CMS Monte Carlo production in the WLCG computing Grid

Monte Carlo production in CMS has received a major boost in performance and scale since the past CHEP06 conference. The production system has been re-engineered in order to incorporate the experience gained in running the previous system and to integrate production with the new CMS event data model, data management system and data processing framework. The system is interfaced to the two major computing Grids used by CMS, the LHC Computing Grid (LCG) and the Open Science Grid (OSG). Operational experience and integration aspects of the new CMS Monte Carlo production system is presented together with an analysis of production statistics. The new system automatically handles job submission, resource monitoring, job queuing, job distribution according to the available resources, data merging, registration of data into the data bookkeeping, data location, data transfer and placement systems. Compared to the previous production system automation, reliability and performance have been considerably improved. A more efficient use of computing resources and a better handling of the inherent Grid unreliability have resulted in an increase of production scale by about an order of magnitude, capable of running in parallel at the order of ten thousand jobs and yielding more than two million events per day

The CMS Monte Carlo Production System: Development and Design

The CMS production system has undergone a major architectural upgrade from its predecessor, with the goal of reducing the operational manpower needed and preparing for the large scale production required by the CMS physics plan. The new production system is a tiered architecture that facilitates robust and distributed production request processing and takes advantage of the multiple Grid and farm resources available to the CMS experiment

Indicators of sustainable fishing for South African sardine Sardinops sagax and anchovy Engraulis encrasicolus

Six indicators were investigated for South African sardine Sardinops sagax and anchovy Engraulis encrasicolus: mean length of catch, length-at-50% maturity, total mortality, exploitation rate, ratio of bycatch, and centre of gravity of commercial catches. Sardine length-at-50% maturity is the most promising as a descriptive indicator because it is positively correlated with population size for an extensive time period (1953–2005). The remaining indicators were limited by shorter data-series (1984–2005). However, mean length of catch, ratio of bycatch and exploitation rate were found to be useful when considered in conjunction with other indicators. The centre of gravity of commercial sardine catches has shown a significant eastward shift from the West Coast, whereas that of anchovy has remained off that coast. Ratio of bycatch indicates that school composition is a reliable descriptive indicator of relative abundance in the two species. Fewer indicators for anchovy were useful, which is attributed to this species’ flexible life-history pattern

Feasibility and reliability of PRISMA-Medical for specialty-based incident analysis

Aims and objectives: In this study, the feasibility and reliability of the Prevention Recovery Information System for Monitoring and Analysis (PRISMA)-Medical method for systematic, specialty-based analysis and classification of incidents in the neonatal intensive care unit (NICU) were determined. Methods: After the introduction of a Neonatology System for Analysis and Feedback on Medical Events (NEOSAFE) in eight tertiary care NICUs and one paediatric surgical ICU, PRISMA-Medical was started to be used to identify root causes of voluntary reported incidents by multidisciplinary unit patient safety committees. Committee members were PRISMA-trained and familiar with the department and its processes. In this study, the results of PRISMA-analysis of incidents reported during the first year are described. At t¿=¿3 months and t¿=¿12 months after introduction, test cases were performed to measure agreement at three levels of root cause classification using PRISMA-Medical. Inter-rater reliability was determined by calculating generalised ¿ values for each level of classification. Results: During the study period, 981 out of 1786 eligible incidents (55%) were analysed for underlying root causes. In total, 2313 root causes were identified and classified, giving an average of 2.4 root causes for every incident. Although substantial agreement (¿ 0.70–0.81) was reached at the main level of root cause classification of the test cases (discrimination between technical, organisational and human failure) and agreement among the committees at the second level (discrimination between skill-based, rule-based and knowledge-based errors) was acceptable (¿ 0.53–0.59), discrimination between rule-based errors (the third level of classification) was more difficult to assess (¿ 0.40–0.47). Conclusion: With some restraints, PRISMA-Medical proves to be both feasible and acceptably reliable to identify and classify multiple causes of medical events in the NICU

Diet and feeding intensity of sardine Sardina pilchardus: correlation with satellite-derived chlorophyll data

