A Blueprint for a Contemporary Storage Element, building a new WLCG storage system with widely available hardware and software components: Ceph, XRootD, and Prometheus

When a new long-term storage facility was needed at the Lancaster WLCG Tier-2 Site, an architecture was chosen involving CephFS as a failure-tolerant back-end volume, and load-balanced XRootD as an endpoint exposing the volume via the HTTPS/DAVS protocols increasingly favoured by the WLCG and other users. This allows operations to continue in the face of disc/node failures with minimal management, and enables good utilization of network connectivity for remote access. We deployed a Prometheus/Loki/Grafana monitoring/alerting stack for timely detection and resolution of failures in such a production environment. Some custom scripts were required to adapt the off-the-shelf functional components with monitoring. With such a monitoring system in place, failures such as disc defects, data corruption and resource exhaustion in long-running processes can be anticipated, and their management planned. We describe the hardware platform and our requirements on it, and detail the software architecture from initial design, through adaptations to face challenges encountered during production, to present condition. Developments and contributions to related projects that help to fully exploit our design decisions are described. We include performance metrics of the system, the lessons learned during production, and our future plans

The Bruininks-Oseretsky Test of Motor Proficiency-Short Form is reliable in children living in remote Australian Aboriginal communities

BACKGROUND: The Lililwan Project is the first population-based study to determine Fetal Alcohol Spectrum Disorders (FASD) prevalence in Australia and was conducted in the remote Fitzroy Valley in North Western Australia. The diagnostic process for FASD requires accurate assessment of gross and fine motor functioning using standardised cut-offs for impairment. The Bruininks-Oseretsky Test of Motor Proficiency, Second Edition (BOT-2) is a norm-referenced assessment of motor function used worldwide and in FASD clinics in North America. It is available in a Complete Form with 53 items or a Short Form with 14 items. Its reliability in measuring motor performance in children exposed to alcohol in utero or living in remote Australian Aboriginal communities is unknown. METHODS: A prospective inter-rater and test-retest reliability study was conducted using the BOT-2 Short Form. A convenience sample of children (n = 30) aged 7 to 9 years participating in the Lililwan Project cohort (n = 108) study, completed the reliability study. Over 50% of mothers of Lililwan Project children drank alcohol during pregnancy. Two raters simultaneously scoring each child determined inter-rater reliability. Test-retest reliability was determined by assessing each child on a second occasion using predominantly the same rater. Reliability was analysed by calculating Intra-Class correlation Coefficients, ICC(2,1), Percentage Exact Agreement (PEA) and Percentage Close Agreement (PCA) and measures of Minimal Detectable Change (MDC) were calculated. RESULTS: Thirty Aboriginal children (18 male, 12 female: mean age 8.8 years) were assessed at eight remote Fitzroy Valley communities. The inter-rater reliability for the BOT-2 Short Form score sheet outcomes ranged from 0.88 (95%CI, 0.77 – 0.94) to 0.92 (95%CI, 0.84 – 0.96) indicating excellent reliability. The test-retest reliability (median interval between tests being 45.5 days) for the BOT-2 Short Form score sheet outcomes ranged from 0.62 (95%CI, 0.34 – 0.80) to 0.73 (95%CI, 0.50 – 0.86) indicating fair to good reliability. The raw score MDC was 6.12. CONCLUSION: The BOT-2 Short Form has acceptable reliability for use in remote Australian Aboriginal communities and will be useful in determining motor deficits in children exposed to alcohol prenatally. This is the first known study evaluating the reliability of the BOT-2 Short Form, either in the context of assessment for FASD or in Aboriginal children

Identification of a BRCA2-Specific modifier locus at 6p24 related to breast cancer risk

