DOOp, an automated wrapper for DAOSPEC

Large spectroscopic surveys such as the Gaia-ESO Survey produce huge quantities of data. Automatic tools are necessary to efficiently handle this material. The measurement of equivalent widths in stellar spectra is traditionally done by hand or with semi-automatic procedures that are time-consuming and not very robust with respect to the repeatability of the results. The program DAOSPEC is a tool that provides consistent measurements of equivalent widths in stellar spectra while requiring a minimum of user intervention. However, it is not optimised to deal with large batches of spectra, as some parameters still need to be modified and checked by the user. Exploiting the versatility and portability of BASH, we have built a pipeline called DAOSPEC Option Optimiser (DOOp) automating the procedure of equivalent widths measurement with DAOSPEC. DOOp is organised in different modules that run one after the other to perform specific tasks, taking care of the optimisation of the parameters needed to provide the final equivalent widths, and providing log files to ensure better control over the procedure. In this paper, making use of synthetic and observed spectra, we compare the performance of DOOp with other methods, including DAOSPEC used manually. The measurements made by DOOp are identical to the ones produced by DAOSPEC when used manually, while requiring less user intervention, which is convenient when dealing with a large quantity of spectra. DOOp shows its best performance on high-resolution spectra (R>20 000) and high signal-to-noise ratio (S/N>30), with uncertainties ranging from 6 m{\AA} to 2 m{\AA}. The only subjective parameter that remains is the normalisation, as the user still has to make a choice on the order of the polynomial used for the continuum fitting. As a test, we use the equivalent widths measured by DOOp to re-derive the stellar parameters of four well-studied stars

Glycaemic variability, infections and mortality in a medical-surgical intensive care unit.

In critically ill patients, glycaemic variability (GV) was reported as a better predictor of mortality than mean blood glucose level (BGL). We compared the ability of different GV indices and mean BGLs to predict mortality and intensive care unit-acquired infections in a population of ICU patients.Retrospective study on adult ICU patients with ≥ three BGL measurements. GV was assessed by SD, coefficient of variation (CV) and mean amplitude of glycaemic excursion (MAGE), and by one timeweighted index, the glycaemic lability index (GLI), and compared with mean BGL. We studied 2782 patients admitted to the 12-bed medical-surgical ICU of a teaching hospital from January 2004 until December 2010.Logistic regression analyses were performed to assess the association between GV and ICU mortality and ICU-acquired infections. The areas under receiver operating characteristic curves were calculated to compare the discriminatory ability of GV and mean BGL for infections and mortality.Mortality was 16.6%, and 30% of patients had at least one infection. Patients with infections or diabetes or who were treated with insulin had a higher mean BGL and GV than other patients. GLI, SD, CV and MAGE were significantly associated with infections and mortality; mean BGL was not. Quartiles of increasing GLI were independently associated with higher mortality and an increased infection rate. Patients in the upper quartile of mean BGL and GLI had the strongest association with infections (odds ratio, 5.044 [95% CI, 1.695-15.007]; P = 0.004).High GV is associated with higher risk of ICUCrit acquired infection and mortality

Multiple system atrophy is distinguished from idiopathic Parkinson's disease bythe arginine growth hormone stimulation test

Objective: Multiple system atrophy (MSA) may be difficult to distinguish from idiopathic Parkinson’s disease (PD). Our aim was to evaluate the accuracy of the arginine growth hormone (GH) stimulation test in distinguishing between MSA and PD in large populations of patients. Methods: We measured the GH response to arginine in 69 MSA (43 MSAp [parkinsonism as the main motor feature] and 26 MSAc [cerebellar features predominated]) patients, 35 PD patients, and 90 healthy control subjects. We used receiver-operating curve analysis to establish the arginine cutoff value that best differentiated between MSA and PD. Results: The GH response to arginine was significantly lower (p 0.01) in MSA than in either PD patients or control subjects. At a cutoff level of 4g/L, arginine distinguished MSAp from PD with a sensitivity and specificity of 91% and MSAc from PD with a sensitivity of 96% and specificity of 91%. The arginine test had a positive predictive value for MSA of 95%. The GH response to arginine was not affected by disease duration or severity, MSA motor subtype, pyramidal signs, response to dopaminergic therapy, or magnetic resonance imaging findings. Interpretation: The GH response to arginine differentiates MSA from PD with a high diagnostic accuracy. The results suggest an impairment of cholinergic central systems modulating GH release in MSA

Type 1 plasminogen activator inhibitor as a common risk factor for cancer and ischaemic vascular disease: the EPICOR study