Spatio-temporal variability of the diet of sardine Sardina pilchardus off Portugal was examined through analysis of the stomach contents of fish collected every 14 d from the west and south of Portugal during 2003/2004. Dietary composition of the modal sardine length class was assessed by determining the frequency of occurrence and carbon content of identified prey, and these 2 parameters were combined to estimate a modified index of relative importance of prey (mIRI). The most important prey for sardines were zooplankton, comprising crustacean eggs, copepods, decapods, cirripedes and fish eggs, dinoflagellates and diatoms (particularly the toxin-producer\ud genus Pseudo-nitzschia), which together accounted for >90% of the estimated dietary carbon. Dietary seasonality was similar for both areas, except that the contribution of phytoplankton was higher for fish from the west Portuguese coast, where upwelling events are stronger and recurrent during spring and summer months. The predominance of prey <750 μm in sardine diet suggests that filter feeding is the dominant feeding mode used in the wild. Feeding intensity was similar for both sexes and for fish of different length classes and was higher on the west coast than in the south, which is probably related to the higher productivity of the west coast. Although there was high inter-annual variability in feeding intensity, this parameter was highest for both areas during spring and winter months. Temporal variability in satellite-derived chlorophyll a matched the temporal variability in the dietary contribution by phytoplankton and of sardine feeding intensity, suggesting further investigation of the potential use of satellite-derived chlorophyll a data as a proxy for sardine feeding intensity

Distributed Computing Grid Experiences in CMS

The CMS experiment is currently developing a computing system capable of serving, processing and archiving the large number of events that will be generated when the CMS detector starts taking data. During 2004 CMS undertook a large scale data challenge to demonstrate the ability of the CMS computing system to cope with a sustained data-taking rate equivalent to 25% of startup rate. Its goals were: to run CMS event reconstruction at CERN for a sustained period at 25 Hz input rate; to distribute the data to several regional centers; and enable data access at those centers for analysis. Grid middleware was utilized to help complete all aspects of the challenge. To continue to provide scalable access from anywhere in the world to the data, CMS is developing a layer of software that uses Grid tools to gain access to data and resources, and that aims to provide physicists with a user friendly interface for submitting their analysis jobs. This paper describes the data challenge experience with Grid infrastructure and the current development of the CMS analysis system

Risk Factors for Necrotizing Enterocolitis:A Prospective Multicenter Case-Control Study

BACKGROUND: The identification of independent clinical risk factors for necrotizing enterocolitis (NEC) may contribute to early selection of infants at risk, allowing for the development of targeted strategies aimed at the prevention of NEC. OBJECTIVE: The objective of this study was to identify independent risk factors contributing to the development of NEC in a large multicenter cohort. METHODS: This prospective cohort study was performed in 9 neonatal intensive care units. Infants born at a gestational age &lt;/=30 weeks were included. Demographic and clinical data were collected daily until day 28 postnatally. Factors predictive of the development of NEC were identified using univariate and multivariable analyses in a 1: 5 matched case-control cohort. RESULTS: In total, 843 infants (56 NEC cases) were included in this study. In the case-control cohort, univariate analysis identified sepsis prior to the onset of NEC and formula feeding to be associated with an increased risk of developing NEC, whereas the administration of antibiotics directly postpartum was inversely associated with NEC. In a multivariable logistic regression model, enteral feeding type and the number of days parenterally fed remained statistically significantly associated with NEC, whereas the administration of antibiotics directly after birth was associated with a lower risk of developing NEC. CONCLUSIONS: Formula feeding and prolonged (duration of) parenteral feeding were associated with an increased risk of NEC. Contrary to expectations, the initiation of treatment with antibiotics within 24 h after birth was inversely associated with NEC

Rehabilitation Enablement in Chronic Heart Failure—a facilitated self-care rehabilitation intervention in patients with heart failure with preserved ejection fraction (REACH-HFpEF) and their caregivers:rationale and protocol for a single-centre pilot randomised controlled trial