Common genetic variants contribute to the observed variation in breast cancer risk for BRCA2 mutation carriers; those known to date have all been found through population-based genome-wide association studies (GWAS). To comprehensively identify breast cancer risk modifying loci for BRCA2 mutation carriers, we conducted a deep replication of an ongoing GWAS discovery study. Using the ranked P-values of the breast cancer associations with the imputed genotype of 1.4 M SNPs, 19,029 SNPs were selected and designed for inclusion on a custom Illumina array that included a total of 211,155 SNPs as part of a multi-consortial project. DNA samples from 3,881 breast cancer affected and 4,330 unaffected BRCA2 mutation carriers from 47 studies belonging to the Consortium of Investigators of Modifiers of BRCA1/2 were genotyped and available for analysis. We replicated previously reported breast cancer susceptibility alleles in these BRCA2 mutation carriers and for several regions (including FGFR2, MAP3K1, CDKN2A/B, and PTHLH) identified SNPs that have stronger evidence of association than those previously published. We also identified a novel susceptibility allele at 6p24 that was inversely associated with risk in BRCA2 mutation carriers (rs9348512; per allele HR = 0.85, 95% CI 0.80-0.90, P = 3.9×10−8). This SNP was not associated with breast cancer risk either in the general population or in BRCA1 mutation carriers. The locus lies within a region containing TFAP2A, which encodes a transcriptional activation protein that interacts with several tumor suppressor genes. This report identifies the first breast cancer risk locus specific to a BRCA2 mutation background. This comprehensive update of novel and previously reported breast cancer susceptibility loci contributes to the establishment of a panel of SNPs that modify breast cancer risk in BRCA2 mutation carriers. This panel may have clinical utility for women with BRCA2 mutations weighing options for medical prevention of breast cancer

Very silly party politics : surrealism and satire in the ‘Pythonesque’

2019 sees the 50th anniversary of the iconic British television comedy series Monty Python’s Flying Circus (BBC: 1969-74). This article focuses on the concept of ‘Pythonesque’, placing the broadly political satirical content that is evident within the Pythons’ mainstream TV work and in selected subsequent film work at the centre of the notion of ‘Pythonesque’. It will be suggested, moreover, that the Pythons’ socio-cultural critical position is embedded in a long established British literary satirical tradition. Further, this article will aim to show that ‘Pythonesque’ incongruity, whilst adopting the aesthetic of the nihilistic cabaret of the Dadaists, was further influenced by the contemporary strain of British vernacular surrealism that permeated twentieth century popular performance through Music Hall, Variety comedy and The Goons, and also borrows Surrealist satirical perspectives. This evaluation of ‘Pythonesque’ fusion of satirical and surreal elements will posit that the comedians were simultaneously behind the times; of their time; and, in their prescience, some ways ahead of their time in their construction of humorous commentary on British societal mores and their vividly underscoring of the absurdity of the institutions they targeted. Key Words: Monty Python, Satire, Surrealism, Comedy, ‘Pythonesque

Ulnar-sided wrist pain. Part I: anatomy and physical examination

Ulnar-sided wrist pain is a common complaint, and it presents a diagnostic challenge for hand surgeons and radiologists. The complex anatomy of this region, combined with the small size of structures and subtle imaging findings, compound this problem. A thorough understanding of ulnar-sided wrist anatomy and a systematic clinical examination of this region are essential in arriving at an accurate diagnosis. In part I of this review, ulnar-sided wrist anatomy and clinical examination are discussed for a more comprehensive understanding of ulnar-sided wrist pain