OBJECTIVES: We examined the association of plasminogen activator inhibitor-1 (PAI-1) levels with colorectal cancer, breast cancer, acute coronary syndrome (ACS) and ischaemic stroke. DESIGN: Nested case-cohort study. SETTING: The European Prospective Investigation into Cancer and Nutrition-Italy cohort. PARTICIPANTS: A centre-stratified random sample of 850 participants (286 men, 564 women) was selected as subcohort and compared with 303 colorectal cancers, 617 breast cancers, 688 ACS and 158 ischaemic strokes, in a mean follow-up of 9.11 years. MAIN OUTCOMES AND MEASURES: Primary incident cases of colon cancer, breast cancer, ACS and ischaemic stroke. PAI-1 levels were measured in citrated plasma by ELISA. HR and 95% CI, adjusted by relevant confounders and stratified by centre, were estimated by a Cox regression model using Prentice method. RESULTS: Individuals in the highest compared with the lowest quartile of PAI-1 had significantly increased risk of colorectal cancer (RR=2.28; 95% CI 1.46 to 3.55; P for trend<0.0012), breast cancer (HR=1.70; 95% CI 1.21 to 2.39; p<0.0055), ACS (HR=2.57; 95% CI 1.75 to 3.77; p<0.001) and ischaemic stroke (HR=2.27; 95% CI 1.28 to 4.03; p<0.0017), after adjustment for sex and age. Additional adjustment for disease-specific confounders, insulin or other metabolic variables did not modify the associations. Risk of colon cancer was stronger for men and for whole and distal colon localisation. Risk for breast cancer was stronger in postmenopausal women. CONCLUSIONS: Our data provide the first evidence that elevated levels of PAI-1 are potential risk factors for colorectal and breast cancer and a common pathway for cancer and cardiovascular disease

DOOp: DAOSPEC Output Optimizer pipeline

The DAOSPEC Output Optimizer pipeline (DOOp) runs efficient and convenient equivalent widths measurements in batches of hundreds of spectra. It uses a series of BASH scripts to work as a wrapper for the FORTRAN code DAOSPEC (ascl:1011.002) and uses IRAF (ascl:9911.002) to automatically fix some of the parameters that are usually set by hand when using DAOSPEC. This allows batch-processing of quantities of spectra that would be impossible to deal with by hand. DOOp was originally built for the large quantity of UVES and GIRAFFE spectra produced by the Gaia-ESO Survey, but just like DAOSPEC, it can be used on any high resolution and high signal-to-noise ratio spectrum binned on a linear wavelength scale

Present and Future CP Measurements

We review theoretical and experimental results on CP violation summarizing the discussions in the working group on CP violation at the UK phenomenology workshop 2000 in Durham.Comment: 104 pages, Latex, to appear in Journal of Physics

The sacral chordoma margin

[Objective]: Aim of the manuscript is to discuss how to improve margins in sacral chordoma. [Background]: Chordoma is a rare neoplasm, arising in half cases from the sacrum, with reported local failure in >50% after surgery. [Methods]: A multidisciplinary meeting of the “Chordoma Global Consensus Group” was held in Milan in 2017, focusing on challenges in defining and achieving optimal margins in chordoma with respect to surgery, definitive particle radiation therapy (RT) and medical therapies. This review aims to report on the outcome of the consensus meeting and to provide a summary of the most recent evidence in this field. Possible new ways forward, including on-going international clinical studies, are discussed. [Results]: En-bloc tumor-sacrum resection is the cornerstone of treatment of primary sacral chordoma, aiming to achieve negative microscopic margins. Radical definitive particle therapy seems to offer a similar outcome compared to surgery, although confirmation in comparative trials is lacking; besides there is still a certain degree of technical variability across institutions, corresponding to different fields of treatment and different tumor coverage. To address some of these questions, a prospective, randomized international study comparing surgery versus definitive high-dose RT is ongoing. Available data do not support the routine use of any medical therapy as (neo)adjuvant/cytoreductive treatment. [Conclusion]: Given the significant influence of margins status on local control in patients with primary localized sacral chordoma, the clear definition of adequate margins and a standard local approach across institutions for both surgery and particle RT is vital for improving the management of these patients

Observation of Exclusive Gamma Gamma Production in p pbar Collisions at sqrt{s}=1.96 TeV

We have observed exclusive \gamma\gamma production in proton-antiproton collisions at \sqrt{s}=1.96 TeV, using data from 1.11 \pm 0.07 fb^{-1} integrated luminosity taken by the Run II Collider Detector at Fermilab. We selected events with two electromagnetic showers, each with transverse energy E_T > 2.5 GeV and pseudorapidity |\eta| < 1.0, with no other particles detected in -7.4 < \eta < +7.4. The two showers have similar E_T and azimuthal angle separation \Delta\phi \sim \pi; 34 events have two charged particle tracks, consistent with the QED process p \bar{p} to p + e^+e^- + \bar{p} by two-photon exchange, while 43 events have no charged tracks. The number of these events that are exclusive \pi^0\pi^0 is consistent with zero and is < 15 at 95% C.L. The cross section for p\bar{p} to p+\gamma\gamma+\bar{p} with |\eta(\gamma)| < 1.0 and E_T(\gamma) > 2.5$ GeV is 2.48^{+0.40}_{-0.35}(stat)^{+0.40}_{-0.51}(syst) pb.Comment: 7 pages, 4 figure