Real Time Global Tests of the ALICE High Level Trigger Data Transport Framework

The High Level Trigger (HLT) system of the ALICE experiment is an online event filter and trigger system designed for input bandwidths of up to 25 GB/s at event rates of up to 1 kHz. The system is designed as a scalable PC cluster, implementing several hundred nodes. The transport of data in the system is handled by an object-oriented data flow framework operating on the basis of the publisher-subscriber principle, being designed fully pipelined with lowest processing overhead and communication latency in the cluster. In this paper, we report the latest measurements where this framework has been operated on five different sites over a global north-south link extending more than 10,000 km, processing a ``real-time'' data flow.Comment: 8 pages 4 figure

From ‘other’ to involved: User involvement in research: An emerging paradigm

This article has been made available through the Brunel Open Access Publishing Fund. Copyright @ 2013 The Author(s). This is an Open Access article. Non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly attributed, cited, and is not altered, transformed, or built upon in any way, is permitted. The moral rights of the named author(s) have been asserted.This article explores the issue of ‘othering’ service users and the role that involving them, particularly in social policy and social work research may play in reducing this. It takes, as its starting point, the concept of ‘social exclusion’, which has developed in Europe and the marginal role that those who have been included in this construct have played in its development and the damaging effects this may have. The article explores service user involvement in research and is itself written from a service user perspective. It pays particular attention to the ideological, practical, theoretical, ethical and methodological issues that such user involvement may raise for research. It examines problems that both research and user involvement may give rise to and also considers developments internationally to involve service users/subjects of research, highlighting some of the possible implications and gains of engaging service user knowledge in research and the need for this to be evaluated

Reflections and Experiences of a Co-Researcher involved in a Renal Research Study

Background Patient and Public Involvement (PPI) is seen as a prerequisite for health research. However, current Patient and public involvement literature has noted a paucity of recording of patient and public involvement within research studies. There have been calls for more recordings and reflections, specifically on impact. Renal medicine has also had similar criticisms and any reflections on patient and public involvement has usually been from the viewpoint of the researcher. Roles of patient and public involvement can vary greatly from sitting on an Advisory Group to analysing data. Different PPI roles have been described within studies; one being a co-researcher. However, the role of the co-researcher is largely undefined and appears to vary from study to study. Methods The aims of this paper are to share one first time co-researcher's reflections on the impact of PPI within a mixed methods (non-clinical trial) renal research study. A retrospective, reflective approach was taken using data available to the co-researcher as part of the day-to-day research activity. Electronic correspondence and documents such as meeting notes, minutes, interview thematic analysis and comments on documents were re-examined. The co-researcher led on writing this paper. Results This paper offers a broad definition of the role of the co-researcher. The co-researcher reflects on undertaking and leading on the thematic analysis of interview transcripts, something she had not previously done before. The co-researcher identified a number of key themes; the differences in time and responsibility between being a coresearcher and an Advisory Group member; how the role evolved and involvement activities could match the co-researchers strengths (and the need for flexibility); the need for training and support and lastly, the time commitment. It was also noted that it is preferable that a co-researcher needs to be involved from the very beginning of the grant application. Conclusions The reflections, voices and views of those undertaking PPI has been largely underrepresented in the literature. The role of co-researcher was seen to be rewarding but demanding, requiring a large time commitment. It is hoped that the learning from sharing this experience will encourage others to undertake this role, and encourage researchers to reflect on the needs of those involved.Peer reviewedFinal Published versio

Understanding the errors of SHAPE-directed RNA structure modeling

Single-nucleotide-resolution chemical mapping for structured RNA is being rapidly advanced by new chemistries, faster readouts, and coupling to computational algorithms. Recent tests have shown that selective 2'-hydroxyl acylation by primer extension (SHAPE) can give near-zero error rates (0-2%) in modeling the helices of RNA secondary structure. Here, we benchmark the method using six molecules for which crystallographic data are available: tRNA(phe) and 5S rRNA from Escherichia coli, the P4-P6 domain of the Tetrahymena group I ribozyme, and ligand-bound domains from riboswitches for adenine, cyclic di-GMP, and glycine. SHAPE-directed modeling of these highly structured RNAs gave an overall false negative rate (FNR) of 17% and a false discovery rate (FDR) of 21%, with at least one helix prediction error in five of the six cases. Extensive variations of data processing, normalization, and modeling parameters did not significantly mitigate modeling errors. Only one varation, filtering out data collected with deoxyinosine triphosphate during primer extension, gave a modest improvement (FNR = 12%, and FDR = 14%). The residual structure modeling errors are explained by the insufficient information content of these RNAs' SHAPE data, as evaluated by a nonparametric bootstrapping analysis. Beyond these benchmark cases, bootstrapping suggests a low level of confidence (<50%) in the majority of helices in a previously proposed SHAPE-directed model for the HIV-1 RNA genome. Thus, SHAPE-directed RNA modeling is not always unambiguous, and helix-by-helix confidence estimates, as described herein, may be critical for interpreting results from this powerful methodology.Comment: Biochemistry, Article ASAP (Aug. 15, 2011

Three-dimensionally Ordered Macroporous Structure Enabled Nanothermite Membrane of Mn2O3/Al