Crop Updates 2005 - Lupins and Pulses

This session covers sixty five papers from different authors: 1. 2004 LUPIN AND PULSE INDUSTRY HIGHLIGHTS, Peter White Department of Agriculture 2. BACKGROUND, Peter White Department of Agriculture 2004 REGIONAL ROUNDUP 3. Northern Agricultural Region, Martin Harries, Department of Agriculture 4. Central Agricultural Region, Ian Pritchard, Department of Agriculture 5. Great Southern and Lakes, Rodger Beermier, Department of Agriculture 6. Esperance Port Zone, Mark Seymour, Department of Agriculture, and David Syme, The Grain Pool of WA LUPIN AND PULSE PRODUCTION AGRONOMY AND GENETIC IMPROVEMENT 7. Lupin, Martin Harries, Department of Agriculture 8. Narrow-leafed lupin breeding, Bevan Buirchell, Department of Agriculture 9. Yellow lupin breeding in Western Australia, Kedar Adhikari, Mark Sweetingham and Bevan Buirchell, Department of Agriculture 10. WALAB2000 - First Anthracnose resistant albus lupins, Kedar Adhikari, Bevan Buirchell, MarkSweetingham and Geoff Thomas, Department of Agriculture 11. Improving lupin grain quality and yield through genetic manipulation of key physiological traits, Jon Clements1 and Bevan Buirchell2,1CLIMA, The University of Western Australia 2Department of Agriculture 12. Lupin alkaloids in four Australian species, Shao Fang Wang, Chemistry Centre (WA), CLIMA, The University of Western Australia 13. Improving lupin tolerance to herbicides of metribuzin, isoxaflutole and carfentrazone-ethyl, Ping Si1, Mark Sweetingham12, Bevan Buirchell12, David Bowran2 and Huaan Yang12 , 1CLIMA, The University of Western Australia, 2Department of Agriculture 14. Combined cultural and shielded sprayer herbicide application for weed management, Martin Harries and Mike Baker Department of Agriculture 15. Field testing of lupin seed of various sources with and without post maturity, pre harvest rain for field establishment, Martin Harries, Wayne Parker, Mike Baker, Department of Agriculture 16. Lupin seed rate by wide row spacing, Martin Harries, Bob French, Damien Owen D’arcy, Department of Agriculture 17. How environment influences row spacing response in lupins, Bob French, Department of Agriculture 18. The effect of wider row spacing on lupin architecture, growth and nutrient uptake dynamics, Bill Bowden and Craig Scanlan, Department of Agriculture 19. Fertiliser placement and application rate in wide rows, Martin Harries, Damien Owen D’arcy, Department of Agriculture 20. The pros and cons of cowing lupins in ‘wide’ rows, Wayne Parker, Bob French and Martin Harries, Department of Agriculture 21. Investigation into the influence of row orientation in lupin crops, Jeff Russell1 and Angie Roe2, 1Department of Agriculture, 2Farm Focus Consultants 22. Making the most of Mandelup, Greg Shea and Chris Matthews, Department of Agriculture 23. The effect of wild radish density and lupin cultivars on their competition at Merredin, Shahab Pathan, Abul Hashem and Bob French, Department of Agriculture 24. The potential of pearl lupin (Lupinus mutabilis) for southern Australia, Jon Clements1, Mark Sweetingham2, Bevan Buirchell2, Sofia Sipsas2, Geoff Thomas2, John Quealy1, Roger Jones2, Clive Francis1, Colin Smith2 and Gordon Francis1, 1CLIMA, University of Western Australia 2Department of Agriculture 25. Field pea, Mark Seymour, Department of Agriculture 26. Breeding highlights, Tanveer. Khan and Bob French, Department of Agriculture 27. Variety evaluation, Tanveer Khan, Kerry Regan, Jenny Garlinge and Rod Hunter, Department of Agriculture 28. Large scale field pea variety trials, Martin Harries, Department of Agriculture 29. Kaspa demonstrations, Rodger Beermier, Mark Seymour, Ian Pritchard, Graham Mussell, Department of Agriculture 30. Field pea harvesting demonstration at Merredin, Glen Riethmuller, Greg Shea and Bob French, Department of Agriculture 31. Does Kaspa respond differently to disease, fungicides, time of sowing or seed rate, Mark Seymour, Department of Agriculture 32. Field pea response to foliar Manganese in mallee district, Mark Seymour, Department of Agriculture 33. Kaspa harvesting observations 2004, Mark Seymour, Ian Pritchard, Glen Riethmuller, Department of Agriculture 34. ‘Blackspot Manager’ for understanding blackspot of peas and ascochyta blight management, Moin Salam and Jean Galloway, Department of Agriculture 35. 