COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access

Metabolomics has become a crucial phenotyping technique in a range of research fields including medicine, the life sciences, biotechnology and the environmental sciences. This necessitates the transfer of experimental information between research groups, as well as potentially to publishers and funders. After the initial efforts of the metabolomics standards initiative, minimum reporting standards were proposed which included the concepts for metabolomics databases. Built by the community, standards and infrastructure for metabolomics are still needed to allow storage, exchange, comparison and re-utilization of metabolomics data. The Framework Programme 7 EU Initiative ‘coordination of standards in metabolomics’ (COSMOS) is developing a robust data infrastructure and exchange standards for metabolomics data and metadata. This is to support workflows for a broad range of metabolomics applications within the European metabolomics community and the wider metabolomics and biomedical communities’ participation. Here we announce our concepts and efforts asking for re-engagement of the metabolomics community, academics and industry, journal publishers, software and hardware vendors, as well as those interested in standardisation worldwide (addressing missing metabolomics ontologies, complex-metadata capturing and XML based open source data exchange format), to join and work towards updating and implementing metabolomics standards

Effectiveness of EDACS Versus ADAPT Accelerated Diagnostic Pathways for Chest Pain: A Pragmatic Randomized Controlled Trial Embedded Within Practice

Study objective A 2-hour accelerated diagnostic pathway based on the Thrombolysis in Myocardial Infarction score, ECG, and troponin measures (ADAPT-ADP) increased early discharge of patients with suspected acute myocardial infarction presenting to the emergency department compared with standard care (from 11% to 19.3%). Observational studies suggest that an accelerated diagnostic pathway using the Emergency Department Assessment of Chest Pain Score (EDACS-ADP) may further increase this proportion. This trial tests for the existence and size of any beneficial effect of using the EDACS-ADP in routine clinical care. Methods This was a pragmatic randomized controlled trial of adults with suspected acute myocardial infarction, comparing the ADAPT-ADP and the EDACS-ADP. The primary outcome was the proportion of patients discharged to outpatient care within 6 hours of attendance, without subsequent major adverse cardiac event within 30 days. Results Five hundred fifty-eight patients were recruited, 279 in each arm. Sixty-six patients (11.8%) had a major adverse cardiac event within 30 days (ADAPT-ADP 29; EDACS-ADP 37); 11.1% more patients (95% confidence interval 2.8% to 19.4%) were identified as low risk in EDACS-ADP (41.6%) than in ADAPT-ADP (30.5%). No low-risk patients had a major adverse cardiac event within 30 days (0.0% [0.0% to 1.9%]). There was no difference in the primary outcome of proportion discharged within 6 hours (EDACS-ADP 32.3%; ADAPT-ADP 34.4%; difference −2.1% [−10.3% to 6.0%], P=.65). Conclusion There was no difference in the proportion of patients discharged early despite more patients being classified as low risk by the EDACS-ADP than the ADAPT-ADP. Both accelerated diagnostic pathways are effective strategies for chest pain assessment and resulted in an increased rate of early discharges compared with previously reported rates

Quadrupole moments of odd-A ⁵³⁻⁶³Mn: Onset of collectivity towards N = 40

The spectroscopic quadrupole moments of the odd–even Mn isotopes between N=28 and N=38 have been measured using bunched-beam collinear laser spectroscopy at ISOLDE, CERN. In order to increase sensitivity to the quadrupole interaction, the measurements have been done using a transition in the ion rather than in the atom, with the additional advantage of better spectroscopic efficiency. Since the chosen transition is from a metastable state, optical pumping in ISOLDE’s cooler and buncher (ISCOOL) was used to populate this state. The extracted quadrupole moments are compared to large-scale shell model predictions using three effective interactions, GXPF1A, LNPS and modified A3DA. The inclusion of both the 1νg9/2and 2νd5/2orbitals in the model space is shown to be necessary to reproduce the observed increase in the quadrupole deformation from N=36 onwards. Specifically, the inclusion of the 2νd5/2orbital induces an increase in neutron and proton excitations across the reduced gaps at N=40and Z=28, leading to an increase in deformation above N=36

BHPR research: qualitative1. Complex reasoning determines patients' perception of outcome following foot surgery in rheumatoid arhtritis

