Chlamydia trachomatis infection increases fallopian tube PROKR2 via TLR2 and NFκB activation resulting in a microenvironment predisposed to ectopic pregnancy

Chlamydia trachomatis and smoking are major risk factors for tubal ectopic pregnancy (EP), but the underlying mechanisms of these associations are not completely understood. Fallopian tube (FT) from women with EP exhibit altered expression of prokineticin receptors 1 and 2 (PROKR1 and PROKR2); smoking increases FT PROKR1, resulting in a microenvironment predisposed to EP. We hypothesize that C. trachomatis also predisposes to EP by altering FT PROKR expression and have investigated this by examining NFkappaB activation via ligation of the Toll-like receptor (TLR) family of cell-surface pattern recognition receptors. PROKR2 mRNA was higher in FT from women with evidence of past C. trachomatis infection than in those without (P < 0.05), and was also increased in FT explants and in oviductal epithelial cell line OE-E6/E7 infected with C. trachomatis (P < 0.01) or exposed to UV-killed organisms (P < 0.05). The ability of both live and dead organisms to induce this effect suggests ligation of a cell-surface-expressed receptor. FT epithelium and OE-E6/E7 were both found to express TLR2 and TLR4 by immunohistochemistry. Transfection of OE-E6/E7 cells with dominant-negative TLR2 or IkappaBalpha abrogated the C. trachomatis-induced PROKR2 expression. We propose that ligation of tubal TLR2 and activation of NFkappaB by C. trachomatis leads to increased tubal PROKR2, thereby predisposing the tubal microenvironment to ectopic implantation

The Acoustic Index User’s Guide: A practical manual for defining, generating and understanding current and future acoustic indices

1. Ecoacoustics, the study of environmental sound, is a rapidly growing discipline offering ecological insights at scales ranging from individual organisms to whole ecosystems. Substantial methodological developments over the last 15 years have streamlined extraction of ecological information from audio recordings. One widely used set of methods are acoustic indices, which offer numerical summaries of the spectral, temporal and amplitude patterns in audio recordings. 2. Currently, the specifics of each index’s background, methodology, and the soundscape patterns they are designed to summarise, are spread across multiple sources. Critically, details of index calculation are sometimes scarce, making it challenging for users to understand how index values are generated. Discrepancies in understanding can lead to misuse of acoustic indices or reporting of spurious results. This hinders ecological inference, replicability, and discourages adoption of these tools for conservation and ecosystem monitoring, where they might otherwise provide useful insight.  3. Here we present the Acoustic Index User’s Guide - an interactive RShiny web app that defines and deconstructs eight of the most commonly used acoustic indices to facilitate consistent application across the discipline. We break the acoustic indices calculations down into easy-to-follow steps to better enable practical application and critical interpretation of acoustic indices. We demonstrate typical soundscape patterns using a suite of 91 example audio recordings: 66 real-world soundscapes from terrestrial, aquatic, and subterranean systems around the world, and 25 synthetic files demonstrating archetypal soundscape patterns. Our interpretation figures signpost specific soundscape patterns likely to be reflected in acoustic indices’ values. 4. This RShiny app is a living resource; additional acoustic indices will be added in the future through collaboration with authors of pre-existing and new indices. The app also serves as a best-practice template for the information required when publishing new acoustic indices, so that authors can facilitate the widest possible understanding and uptake of their indices. In turn, improved understanding of acoustic indices will aid effective hypothesis generation, application, and interpretation in ecological research, ecosystem monitoring, and conservation management.Additional authors: Magnus Janson, Thomas Luypaert, Oliver C. Metcalf, Anna E. Nousek-McGregor, Frederica Poznansky, Samuel R. P.-J. Ross, Sarab Sethi, Siobhan Smyt

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

Training future generations to deliver evidence-based conservation and ecosystem management