This is the final version of the article. Available from the publisher via the DOI in this record.INTRODUCTION: The Rehabilitation EnAblement in CHronic Heart Failure in patients with Heart Failure (HF) with preserved ejection fraction (REACH-HFpEF) pilot trial is part of a research programme designed to develop and evaluate a facilitated, home-based, self-help rehabilitation intervention to improve self-care and quality of life (QoL) in heart failure patients and their caregivers. We will assess the feasibility of a definitive trial of the REACH-HF intervention in patients with HFpEF and their caregivers. The impact of the REACH-HF intervention on echocardiographic outcomes and bloodborne biomarkers will also be assessed. METHODS AND ANALYSIS: A single-centre parallel two-group randomised controlled trial (RCT) with 1:1 individual allocation to the REACH-HF intervention plus usual care (intervention) or usual care alone (control) in 50 HFpEF patients and their caregivers. The REACH-HF intervention comprises a REACH-HF manual with supplementary tools, delivered by trained facilitators over 12 weeks. A mixed methods approach will be used to assess estimation of recruitment and retention rates; fidelity of REACH-HF manual delivery; identification of barriers to participation and adherence to the intervention and study protocol; feasibility of data collection and outcome burden. We will assess the variance in study outcomes to inform a definitive study sample size and assess methods for the collection of resource use and intervention delivery cost data to develop the cost-effectiveness analyses framework for any future trial. Patient outcomes collected at baseline, 4 and 6 months include QoL, psychological well-being, exercise capacity, physical activity and HF-related hospitalisation. Caregiver outcomes will also be assessed, and a substudy will evaluate impact of the REACH-HF manual on resting global cardiovascular function and bloodborne biomarkers in HFpEF patients. ETHICS AND DISSEMINATION: The study is approved by the East of Scotland Research Ethics Service (Ref: 15/ES/0036). Findings will be disseminated via journals and presentations to clinicians, commissioners and service users. TRIAL REGISTRATION NUMBER: ISRCTN78539530; Pre-results .This paper presents independent research funded by the National Institute for Health Research (NIHR) under its Programme Grants for Applied Research Programme (Grant Reference Number RP-PG-1210-12004). NB, CA, CJG and RST are also supported by the National Institute for Health Research (NIHR) Collaboration for Leadership in Applied Health Research and Care (CLAHRC) South West Peninsula at the Royal Devon and Exeter NHS Foundation Trust; KJ by CLAHRC West Midlands and SS by CLAHRC East-Midlands. The views expressed are those of the authors and not necessarily those of the NHS, the NIHR or the Department of Healt

Revisiting diagenesis on the Ontong Java Plateau: Evidence for authigenic crust precipitation in Globorotalia tumida

The calcite tests of foraminifera lie in marine sediments for thousands to millions of years, before being analysed to generate trace element and isotope palaeoproxy records. These sediments constitute a distinct physio-chemical environment from the conditions in which the tests formed. Storage in sediments can modify the trace element and isotopic content of foraminiferal calcite through diagenetic alteration, which has the potential to confound their palaeoceanographic interpretation. A previous study of G. tumida from the Ontong Java Plateau, western equatorial Pacific, found that preferential dissolution of higher-Mg chamber calcite, and the preservation of a low-Mg crust on the tests significantly reduced whole-test Mg/Ca and Sr/Ca [Brown and Elderfield, 1996]. Here, we revisit these specimens with a combination of synchrotron X-ray computed tomography (sXCT) and electron probe micro-analyses (EPMA) to re-evaluate the nature of their diagenetic alteration. The dissolution of higher-Mg calcite with depth was directly observed in the sXCT data, confirming the inference of the previous study. The sXCT data further reveal a thickening of the chemically and structurally distinct calcite crust with depth. We propose that these crusts have a diagenetic origin, driven by the simultaneous dissolution of high-Mg chamber calcite and precipitation of low-Mg crust from the resulting modified pore-water solution. While the breadth of the study is limited by the nature of the techniques, the observation of both dissolution and re-precipitation of foraminiferal calcite serves to demonstrate the action of two simultaneous diagenetic alteration processes, with significant impacts on the resulting palaeoproxy signals.The authors would like to acknowledge Aleksey Sadekov, Gerald Langer, India Weidle, Alberto de Fanis, Andrew Bodey, Joan Vila-Comamala and Ulrich Wagner for their help with the project. The work was funded by the Diamond Light Source and by the ERC (2010-NEWLOG ADG-267931 grant to HE).This is the author accepted manuscript. The final version is available from Wiley via http://dx.doi.org/10.1002/2014PA00275