Mn2O3 has been selected to realize nanothermite membrane for the first time in the literature. Mn2O3/Al nanothermite has been synthesized by magnetron sputtering a layer of Al film onto three-dimensionally ordered macroporous (3DOM) Mn2O3 skeleton. The energy release is significantly enhanced owing to the unusual 3DOM structure, which ensures Al and Mn2O3 to integrate compactly in nanoscale and greatly increase effective contact area. The morphology and DSC curve of the nanothermite membrane have been investigated at various aluminizing times. At the optimized aluminizing time of 30 min, energy release reaches a maximum of 2.09 kJ∙g−1, where the Al layer thickness plays a decisive role in the total energy release. This method possesses advantages of high compatibility with MEMS and can be applied to other nanothermite systems easily, which will make great contribution to little-known nanothermite research

Prospects for K+→π+ννˉK^+ \to \pi^+ \nu \bar{ \nu } at CERN in NA62

The NA62 experiment will begin taking data in 2015. Its primary purpose is a 10% measurement of the branching ratio of the ultrarare kaon decay $K^+ \to \pi^+ \nu \bar{ \nu }$, using the decay in flight of kaons in an unseparated beam with momentum 75 GeV/c.The detector and analysis technique are described here.Comment: 8 pages for proceedings of 50 Years of CP

Exploring the challenge of health research priority setting in partnership: reflections on the methodology used by the James Lind Alliance Pressure Ulcer Priority Setting Partnership

Background: Studies identifying a mismatch between the priorities of academics and clinicians and those of people with direct experience of a health condition pose a challenge to the assumption that professional researchers can represent the interests of patients and the public in setting priorities for health research. The James Lind Alliance (JLA) brings patients, carers and clinicians together in Priority Setting Partnerships (PSPs) to identify and prioritise shared uncertainties about the effects of treatment. There is no formal evaluation yet to examine the different approaches used by individual PSPs and the impact these methods have on the quality of the partnership and subsequent outputs. There is no gold standard method for health research topic identification and priority setting and reporting on public involvement in this area is predominantly descriptive rather than evaluative. Methods and Findings: The JLA Pressure Ulcer PSP (JLAPUP) was developed and worked between 2009 and 2013 to identify and prioritise the top 10 ‘uncertainties’, or ‘unanswered questions’, about the effects of pressure ulcer interventions. JLAPUP identified a mismatch between the nature and quality of RCTs in pressure ulcer prevention and treatment and the kind of research evidence desired by patients or service users, carers and health professionals. Results and methods have been reported fully elsewhere. The consultative and deliberative methods used to establish health research priorities in PSPs are fundamentally interpretive. PSPs are therefore an arena in which ‘hard’ evidence-informed ideals meet ‘soft’ participatory practices. This article provides an account of the challenges faced in one particular PSP. We explain the rationale for the approaches taken, difficulties faced and the limitations at each stage, because these aspects are particularly under-reported. The JLAPUP case is used to identify possible areas for evaluation and reporting across PSPs. Conclusion: Engaging people with very different health and life experiences in the complexities of health science based discussions of uncertainty is challenging. This is particularly the case when engaging groups routinely excluded from participating in health research, for example, older people with multiple comorbidities. The JLA principles of transparency, inclusivity and avoiding waste in research require paying close critical attention to PSP methodology, including full evaluation and reporting of PSP processes and outcomes. Assessing the impact of PSPs is contingent on the decision making processes of commissioners and funders

Re-structuring hedges: rejuvenation management can improve the long term quality of hedgerow habitats for wildlife in the UK

Hedgerows provide key wildlife habitat in intensive agricultural landscapes, but are declining in length and structural condition due to a lack of rejuvenation management, neglect and over-frequent trimming with mechanised flails. Here, we test cheaper, alternative methods to traditional hedge laying methods using a multi-site manipulative field experiment. In the first quantitative test of new approaches to hedge rejuvenation management, hedge regrowth, structure, berry provision for over-wintering wildlife and cost of rejuvenation were assessed in response to five methods, for three years following rejuvenation. Three ‘laying’ methods and coppicing were effective at improving hedgerow condition by stimulating basal regrowth, thus increasing the density of woody material at the base and reducing gap size. The pros and cons of coppicing are discussed in relation to its impact on different wildlife groups, and it is recommended in limited circumstances. Differences between the three ‘laying’ methods reduced over time, so a cheaper conservation hedging method is recommended as an alternative to traditional hedge laying. This new approach to hedge management offers the potential to restore twice the length of hedgerow currently rejuvenated under agri-environment schemes

Precision Determination of the Neutron Spin Structure Function g1n

We report on a precision measurement of the neutron spin structure function $g^n_1$ using deep inelastic scattering of polarized electrons by polarized ^3He. For the kinematic range 0.014<x<0.7 and 1 (GeV/c)^2< Q^2< 17 (GeV/c)^2, we obtain $\int^{0.7}_{0.014} g^n_1(x)dx = -0.036 \pm 0.004 (stat) \pm 0.005 (syst)$ at an average $Q^2=5 (GeV/c)^2$. We find relatively large negative values for $g^n_1$ at low $x$. The results call into question the usual Regge theory method for extrapolating to x=0 to find the full neutron integral $\int^1_0 g^n_1(x)dx$, needed for testing quark-parton model and QCD sum rules.Comment: 5 pages, 3 figures To be published in Phys. Rev. Let