The XMM-Newton serendipitous survey. VII. The third XMM-Newton serendipitous source catalogue

Thanks to the large collecting area (3 x ~1500 cm$^2$ at 1.5 keV) and wide field of view (30' across in full field mode) of the X-ray cameras on board the European Space Agency X-ray observatory XMM-Newton, each individual pointing can result in the detection of hundreds of X-ray sources, most of which are newly discovered. Recently, many improvements in the XMM-Newton data reduction algorithms have been made. These include enhanced source characterisation and reduced spurious source detections, refined astrometric precision, greater net sensitivity and the extraction of spectra and time series for fainter sources, with better signal-to-noise. Further, almost 50\% more observations are in the public domain compared to 2XMMi-DR3, allowing the XMM-Newton Survey Science Centre (XMM-SSC) to produce a much larger and better quality X-ray source catalogue. The XMM-SSC has developed a pipeline to reduce the XMM-Newton data automatically and using improved calibration a new catalogue version has been produced from XMM-Newton data made public by 2013 Dec. 31 (13 years of data). Manual screening ensures the highest data quality. This catalogue is known as 3XMM. In the latest release, 3XMM-DR5, there are 565962 X-ray detections comprising 396910 unique X-ray sources. For the 133000 brightest sources, spectra and lightcurves are provided. For all detections, the positions on the sky, a measure of the quality of the detection, and an evaluation of the X-ray variability is provided, along with the fluxes and count rates in 7 X-ray energy bands, the total 0.2-12 keV band counts, and four hardness ratios. To identify the detections, a cross correlation with 228 catalogues is also provided for each X-ray detection. 3XMM-DR5 is the largest X-ray source catalogue ever produced. Thanks to the large array of data products, it is an excellent resource in which to find new and extreme objects.Comment: 23 pages, version accepted for publication in A&

Relationship between aerodynamic roughness length and bulk sedge leaf area index in a mixed-species boreal mire complex

Leaf area index (LAI) is an important parameter in natural ecosystems, representing the seasonal development of vegetation and photosynthetic potential. However, direct measurement techniques require labor-intensive field campaigns that are usually limited in time, while remote sensing approaches often do not yield reliable estimates. Here we propose that the bulk LAI of sedges (LAI(s)) can be estimated alternatively from a micrometeorological parameter, the aerodynamic roughness length for momentum (z(0)). z(0) can be readily calculated from high-response turbulence and other meteorological data, typically measured continuously and routinely available at ecosystem research sites. The regressions of LAI versus z(0) were obtained using the data from two Finnish natural sites representative of boreal fen and bog ecosystems. LAI(s) was found to be well correlated with z(0) and sedge canopy height. Superior method performance was demonstrated in the fen ecosystem where the sedges make a bigger contribution to overall surface roughness than in bogs.Peer reviewe

Paschen-alpha Emission in the Gravitationally Lensed Galaxy SMM J163554.2+661225

We report the detection of the Paschen-alpha emission line in the z=2.515 galaxy SMM J163554.2+661225 using Spitzer spectroscopy. SMM J163554.2+661225 is a sub-millimeter-selected infrared (IR)-luminous galaxy maintaining a high star-formation rate (SFR), with no evidence of an AGN from optical or infrared spectroscopy, nor X-ray emission. This galaxy is lensed gravitationally by the cluster Abell 2218, making it accessible to Spitzer spectroscopy. Correcting for nebular extinction derived from the H-alpha and Pa-alpha lines, the dust-corrected luminosity is L(Pa-alpha) = (2.57+/-0.43) x 10^43 erg s^-1, which corresponds to an ionization rate, Q = (1.6+/-0.3) x 10^55 photons s^-1. The instantaneous SFR is 171+/-28 solar masses per year, assuming a Salpeter-like initial mass function. The total IR luminosity derived using 70, 450, and 850 micron data is L(IR) = (5-10) x 10^11 solar luminosities, corrected for gravitational lensing. This corresponds to a SFR=90-180 solar masses per year, where the upper range is consistent with that derived from the Paschen-alpha luminosity. While the L(8 micron) / L(Pa-alpha) ratio is consistent with the extrapolated relation observed in local galaxies and star-forming regions, the rest-frame 24 micron luminosity is significantly lower with respect to local galaxies of comparable Paschen-alpha luminosity. Thus, SMM J163554.2+661225 arguably lacks a warmer dust component (T ~ 70 K), which is associated with deeply embedded star formation, and which contrasts with local galaxies with comparable SFRs. Rather, the starburst is consistent with star-forming local galaxies with intrinsic luminosities, L(IR) ~ 10^10 solar luminosities, but "scaled-up" by a factor of 10-100.Comment: Published in the Astrophysical Journal. 14 pages in emulateapj format, 9 figures (many in color