1. To be effective, the next generation of conservation practitioners and managers need to be critical thinkers with a deep understanding of how to make evidence-based decisions and of the value of evidence synthesis. 2. If, as educators, we do not make these priorities a core part of what we teach, we are failing to prepare our students to make an effective contribution to conservation practice. 3. To help overcome this problem we have created open access online teaching materials in multiple languages that are stored in Applied Ecology Resources. So far, 117 educators from 23 countries have acknowledged the importance of this and are already teaching or about to teach skills in appraising or using evidence in conservation decision-making. This includes 145 undergraduate, postgraduate or professional development courses. 4. We call for wider teaching of the tools and skills that facilitate evidence-based conservation and also suggest that providing online teaching materials in multiple languages could be beneficial for improving global understanding of other subject areas.Peer reviewe

HeAlth System StrEngThening in four sub-Saharan African countries (ASSET) to achieve high-quality, evidence-informed surgical, maternal and newborn, and primary care: protocol for pre-implementation phase studies

To achieve universal health coverage, health system strengthening (HSS) is required to support the of delivery of high-quality care. The aim of the National Institute for Health Research Global Research Unit on HeAlth System StrEngThening in Sub-Saharan Africa (ASSET) is to address this need in a four-year programme, with three healthcare platforms involving eight work-packages. Key to effective health system strengthening (HSS) is the pre-implementation phase of research where efforts focus on applying participatory methods to embed the research programme within the existing health system. To conceptualise the approach, we provide an overview of the key methods applied across work-package to address this important phase of research conducted between 2017 and 2021. Work-packages are being undertaken in publicly funded health systems in rural and urban areas in Ethiopia, Sierra Leone, South Africa, and Zimbabwe. Stakeholders including patients and their caregivers, community representatives, clinicians, managers, administrators, and policymakers are the main research participants. In each work-package, initial activities engage stakeholders and build relationships to ensure co-production and ownership of HSSIs. A mixed-methods approach is then applied to understand and address determinants of high-quality care delivery. Methods such as situation analysis, cross-sectional surveys, interviews and focus group discussions are adopted to each work-package aim and context. At the end of the pre-implementation phase, findings are disseminated using focus group discussions and participatory Theory of Change workshops where stakeholders from each work package use findings to select HSSIs and develop a programme theory. ASSET places a strong emphasis of the pre-implementation phase in order to provide an in-depth and systematic diagnosis of the existing heath system functioning, needs for strengthening and stakeholder engagement. This common approach will inform the design and evaluation of the HSSIs to increase effectiveness across work packages and contexts, to better understand what works, for whom, and how

The Acoustic Index User’s Guide: A practical manual for defining, generating and understanding current and future acoustic indices

1. Ecoacoustics, the study of environmental sound, is a rapidly growing discipline offering ecological insights at scales ranging from individual organisms to whole ecosystems. Substantial methodological developments over the last 15 years have streamlined extraction of ecological information from audio recordings. One widely used set of methods are acoustic indices, which offer numerical summaries of the spectral, temporal and amplitude patterns in audio recordings. 2. Currently, the specifics of each index’s background, methodology, and the soundscape patterns they are designed to summarise, are spread across multiple sources. Critically, details of index calculation are sometimes scarce, making it challenging for users to understand how index values are generated. Discrepancies in understanding can lead to misuse of acoustic indices or reporting of spurious results. This hinders ecological inference, replicability, and discourages adoption of these tools for conservation and ecosystem monitoring, where they might otherwise provide useful insight.  3. Here we present the Acoustic Index User’s Guide - an interactive RShiny web app that defines and deconstructs eight of the most commonly used acoustic indices to facilitate consistent application across the discipline. We break the acoustic indices calculations down into easy-to-follow steps to better enable practical application and critical interpretation of acoustic indices. We demonstrate typical soundscape patterns using a suite of 91 example audio recordings: 66 real-world soundscapes from terrestrial, aquatic, and subterranean systems around the world, and 25 synthetic files demonstrating archetypal soundscape patterns. Our interpretation figures signpost specific soundscape patterns likely to be reflected in acoustic indices’ values. 4. This RShiny app is a living resource; additional acoustic indices will be added in the future through collaboration with authors of pre-existing and new indices. The app also serves as a best-practice template for the information required when publishing new acoustic indices, so that authors can facilitate the widest possible understanding and uptake of their indices. In turn, improved understanding of acoustic indices will aid effective hypothesis generation, application, and interpretation in ecological research, ecosystem monitoring, and conservation management

