, Christine Zaicou, Department of Agriculture and Food
2. Wheat variety performance on the Central Agricultural Region in 2007, Shahajahan Miyan, Department of Agriculture and Food
3. Response of wheat varieties to sowing time in the Great Southern and Lakes Region in 2007, Brenda Shackley and Steve Penny, Department of Agriculture and Food
4. Wheat variety performance in the South Coastal Region in 2007, Sarah Ellis, Department of Agriculture and Food
5. Flowering dates of wheat varieties in Western Australia in 2007, Darshan Sharma, Brenda Shackley and Christine Zaicou, Department of Agriculture and Food
BARLEY AGRONOMY
6. Barley variety options for Western Australia, Blakely Paynter, Andrea Hills and Jeff Russell, Department of Agriculture and Food
7. Vlaming A – the newest malting barley variety, Blakely Paynter, Jeff Russell and Andrea Hills, Department of Agriculture and Food
8. Barley yields higher in wide rows with stubble retained in a very dry season at Merredin, Glen Riethmuller, Bill Bowden and Paul Blackwell, Department of Agriculture and Food
HERBICIDE TOLERANCE
9. Herbicide tolerance of current/new wheat varieties, Dr Harmohinder Dhammu, Department of Agriculture and Food
10. Herbicide tolerance of new oat varieties, Dr Harmohinder Dhammu, Vince Lambert, and Chris Roberts,Department of Agriculture and Food
NUTRITION
11. Managing nitrogen inputs in malting barley, Andrea Hills and Blakely Paynter, Department of Agriculture and Food
12. Decision tools for optimal N on cereal crops, David and Sally Cox, Jeremy Lemon* and Andrea Hills*, *Department of Agriculture and Food
13. Wheat varieties respond differently to potassium application on potassium responsive soils, Paul Damon and Zed Rengel, Faculty of Natural and Agricultural Sciences, University of Western Australia
DISEASES
14. Leaf disease management in continuous barley in the northern and central grainbelt of WA, Geoff Thomas, Ciara Beard, Anne Smith, Kith Jayasena and Sean Kelly, Department of Agriculture and Food
15. Temperature and moisture requirements of leaf, stem and stripe rusts of wheat, Geoff Thomas, Rob Loughman and Bill MacLeod, Department of Agriculture and Food
16. Fungicide options for controlling diseases in oats, Raj Malik and Blakely Paynter, Department of Agriculture and Food
17. Survey of wheat root diseases under intensive cereal production in Western Australia during 2005-2007, Ravjit Khangura, William MacLeod, Vivien Vanstone, Colin Hanbury, Mehreteab Aberra, Gordon MacNish and Robert Loughman, Department of Agriculture and Food
18. Epidemiology studies on Wheat Streak Mosaic Virus in 2007, Brenda Coutts, Geoff Strickland, Monica Kehoe, Dustin Severtson and Roger Jones, Department of Agriculture and Food
19. Bacterial diseases that affect WA export hay quality, Dominie Wright and Megan Jordan, Department of Agriculture and Food
SOIL
20. Hardpan penetration ability of drought-stressed wheat under pot and field conditions, Xinhua He1, Eli Manyol1, Song-Ai Nio1, Imran Malik1, Tina Botwright-Acuña1,2and Len Wade1,3,1School of Plant Biology, University of Western Australia, 2Tasmanian Institute of Agricultural Research, University of Tasmania, TAS, 3E.H. Graham Centre, Charles Sturt University, NSW
HARVEST MANAGEMENT
21. Calculating the risk – the SEPWA Harvest Calculator, Nigel Metz, South East Premium Wheat Growers Association
22. The relationship between grain moisture and atmospheric conditions in cereal crop harvesting on the South Coast of WA, Nigel Metz, South East Premium Wheat Growers Association (SEPWA)
MARKETS
23. Varietal accreditation for Australian Barley, Linda Price, Barley Australia
STATISTICAL METHODS
24. Applying data mining tools to improve grain quality for growers, Dean Diepeveen1, Leisa Armstrong2, Peter Clarke1, Doug Abrecht1, Rudi Appels2 and Matthew Bellgard3,1Department of Agriculture and Food, Western Australia 2Edith Cowan University, Western Australia, 3Centre of Comparative Genomics, Murdoch Universit
Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas
Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN
Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context
Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts
Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas
This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing
molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin
Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images
Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images
of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL
maps are derived through computational staining using a convolutional neural network trained to
classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and
correlation with overall survival. TIL map structural patterns were grouped using standard
histopathological parameters. These patterns are enriched in particular T cell subpopulations
derived from molecular measures. TIL densities and spatial structure were differentially enriched
among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial
infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic
patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for
the TCGA image archives with insights into the tumor-immune microenvironment
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
STARD 2015: An Updated List of Essential Items for Reporting Diagnostic Accuracy Studies.
Incomplete reporting has been identified as a major source of avoidable waste in biomedical research. Essential information is often not provided in study reports, impeding the identification, critical appraisal, and replication of studies. To improve the quality of reporting of diagnostic accuracy studies, the Standards for Reporting of Diagnostic Accuracy Studies (STARD) statement was developed. Here we present STARD 2015, an updated list of 30 essential items that should be included in every report of a diagnostic accuracy study. This update incorporates recent evidence about sources of bias and variability in diagnostic accuracy and is intended to facilitate the use of STARD. As such, STARD 2015 may help to improve completeness and transparency in reporting of diagnostic accuracy studies