Cardiff University’s Condor Pool: background, case studies, and fEC

Cardiff University’s Condor pool aims to cater for the high throughput computing needs of a wide range of users based in various schools across campus. The paper begins by discussing the background of Cardiff University’s Condor pool. The paper then presents a selection of case studies and outlines our strategy for Condorising applications using submit script generators. Finally the paper presents the findings of a fEC exercise and outlines our policy for attributing directly allocated costs to a particular research project

Detection of Phosphorus and Nitrogen Deficiencies in Corn Using Spectral Radiance Measurements

Applications of remote sensing in crop production are becoming increasingly popular due in part to an increased concern with pollution of surface and ground waters due to over-fertilization of agricultural lands and the need to compensate for spatial variability in a field. Past research in this area has focused primarily on N stress in crops. Other stresses and the interactions have not been fully evaluated. A field experiment was conducted to determine wavelengths and/or combinations of wavelengths that are indicative of P and N deficiency and also the interaction between these in corn (Zea mays L.). The field experiment was a randomized complete block design with four replications using a factorial arrangement of treatments in an irrigated continuous corn system. The treatment included four N rates (0, 67, 134, and 269 kg N ha-1) and four P rates (0, 22, 45, and 67 kg P ha-1). Spectral radiance measurements were taken at various growth stages in increments from 350 to 1000 nm and correlated with plant N and P concentration, plant biomass, grain N and P concentration, and grain yield. Reflectance in the near-infrared (NIR) and blue regions was found to predict early season P stress between growth stages V6 and V8. Late season detection of P stress was not achieved. Plant N concentration was best predicted using reflectance in the red and green regions of the spectrum, while grain yield was estimated using reflectance in the NIR region, with the particular wavelengths of importance changing with growth stage

Fusing the horizons or why context matters: the interdependence of fieldwork and museum study in Mediterranean archaeology

In a recent JMA article (JMA 28.2, December 2015), Robin Osborne argued that Mediterranean archaeology places too much emphasis on fieldwork and too little on museum study. In doing so he has set up an antithesis between two kinds of archaeological practice: the former ‘in the field’, undertaken chiefly by specialists in prehistory, and the latter in the museum, undertaken principally by Classical archaeologists who are also experts in the traditional subjects of sculpture and vase painting. I argue that this antithesis is at best misleading, and a poor guide to how best to turn material evidence into historical knowledge. These issues are explored in relation to a set of case studies where recent survey and fieldwork have shed light on old ‘museum’ material, and where a reappraisal of that material has in turn affected research design in the field as well as historical interpretation. This study concentrates on the results of a number of fieldwork projects (both excavation and survey) covering Archaic and Classical material in eastern Crete, with a particular focus on first on pithoi (storage jars) found in the excavation of houses and then terracotta plaques from various sanctuary deposits. New fieldwork, conducted to modern standards, when combined with a reappraisal of older ‘museum’ material can, when conducted using a range of both new and traditional methods, yield new insights. This combination can offer a true ‘fusion of horizons’, in Gadamer’s (1975) sense

Rapid Optical Fluctuations in the Black Hole Binary, V4641 Sgr

We report on unprecedented short-term variations detected in the optical flux from the black hole binary system, V4641 Sgr. Amplitudes of the optical fluctuations were larger at longer time scales, and surprisingly reached ~60% around a period of ~10 min. The power spectra of fluctuations are characterized by a power law. It is the first case in black hole binaries that the optical emission was revealed to show short-term and large-amplitude variations given by such a power spectrum. The optical emission from black hole binaries is generally dominated by the emission from the outer portion of an accretion disc. The rapid optical fluctuations however indicate that the emission from an inner accretion region significantly contributes to the optical flux. In this case, cyclo-synchrotron emission associated with various scales of magnetic flares is the most promising mechanism for the violently variable optical emission.Comment: 5 pages, 2 figures, accepted for publication in PAS

American Society of Clinical Oncology/College ofAmerican Pathologists guideline recommendations forimmunohistochemical testing of estrogen andprogesterone receptors in breast cancer

Purpose: To develop a guideline to improve theaccuracy of immunohistochemical (IHC) estrogen receptor(ER) and progesterone receptor (PgR) testing in breastcancer and the utility of these receptors as predictivemarkers.Methods: The American Society of Clinical Oncologyand the College of American Pathologists convened aninternational Expert Panel that conducted a systematicreview and evaluation of the literature in partnership withCancer Care Ontario and developed recommendations foroptimal IHC ER/PgR testing performance.Results: Up to 20% of current IHC determinations ofER and PgR testing worldwide may be inaccurate (falsenegative or false positive). Most of the issues with testinghave occurred because of variation in preanalyticvariables, thresholds for positivity, and interpretationcriteria.Recommendations: The Panel recommends that ER andPgR status be determined on all invasive breast cancers andbreast cancer recurrences. A testing algorithm that relieson accurate, reproducible assay performance is proposed.Elements to reliably reduce assay variation are specified. It is recommended that ER and PgR assays be consideredpositive if there are at least 1% positive tumor nuclei in the sample on testing in the presence of expected reactivity of internal (normal epithelial elements) and external controls. The absence of benefit from endocrine therapy for women with ER-negative invasive breast cancers has been confirmed in large overviews of randomized clinical trials.(Arch Pathol Lab Med. 2010;134:907–922

