Community research report

University College Cork introduced its first Community-based Participatory Research (CBPR) module in 2016. The module was funded and supported by Horizon2020 funding, specifically the EnRRICH project (Enhancing Responsible Research and Innovation through Curricula in Higher Education). The module is a 5-credit module for PhD students from all disciplines in the early stages of their PhD at University College Cork. Following two fruitful partnerships in the areas of social justice / equality, community family support services and older persons, there was a keen interested to explore partnerships in markedly different areas such as environmental sustainability. A dialogue ensued with CEF where the opportunity and feasibility to collaborate on the CBPR module was explored

Clinical impact of genomic testing in patients with suspected monogenic kidney disease

Purpose: To determine the diagnostic yield and clinical impact of exome sequencing (ES) in patients with suspected monogenic kidney disease. Methods: We performed clinically accredited singleton ES in a prospectively ascertained cohort of 204 patients assessed in multidisciplinary renal genetics clinics at four tertiary hospitals in Melbourne, Australia. Results: ES identified a molecular diagnosis in 80 (39%) patients, encompassing 35 distinct genetic disorders. Younger age at presentation was independently associated with an ES diagnosis (p < 0.001). Of those diagnosed, 31/80 (39%) had a change in their clinical diagnosis. ES diagnosis was considered to have contributed to management in 47/80 (59%), including negating the need for diagnostic renal biopsy in 10/80 (13%), changing surveillance in 35/80 (44%), and changing the treatment plan in 16/80 (20%). In cases with no change to management in the proband, the ES result had implications for the management of family members in 26/33 (79%). Cascade testing was subsequently offered to 40/80 families (50%). Conclusion: In this pragmatic pediatric and adult cohort with suspected monogenic kidney disease, ES had high diagnostic and clinical utility. Our findings, including predictors of positive diagnosis, can be used to guide clinical practice and health service design

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

A chromosome conformation capture ordered sequence of the barley genome

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Genome-wide association meta-analysis in 269,867 individuals identifies new genetic and functional links to intelligence

Intelligence is highly heritable(1) and a major determinant of human health and well-being(2). Recent genome-wide meta-analyses have identified 24 genomic loci linked to variation in intelligence3-7, but much about its genetic underpinnings remains to be discovered. Here, we present a large-scale genetic association study of intelligence (n = 269,867), identifying 205 associated genomic loci (190 new) and 1,016 genes (939 new) via positional mapping, expression quantitative trait locus (eQTL) mapping, chromatin interaction mapping, and gene-based association analysis. We find enrichment of genetic effects in conserved and coding regions and associations with 146 nonsynonymous exonic variants. Associated genes are strongly expressed in the brain, specifically in striatal medium spiny neurons and hippocampal pyramidal neurons. Gene set analyses implicate pathways related to nervous system development and synaptic structure. We confirm previous strong genetic correlations with multiple health-related outcomes, and Mendelian randomization analysis results suggest protective effects of intelligence for Alzheimer's disease and ADHD and bidirectional causation with pleiotropic effects for schizophrenia. These results are a major step forward in understanding the neurobiology of cognitive function as well as genetically related neurological and psychiatric disorders.Peer reviewe

BHPR research: qualitative1. Complex reasoning determines patients' perception of outcome following foot surgery in rheumatoid arhtritis

Background: Foot surgery is common in patients with RA but research into surgical outcomes is limited and conceptually flawed as current outcome measures lack face validity: to date no one has asked patients what is important to them. This study aimed to determine which factors are important to patients when evaluating the success of foot surgery in RA Methods: Semi structured interviews of RA patients who had undergone foot surgery were conducted and transcribed verbatim. Thematic analysis of interviews was conducted to explore issues that were important to patients. Results: 11 RA patients (9 ♂, mean age 59, dis dur = 22yrs, mean of 3 yrs post op) with mixed experiences of foot surgery were interviewed. Patients interpreted outcome in respect to a multitude of factors, frequently positive change in one aspect contrasted with negative opinions about another. Overall, four major themes emerged. Function: Functional ability & participation in valued activities were very important to patients. Walking ability was a key concern but patients interpreted levels of activity in light of other aspects of their disease, reflecting on change in functional ability more than overall level. Positive feelings of improved mobility were often moderated by negative self perception ("I mean, I still walk like a waddling duck”). Appearance: Appearance was important to almost all patients but perhaps the most complex theme of all. Physical appearance, foot shape, and footwear were closely interlinked, yet patients saw these as distinct separate concepts. Patients need to legitimize these feelings was clear and they frequently entered into a defensive repertoire ("it's not cosmetic surgery; it's something that's more important than that, you know?”). Clinician opinion: Surgeons' post operative evaluation of the procedure was very influential. The impact of this appraisal continued to affect patients' lasting impression irrespective of how the outcome compared to their initial goals ("when he'd done it ... he said that hasn't worked as good as he'd wanted to ... but the pain has gone”). Pain: Whilst pain was important to almost all patients, it appeared to be less important than the other themes. Pain was predominately raised when it influenced other themes, such as function; many still felt the need to legitimize their foot pain in order for health professionals to take it seriously ("in the end I went to my GP because it had happened a few times and I went to an orthopaedic surgeon who was quite dismissive of it, it was like what are you complaining about”). Conclusions: Patients interpret the outcome of foot surgery using a multitude of interrelated factors, particularly functional ability, appearance and surgeons' appraisal of the procedure. While pain was often noted, this appeared less important than other factors in the overall outcome of the surgery. Future research into foot surgery should incorporate the complexity of how patients determine their outcome Disclosure statement: All authors have declared no conflicts of interes

The genetic architecture of the human cerebral cortex

The cerebral cortex underlies our complex cognitive capabilities, yet little is known about the specific genetic loci that influence human cortical structure. To identify genetic variants that affect cortical structure, we conducted a genome-wide association meta-analysis of brain magnetic resonance imaging data from 51,665 individuals. We analyzed the surface area and average thickness of the whole cortex and 34 regions with known functional specializations. We identified 199 significant loci and found significant enrichment for loci influencing total surface area within regulatory elements that are active during prenatal cortical development, supporting the radial unit hypothesis. Loci that affect regional surface area cluster near genes in Wnt signaling pathways, which influence progenitor expansion and areal identity. Variation in cortical structure is genetically correlated with cognitive function, Parkinson's disease, insomnia, depression, neuroticism, and attention deficit hyperactivity disorder