ABCB1 (MDR1) polymorphisms and ovarian cancer progression and survival: A comprehensive analysis from the Ovarian Cancer Association Consortium and The Cancer Genome Atlas

<b>Objective</b> <i>ABCB1</i> encodes the multi-drug efflux pump P-glycoprotein (P-gp) and has been implicated in multi-drug resistance. We comprehensively evaluated this gene and flanking regions for an association with clinical outcome in epithelial ovarian cancer (EOC).<p></p> <b>Methods</b> The best candidates from fine-mapping analysis of 21 <i>ABCB1</i> SNPs tagging C1236T (rs1128503), G2677T/A (rs2032582), and C3435T (rs1045642) were analysed in 4616 European invasive EOC patients from thirteen Ovarian Cancer Association Consortium (OCAC) studies and The Cancer Genome Atlas (TCGA). Additionally we analysed 1,562 imputed SNPs around ABCB1 in patients receiving cytoreductive surgery and either ‘standard’ first-line paclitaxel–carboplatin chemotherapy (n = 1158) or any first-line chemotherapy regimen (n = 2867). We also evaluated ABCB1 expression in primary tumours from 143 EOC patients.<p></p> <b>Result</b> Fine-mapping revealed that rs1128503, rs2032582, and rs1045642 were the best candidates in optimally debulked patients. However, we observed no significant association between any SNP and either progression-free survival or overall survival in analysis of data from 14 studies. There was a marginal association between rs1128503 and overall survival in patients with nil residual disease (HR 0.88, 95% CI 0.77–1.01; p = 0.07). In contrast, <i>ABCB1</i> expression in the primary tumour may confer worse prognosis in patients with sub-optimally debulked tumours.<p></p> <b>Conclusion</b> Our study represents the largest analysis of <i>ABCB1</i> SNPs and EOC progression and survival to date, but has not identified additional signals, or validated reported associations with progression-free survival for rs1128503, rs2032582, and rs1045642. However, we cannot rule out the possibility of a subtle effect of rs1128503, or other SNPs linked to it, on overall survival.<p></p&gt

Computer Law Institute

Materials from the Computer Law Institute held by UK/CLE in May 1999

Mechanisms of Severe Acute Respiratory Syndrome Coronavirus-Induced Acute Lung Injury

ABSTRACT Systems biology offers considerable promise in uncovering novel pathways by which viruses and other microbial pathogens interact with host signaling and expression networks to mediate disease severity. In this study, we have developed an unbiased modeling approach to identify new pathways and network connections mediating acute lung injury, using severe acute respiratory syndrome coronavirus (SARS-CoV) as a model pathogen. We utilized a time course of matched virologic, pathological, and transcriptomic data within a novel methodological framework that can detect pathway enrichment among key highly connected network genes. This unbiased approach produced a high-priority list of 4 genes in one pathway out of over 3,500 genes that were differentially expressed following SARS-CoV infection. With these data, we predicted that the urokinase and other wound repair pathways would regulate lethal versus sublethal disease following SARS-CoV infection in mice. We validated the importance of the urokinase pathway for SARS-CoV disease severity using genetically defined knockout mice, proteomic correlates of pathway activation, and pathological disease severity. The results of these studies demonstrate that a fine balance exists between host coagulation and fibrinolysin pathways regulating pathological disease outcomes, including diffuse alveolar damage and acute lung injury, following infection with highly pathogenic respiratory viruses, such as SARS-CoV.IMPORTANCESevere acute respiratory syndrome coronavirus (SARS-CoV) emerged in 2002 and 2003, and infected patients developed an atypical pneumonia, acute lung injury (ALI), and acute respiratory distress syndrome (ARDS) leading to pulmonary fibrosis and death. We identified sets of differentially expressed genes that contribute to ALI and ARDS using lethal and sublethal SARS-CoV infection models. Mathematical prioritization of our gene sets identified the urokinase and extracellular matrix remodeling pathways as the most enriched pathways. By infecting Serpine1-knockout mice, we showed that the urokinase pathway had a significant effect on both lung pathology and overall SARS-CoV pathogenesis. These results demonstrate the effective use of unbiased modeling techniques for identification of high-priority host targets that regulate disease outcomes. Similar transcriptional signatures were noted in 1918 and 2009 H1N1 influenza virus-infected mice, suggesting a common, potentially treatable mechanism in development of virus-induced ALI