Training future generations to deliver evidence-based conservation and ecosystem management

1. To be effective, the next generation of conservation practitioners and managers need to be critical thinkers with a deep understanding of how to make evidence-based decisions and of the value of evidence synthesis. 2. If, as educators, we do not make these priorities a core part of what we teach, we are failing to prepare our students to make an effective contribution to conservation practice. 3. To help overcome this problem we have created open access online teaching materials in multiple languages that are stored in Applied Ecology Resources. So far, 117 educators from 23 countries have acknowledged the importance of this and are already teaching or about to teach skills in appraising or using evidence in conservation decision-making. This includes 145 undergraduate, postgraduate or professional development courses. 4. We call for wider teaching of the tools and skills that facilitate evidence-based conservation and also suggest that providing online teaching materials in multiple languages could be beneficial for improving global understanding of other subject areas.Additional co-authors: Eduardo C. Arellano, Jan Axmacher, Holly Barclay, Lesley Batty, Ana Benítez-López, Joseph R. Bennett, Maureen J. Berg, Sandro Bertolino, Duan Biggs, Friederike C. Bolam, Tim Bray, Barry W. Brook, Joseph W. Bull, Zuzana Burivalova, Mar Cabeza, Alienor L. M. Chauvenet, Alec P. Christie, Lorna Cole, Alison J. Cotton, Sam Cotton, Sara A. O. Cousins, Dylan Craven, Will Cresswell, Jeremy J. Cusack, Sarah E. Dalrymple, Zoe G. Davies, Anita Diaz, Jennifer A. Dodd, Adam Felton, Erica Fleishman, Charlie J. Gardner, Ruth Garside, Arash Ghoddousi, James J. Gilroy, David A. Gill, Jennifer A. Gill, Louise Glew, Matthew J. Grainger, Amelia A. Grass, Stephanie Greshon, Jamie Gundry, Tom Hart, Charlotte R. Hopkins, Caroline Howe, Arlyne Johnson, Kelly W. Jones, Neil R. Jordan, Taku Kadoya, Daphne Kerhoas, Julia Koricheva, Tien Ming Lee, Szabolcs Lengyel, Stuart W. Livingstone, Ashley Lyons, Gráinne McCabe, Jonathan Millett, Chloë Montes Strevens, Adam Moolna, Hannah L. Mossman, Nibedita Mukherjee, Andrés Muñoz-Sáez, Nuno Negrões, Olivia Norfolk, Takeshi Osawa, Sarah Papworth, Jérôme Pellet, Andrea D. Phillott, Joshua M. Plotnik, Dolly Priatna, Alejandra G. Ramos, Nicola Randall, Rob M. Richards, Euan G. Ritchie, David L. Roberts, Ricardo Rocha, Jon Paul Rodríguez, Roy Sanderson, Takehiro Sasaki, Sini Savilaakso, Carl Sayer, Cagan Sekercioglu, Masayuki Senzaki, Grania Smith, Robert J. Smith, Masashi Soga, Carl D. Soulsbury, Mark D. Steer, Gavin Stewart, E. F. Strange, Andrew J. Suggitt, Ralph R. J. Thompson, Stewart Thompson, Ian Thornhill, R. J. Trevelyan, Hope O. Usieta, Oscar Venter, Amanda D. Webber, Rachel L. White, Mark J. Whittingham, Andrew Wilby, Richard W. Yarnell, Veronica Zamora-Gutierrez, William J. Sutherlan