A novel formulation of inhaled sodium cromoglicate (PA101) in idiopathic pulmonary fibrosis and chronic cough: a randomised, double-blind, proof-of-concept, phase 2 trial

Background Cough can be a debilitating symptom of idiopathic pulmonary fibrosis (IPF) and is difficult to treat. PA101 is a novel formulation of sodium cromoglicate delivered via a high-efficiency eFlow nebuliser that achieves significantly higher drug deposition in the lung compared with the existing formulations. We aimed to test the efficacy and safety of inhaled PA101 in patients with IPF and chronic cough and, to explore the antitussive mechanism of PA101, patients with chronic idiopathic cough (CIC) were also studied. Methods This pilot, proof-of-concept study consisted of a randomised, double-blind, placebo-controlled trial in patients with IPF and chronic cough and a parallel study of similar design in patients with CIC. Participants with IPF and chronic cough recruited from seven centres in the UK and the Netherlands were randomly assigned (1:1, using a computer-generated randomisation schedule) by site staff to receive PA101 (40 mg) or matching placebo three times a day via oral inhalation for 2 weeks, followed by a 2 week washout, and then crossed over to the other arm. Study participants, investigators, study staff, and the sponsor were masked to group assignment until all participants had completed the study. The primary efficacy endpoint was change from baseline in objective daytime cough frequency (from 24 h acoustic recording, Leicester Cough Monitor). The primary efficacy analysis included all participants who received at least one dose of study drug and had at least one post-baseline efficacy measurement. Safety analysis included all those who took at least one dose of study drug. In the second cohort, participants with CIC were randomly assigned in a study across four centres with similar design and endpoints. The study was registered with ClinicalTrials.gov (NCT02412020) and the EU Clinical Trials Register (EudraCT Number 2014-004025-40) and both cohorts are closed to new participants. Findings Between Feb 13, 2015, and Feb 2, 2016, 24 participants with IPF were randomly assigned to treatment groups. 28 participants with CIC were enrolled during the same period and 27 received study treatment. In patients with IPF, PA101 reduced daytime cough frequency by 31·1% at day 14 compared with placebo; daytime cough frequency decreased from a mean 55 (SD 55) coughs per h at baseline to 39 (29) coughs per h at day 14 following treatment with PA101, versus 51 (37) coughs per h at baseline to 52 (40) cough per h following placebo treatment (ratio of least-squares [LS] means 0·67, 95% CI 0·48–0·94, p=0·0241). By contrast, no treatment benefit for PA101 was observed in the CIC cohort; mean reduction of daytime cough frequency at day 14 for PA101 adjusted for placebo was 6·2% (ratio of LS means 1·27, 0·78–2·06, p=0·31). PA101 was well tolerated in both cohorts. The incidence of adverse events was similar between PA101 and placebo treatments, most adverse events were mild in severity, and no severe adverse events or serious adverse events were reported. Interpretation This study suggests that the mechanism of cough in IPF might be disease specific. Inhaled PA101 could be a treatment option for chronic cough in patients with IPF and warrants further investigation

Determinants of recovery from post-COVID-19 dyspnoea: analysis of UK prospective cohorts of hospitalised COVID-19 patients and community-based controls

Background The risk factors for recovery from COVID-19 dyspnoea are poorly understood. We investigated determinants of recovery from dyspnoea in adults with COVID-19 and compared these to determinants of recovery from non-COVID-19 dyspnoea. Methods We used data from two prospective cohort studies: PHOSP-COVID (patients hospitalised between March 2020 and April 2021 with COVID-19) and COVIDENCE UK (community cohort studied over the same time period). PHOSP-COVID data were collected during hospitalisation and at 5-month and 1-year follow-up visits. COVIDENCE UK data were obtained through baseline and monthly online questionnaires. Dyspnoea was measured in both cohorts with the Medical Research Council Dyspnoea Scale. We used multivariable logistic regression to identify determinants associated with a reduction in dyspnoea between 5-month and 1-year follow-up. Findings We included 990 PHOSP-COVID and 3309 COVIDENCE UK participants. We observed higher odds of improvement between 5-month and 1-year follow-up among PHOSP-COVID participants who were younger (odds ratio 1.02 per year, 95% CI 1.01–1.03), male (1.54, 1.16–2.04), neither obese nor severely obese (1.82, 1.06–3.13 and 4.19, 2.14–8.19, respectively), had no pre-existing anxiety or depression (1.56, 1.09–2.22) or cardiovascular disease (1.33, 1.00–1.79), and shorter hospital admission (1.01 per day, 1.00–1.02). Similar associations were found in those recovering from non-COVID-19 dyspnoea, excluding age (and length of hospital admission). Interpretation Factors associated with dyspnoea recovery at 1-year post-discharge among patients hospitalised with COVID-19 were similar to those among community controls without COVID-19. Funding PHOSP-COVID is supported by a grant from the MRC-UK Research and Innovation and the Department of Health and Social Care through the National Institute for Health Research (NIHR) rapid response panel to tackle COVID-19. The views expressed in the publication are those of the author(s) and not necessarily those of the National Health Service (NHS), the NIHR or the Department of Health and Social Care. COVIDENCE UK is supported by the UK Research and Innovation, the National Institute for Health Research, and Barts Charity. The views expressed are those of the authors and not necessarily those of the funders