The Early Youth Engagement in first episode psychosis (EYE-2) study: pragmatic cluster randomised controlled trial of implementation, effectiveness and cost-effectiveness of a team-based motivational engagement intervention to improve engagement

Background: Early Intervention in Psychosis (EIP) services improve health outcomes for young people with psychosis in the medium–long term, but 25% of young people disengage in the first 12 months with costs to their mental health, families, society and the NHS. This study will evaluate the effectiveness, cost-effectiveness and implementation of a team-based motivational Early Youth Engagement (EYE-2) intervention. Method: The study design is a cluster randomised controlled trial (RCT) with economic evaluation, comparing the EYE-2 intervention + standardised EIP service to standardised EIP service alone, with randomisation at the team level. A process evaluation will evaluate the delivery of the intervention qualitatively and quantitatively across contexts. The setting is 20 EIP teams in 5 sites: Manchester, South London, East Anglia, Thames Valley and Hampshire. Participants are young people (14–35 years) with first episode psychosis, and EIP staff. The intervention is the team-based motivational engagement (EYE-2) intervention, delivered alongside standardised EIP services, and supported by additional training, website, booklets and social groups. The comparator is the standardised EIP service. Both interventions are delivered by EIP clinicians. The primary outcome is time to disengagement (time in days from date of allocation to care coordinator to date of last contact following refusal to engage with EIP service, or lack of response to EIP contact for a consecutive 3-month period). Secondary outcomes include mental and physical health, deaths, social and occupational function, recovery, satisfaction and service use at 6, 12, 18 and 24 months. A 12-month within-trial economic evaluation will investigate cost-effectiveness from a societal perspective and from an NHS perspective. Discussion: The trial will provide the first test of an engagement intervention in standardised care, with the potential for significant impact on the mental health and wellbeing of young people and their families, and economic benefits for services. The intervention will be highly scalable, supported by the toolkit including manuals, commissioning guide, training and resources, adapted to meet the needs of the diverse EIP population, and based on an in-depth process evaluation. Trial registration: ISRCTN 51629746 prospectively registered 7th May 2019. Date assigned 10th May 2019

Measurement of the production of a W boson in association with a charm quark in pp collisions at √s = 7 TeV with the ATLAS detector

The production of a W boson in association with a single charm quark is studied using 4.6 fb−1 of pp collision data at s√ = 7 TeV collected with the ATLAS detector at the Large Hadron Collider. In events in which a W boson decays to an electron or muon, the charm quark is tagged either by its semileptonic decay to a muon or by the presence of a charmed meson. The integrated and differential cross sections as a function of the pseudorapidity of the lepton from the W-boson decay are measured. Results are compared to the predictions of next-to-leading-order QCD calculations obtained from various parton distribution function parameterisations. The ratio of the strange-to-down sea-quark distributions is determined to be 0.96+0.26−0.30 at Q 2 = 1.9 GeV2, which supports the hypothesis of an SU(3)-symmetric composition of the light-quark sea. Additionally, the cross-section ratio σ(W + +c¯¯)/σ(W − + c) is compared to the predictions obtained using parton distribution function parameterisations with different assumptions about the s−s¯¯¯ quark asymmetry