Background: Foot surgery is common in patients with RA but research into surgical outcomes is limited and conceptually flawed as current outcome measures lack face validity: to date no one has asked patients what is important to them. This study aimed to determine which factors are important to patients when evaluating the success of foot surgery in RA Methods: Semi structured interviews of RA patients who had undergone foot surgery were conducted and transcribed verbatim. Thematic analysis of interviews was conducted to explore issues that were important to patients. Results: 11 RA patients (9 ♂, mean age 59, dis dur = 22yrs, mean of 3 yrs post op) with mixed experiences of foot surgery were interviewed. Patients interpreted outcome in respect to a multitude of factors, frequently positive change in one aspect contrasted with negative opinions about another. Overall, four major themes emerged. Function: Functional ability & participation in valued activities were very important to patients. Walking ability was a key concern but patients interpreted levels of activity in light of other aspects of their disease, reflecting on change in functional ability more than overall level. Positive feelings of improved mobility were often moderated by negative self perception ("I mean, I still walk like a waddling duck”). Appearance: Appearance was important to almost all patients but perhaps the most complex theme of all. Physical appearance, foot shape, and footwear were closely interlinked, yet patients saw these as distinct separate concepts. Patients need to legitimize these feelings was clear and they frequently entered into a defensive repertoire ("it's not cosmetic surgery; it's something that's more important than that, you know?”). Clinician opinion: Surgeons' post operative evaluation of the procedure was very influential. The impact of this appraisal continued to affect patients' lasting impression irrespective of how the outcome compared to their initial goals ("when he'd done it ... he said that hasn't worked as good as he'd wanted to ... but the pain has gone”). Pain: Whilst pain was important to almost all patients, it appeared to be less important than the other themes. Pain was predominately raised when it influenced other themes, such as function; many still felt the need to legitimize their foot pain in order for health professionals to take it seriously ("in the end I went to my GP because it had happened a few times and I went to an orthopaedic surgeon who was quite dismissive of it, it was like what are you complaining about”). Conclusions: Patients interpret the outcome of foot surgery using a multitude of interrelated factors, particularly functional ability, appearance and surgeons' appraisal of the procedure. While pain was often noted, this appeared less important than other factors in the overall outcome of the surgery. Future research into foot surgery should incorporate the complexity of how patients determine their outcome Disclosure statement: All authors have declared no conflicts of interes

Shape staggering of midshell mercury isotopes from in-source laser spectroscopy compared with density-functional-theory and Monte Carlo shell-model calculations

Neutron-deficient 177−185Hg isotopes were studied using in-source laser resonance-ionization spectroscopy at the CERN-ISOLDE radioactive ion-beam facility in an experiment combining different detection methods tailored to the studied isotopes. These include either α-decay tagging or multireflection time-of-flight gating for isotope identification. The endpoint of the odd-even nuclear shape staggering in mercury was observed directly by measuring for the first time the isotope shifts and hyperfine structures of 177−180Hg. Changes in the mean-square charge radii for all mentioned isotopes, magnetic dipole, and electric quadrupole moments of the odd-A isotopes and arguments in favor of I=7/2 spin assignment for 177,179Hg were deduced. Experimental results are compared with density functional theory (DFT) and Monte Carlo shell model (MCSM) calculations. DFT calculations using Skyrme parametrizations predict a jump in the charge radius around the neutron N=104 midshell, with an odd-even staggering pattern related to the coexistence of nearly degenerate oblate and prolate minima. This near-degeneracy is highly sensitive to many aspects of the effective interaction, a fact that renders perfect agreement with experiments out of reach for current functionals. Despite this inherent difficulty, the SLy5s1 and a modified UNEDF1SO parametrization predict a qualitatively correct staggering that is off by two neutron numbers. MCSM calculations of states with the experimental spins and parities show good agreement for both electromagnetic moments and the observed charge radii. A clear mechanism for the origin of shape staggering within this context is identified: a substantial change in occupancy of the proton πh9/2 and neutron νi13/2 orbitals

Goulder and the Gospels

The value of Michael Goulder's contribution to Gospel studies is underlined by uncovering both strengths and weaknesses in his work. Goulder's theories are divisible into three major areas and are analysed in the three parts of this thesis, Part One on Luke's knowledge of Matthew, Part Two on the creativity of the evangelists and Part Three on the lectionary theory. A screening of 'QC' Words discovers Matthean and Lucan vocabulary in roughly equal proportions, a conclusion detrimental to Goulder's theory that Matthew composed the Q material and that Luke copied it from him. Goulder argues strongly on the Minor Agreements that Matthean, un-Lucan language could indicate Luke's knowledge of Matthew. At least six Minor Agreements satisfy these criteria but one or two satisfy the reverse criteria. Goulder's arguments over the Minor Agreements require revision but still provide problems for a 'hardline' Two-Source Theory. Goulder's case that the L material is the substantial handiwork of the evangelist is plausible given the distinctiveness of many of the features he lists, but the data also suggests that Luke interacted with oral traditions. There is much to commend in Goulder's lectionary theory, particularly the strengths of the correspondences adduced, but there are difficulties which may be insurmountable.</p

UV resonance Raman spectroscopy: a process analytical tool for host cell DNA and RNA dynamics in mammalian cell lines

BACKGROUND Recent advances in Raman spectroscopy have resulted in the development of rapid, in situ Raman probes that can identify and allow the assessment of the quality of complex constituents in mammalian cell culture. One specific Raman technique, UV resonance Raman (UVRR) spectroscopy, has potential as a probe for residual cellular DNA and RNA in mammalian cell culture medium. RESULTS Variations in DNA and RNA UVRR spectral profiles of medium-cellular footprint samples were identified and related to time of harvest and increased cell lysis that is associated with a loss in cell viability. Increased DNA and RNA were also observed in the cell culture supernatant in response to sodium butyrate treatment. Variation in DNA and RNA profiles as a result of both primary and secondary clarification methods during downstream bioprocessing could also be determined with UVRR spectroscopy. CONCLUSIONS This study has demonstrated the utility of UVRR spectroscopy as a tool to monitor variations in residual DNA and RNA that may contaminate cell culture medium. Application of this technique has the potential for both improvement of recovery techniques and assurance of reliable clearance of DNA/RNA to acceptable safety level