250,000 ha of field pea in WA – Is it sustainable? Larn McMurray1 and Mark Seymour2, 1South Australian Research and Development Institute, 2Department of Agriculture 36. Desi chickpea, Wayne Parker, Department of Agriculture 37. Breeding highlights, Tanveer Khan1,2 and Kadambot Siddique2,1Department of Agriculture, 2CLIMA, The University of Western Australia 38. Variety evaluation, Tanveer Khan, Kerry Regan, Jenny Garlinge and Rod Hunter, Department of Agriculture 39. Large scale variety testing of desi chickpeas, Martin Harries, Greg Shea, Mike Baker, Dirranie Kirby, Department of Agriculture 40. Desi variety chickpea trial, Martin Harries and Murray Blyth, Department of Agriculture 41. Seeding rates and row spacing of chickpea desi, Martin Harries, MurrayBlyth, Damien Owen D’arcy, Department of Agriculture 42. Molecular characterisation of chickpea wild relatives, Fucheng Shan, Heather Clarke and Kadambot Siddique, CLIMA, The University of Western Australia 43. Plant phosphorus status has a limited influence on the concentration of phosphorus-mobilising carboxylates in the rhizosphere of chickpea, Madeleine Wouterlood, Hans Lambers and Erik Veneklaas, The University of Western Australia 44. Kabuli chickpea, Kerry Regan, Department of Agriculture, and CLIMA, The University of Western Australia 45. ‘Kimberly Large’ A high quality and high yielding new variety for the Ord River Irrigation Area, Kerry Regan1,2, Kadambot Siddique2, Peter White1,2, Peter Smith1 and Gae Plunkett1,1Department of Agriculture, 2CLIMA, University of Western Australia 46. Development of ascochyta resistant and high quality varieties for Australia, Kadambot Siddique1, Kerry Regan1,2, Tim Pope1 and Mike Baker2, 1CLIMA, The University of Western Australia 2Department of Agriculture 47. Towards double haploids in chickpeas and field pea, Janine Croser, Julia Wilson and Kadambot Siddique, CLIMA, The University of Western Australia 48. Crossing chickpea with wild Cicer relatives to introduce resistance to disease and tolerance to environmental stress, Heather Clarke and Kadambot Siddique, CLIMA, The University of Western Australia 49. Faba bean, Peter White, Department of Agriculture 50. Germplasm evaluation, Peter White1,2, Kerry Regan1,2, Tim Pope2, Martin Harries1, Mark Seymour1, Rodger Beermier1 and Leanne Young1, 1Department of Agriculture, 2CLIMA, The University of Western Australia 51. Lentil, Kerry Regan, Department of Agriculture, and CLIMA, The University of Western Australia 52. Variety and germplasm evaluation, Kerry Regan1,2, Tim Pope2, Leanne Young1, Martin Harries1, Murray Blyth1 and Michael Materne3, 1Department of Agriculture, 2CLIMA, University of Western Australia, 3Department of Primary Industries, Victoria 53. Lathyrus species, Kadambot Siddique1, Kerry Regan2, and Colin Hanbury2, 1CLIMA, the University of Western Australia, 2Department of Agricultur

Mitochondrial physiology

As the knowledge base and importance of mitochondrial physiology to evolution, health and disease expands, the necessity for harmonizing the terminology concerning mitochondrial respiratory states and rates has become increasingly apparent. The chemiosmotic theory establishes the mechanism of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the protonmotive force provides the framework for developing a consistent theoretical foundation of mitochondrial physiology and bioenergetics. We follow the latest SI guidelines and those of the International Union of Pure and Applied Chemistry (IUPAC) on terminology in physical chemistry, extended by considerations of open systems and thermodynamics of irreversible processes. The concept-driven constructive terminology incorporates the meaning of each quantity and aligns concepts and symbols with the nomenclature of classical bioenergetics. We endeavour to provide a balanced view of mitochondrial respiratory control and a critical discussion on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes. Uniform standards for evaluation of respiratory states and rates will ultimately contribute to reproducibility between laboratories and thus support the development of data repositories of mitochondrial respiratory function in species, tissues, and cells. Clarity of concept and consistency of nomenclature facilitate effective transdisciplinary communication, education, and ultimately further discovery