The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse

Gene trapping is a method of generating murine embryonic stem (ES) cell lines containing insertional mutations in known and novel genes. A number of international groups have used this approach to create sizeable public cell line repositories available to the scientific community for the generation of mutant mouse strains. The major gene trapping groups worldwide have recently joined together to centralize access to all publicly available gene trap lines by developing a user-oriented Website for the International Gene Trap Consortium (IGTC). This collaboration provides an impressive public informatics resource comprising ∼45 000 well-characterized ES cell lines which currently represent ∼40% of known mouse genes, all freely available for the creation of knockout mice on a non-collaborative basis. To standardize annotation and provide high confidence data for gene trap lines, a rigorous identification and annotation pipeline has been developed combining genomic localization and transcript alignment of gene trap sequence tags to identify trapped loci. This information is stored in a new bioinformatics database accessible through the IGTC Website interface. The IGTC Website () allows users to browse and search the database for trapped genes, BLAST sequences against gene trap sequence tags, and view trapped genes within biological pathways. In addition, IGTC data have been integrated into major genome browsers and bioinformatics sites to provide users with outside portals for viewing this data. The development of the IGTC Website marks a major advance by providing the research community with the data and tools necessary to effectively use public gene trap resources for the large-scale characterization of mammalian gene function

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

Sedation and Analgesia for Reduction of Pediatric Ileocolic Intussusception

IMPORTANCE: Ileocolic intussusception is an important cause of intestinal obstruction in children. Reduction of ileocolic intussusception using air or fluid enema is the standard of care. This likely distressing procedure is usually performed without sedation or analgesia, but practice variation exists. OBJECTIVE: To characterize the prevalence of opioid analgesia and sedation and assess their association with intestinal perforation and failed reduction. DESIGN, SETTING, AND PARTICIPANTS: This cross-sectional study reviewed medical records of children aged 4 to 48 months with attempted reduction of ileocolic intussusception at 86 pediatric tertiary care institutions in 14 countries from January 2017 to December 2019. Of 3555 eligible medical records, 352 were excluded, and 3203 medical records were eligible. Data were analyzed in August 2022. EXPOSURES: Reduction of ileocolic intussusception. MAIN OUTCOMES AND MEASURES: The primary outcomes were opioid analgesia within 120 minutes of reduction based on the therapeutic window of IV morphine and sedation immediately before reduction of intussusception. RESULTS: We included 3203 patients (median [IQR] age, 17 [9-27] months; 2054 of 3203 [64.1%] males). Opioid use was documented in 395 of 3134 patients (12.6%), sedation 334 of 3161 patients (10.6%), and opioids plus sedation in 178 of 3134 patients (5.7%). Perforation was uncommon and occurred in 13 of 3203 patients (0.4%). In the unadjusted analysis, opioids plus sedation (odds ratio [OR], 5.92; 95% CI, 1.28-27.42; P = .02) and a greater number of reduction attempts (OR, 1.48; 95% CI, 1.03-2.11; P = .03) were significantly associated with perforation. In the adjusted analysis, neither of these covariates remained significant. Reductions were successful in 2700 of 3184 attempts (84.8%). In the unadjusted analysis, younger age, no pain assessment at triage, opioids, longer duration of symptoms, hydrostatic enema, and gastrointestinal anomaly were significantly associated with failed reduction. In the adjusted analysis, only younger age (OR, 1.05 per month; 95% CI, 1.03-1.06 per month; P \u3c .001), shorter duration of symptoms (OR, 0.96 per hour; 95% CI, 0.94-0.99 per hour; P = .002), and gastrointestinal anomaly (OR, 6.50; 95% CI, 2.04-20.64; P = .002) remained significant. CONCLUSIONS AND RELEVANCE: This cross-sectional study of pediatric ileocolic intussusception found that more than two-thirds of patients received neither analgesia nor sedation. Neither was associated with intestinal perforation or failed reduction, challenging the widespread practice of withholding analgesia and sedation for reduction of ileocolic intussusception in children

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

Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin

Recent genomic analyses of pathologically-defined tumor types identify “within-a-tissue” disease subtypes. However, the extent to which genomic signatures are shared across tissues is still unclear. We performed an integrative analysis using five genome-wide platforms and one proteomic platform on 3,527 specimens from 12 cancer types, revealing a unified classification into 11 major subtypes. Five subtypes were nearly identical to their tissue-of-origin counterparts, but several distinct cancer types were found to converge into common subtypes. Lung squamous, head & neck, and a subset of bladder cancers coalesced into one subtype typified by TP53 alterations, TP63 amplifications, and high expression of immune and proliferation pathway genes. Of note, bladder cancers split into three pan-cancer subtypes. The multi-platform classification, while correlated with tissue-of-origin, provides independent information for predicting clinical outcomes. All datasets are available for data-mining from a unified resource to support further biological discoveries and insights into novel therapeutic strategies

Adolescent Wilderness Therapy: The Relationship of Client Outcomes to Reasons for Referral, Motivation for Change, and Clinical Measures

Outdoor behavioral healthcare is a specific model and industry utilizing wilderness therapy (WT), a residential treatment approach comprised of outdoor travel and living for youth experiencing mental health, substance use, and behavioral concerns. We present data from 6417 participants about reasons for referral, admission, and discharge scores from the Youth-Outcome Questionnaire (Y-OQ), youth interest and commitment to treatment, reliable change scores, and the relationship between these variables. One-third of youth entered WT with sub-clinical scores, varying levels of client motivation and voluntariness in relation to clinical outcomes, a diverse range of presenting problems without clear indication of specialized treatment planning, and differing responses to treatment by referral reason. Identifying those not responding to WT and those at risk of deterioration from the time of admission requires further investigation to improve client outcomes for this treatment modality. Recommendations include placing increased importance on accurate and thorough screening and assessment, utilizing baseline and routine outcome monitoring, reducing coercion, and considering specialized intervention

The WI+RE Way

WI+RE (Writing Instruction + Research Education) is a learner-led team of undergraduate and graduate student employees at UCLA Library who apply values-driven design principles and grassroots instructional media production techniques to foster breakthroughs in research, reading, and writing for their fellow learners. The WI+RE Way (UCLA Library WI+RE, 2019c) is a collaboratively authored manifesto for learner-led design co-authored by WI+RE's learner-designers in collaboration with library staff.