Characterizing the Low-Redshift Intergalactic Medium towards PKS1302-102

We present a detailed analysis of the intergalactic metal-line absorption systems in the archival HST/STIS and FUSE ultraviolet spectra of the low-redshift quasar PKS1302-102 (z_QSO = 0.2784). We supplement the archive data with CLOUDY ionization models and a survey of galaxies in the quasar field. There are 15 strong Lya absorbers with column densities logN_HI > 14. Of these, six are associated with at least CIII 977 absorption (logN(C^++) > 13); this implies a redshift density dN_CIII/dz = 36+13/-9 (68% confidence limits) for the five detections with rest equivalent width W_r > 50 mA. Two systems show OVI 1031,1037 absorption in addition to CIII (logN(O^+5) > 14). One is a partial Lyman limit system (logN_HI = 17) with associated CIII, OVI, and SiIII 1206 absorption. There are three tentative OVI systems that do not have CIII detected. For one OVI doublet with both lines detected at 3 sigma with W_r > 50 mA, dN_OVI/dz = 7+9/-4. We also search for OVI doublets without Lya absorption but identify none. From CLOUDY modeling, these metal-line systems have metallicities spanning the range -4 < [M/H] < -0.3. The two OVI systems with associated CIII absorption cannot be single-phase, collisionally-ionized media based on the relative abundances of the metals and kinematic arguments. From the galaxy survey, we discover that the absorption systems are in a diverse set of galactic environments. Each metal-line system has at least one galaxy within 500 km/s and 600 h^-1 kpc with L > 0.1 L_*.Comment: 21 pages in emulatepj form, 24 figures, 10 tables, accepted to Ap

Probing the IGM/Galaxy Connection IV: The LCO/WFCCD Galaxy Survey of 20 Fields Surrounding UV Bright Quasars

We publish the survey for galaxies in 20 fields containing ultraviolet bright quasars (with z_em 0.1 to 0.5) that can be used to study the association between galaxies and absorption systems from the low-z intergalactic medium (IGM). The survey is magnitude limited (R~19.5 mag) and highly complete out to 10' from the quasar in each field. It was designed to detect dwarf galaxies (L ~ 0.1 L*) at an impact parameter rho 1Mpc (z=0.1) from a quasar. The complete sample (all 20 fields) includes R-band photometry for 84718 sources and confirmed redshifts for 2800 sources. This includes 1198 galaxies with 0.005 < z < (z_em - 0.01) at a median redshift of 0.18, which may associated with IGM absorption lines. All of the imaging was acquired with cameras on the Swope 40" telescope and the spectra were obtained via slitmask observations using the WFCCD spectrograph on the Dupont 100" telescope at Las Campanas Observatory (LCO). This paper describes the data reduction, imaging analysis, photometry, and spectral analysis of the survey. We tabulate the principal measurements for all sources in each field and provide the spectroscopic dataset online.Comment: Accepted to the Astrophysical Journal Supplements; 20 pages, only 6 figures shown in this version. See http://www.ucolick.org/~xavier/WFCCDOVI/index.html for a full-length manuscript and other supportive materia

Mining Primary Care Electronic Health Records for Automatic Disease Phenotyping: A Transparent Machine Learning Framework

(1) Background: We aimed to develop a transparent machine-learning (ML) framework to automatically identify patients with a condition from electronic health records (EHRs) via a parsimonious set of features. (2) Methods: We linked multiple sources of EHRs, including 917,496,869 primary care records and 40,656,805 secondary care records and 694,954 records from specialist surgeries between 2002 and 2012, to generate a unique dataset. Then, we treated patient identification as a problem of text classification and proposed a transparent disease-phenotyping framework. This framework comprises a generation of patient representation, feature selection, and optimal phenotyping algorithm development to tackle the imbalanced nature of the data. This framework was extensively evaluated by identifying rheumatoid arthritis (RA) and ankylosing spondylitis (AS). (3) Results: Being applied to the linked dataset of 9657 patients with 1484 cases of rheumatoid arthritis (RA) and 204 cases of ankylosing spondylitis (AS), this framework achieved accuracy and positive predictive values of 86.19% and 88.46%, respectively, for RA and 99.23% and 97.75% for AS, comparable with expert knowledge-driven methods. (4) Conclusions: This framework could potentially be used as an efficient tool for identifying patients with a condition of interest from EHRs, helping clinicians in clinical decision-support process

Frequency and characteristics of disease flares in ankylosing spondylitis

Objective. To examine the characteristics and frequency of disease flares in a cohort of people with AS

Rapid measurement of antituberculosis drug activity in vitro and in macrophages using bioluminescence

OBJECTIVES: Tuberculosis drug development is hampered by the slow growth of Mycobacterium tuberculosis. Bioluminescence, light produced by an enzymatic reaction, constitutes a rapid and highly sensitive measurement of cell metabolic function that can be used as an indirect marker of cell viability in drug screening assays. The aim of this work was to validate and standardize the use of luminescent M. tuberculosis strains to test the activity of antibacterial drugs in vitro and inside macrophages in a 96-well format. METHODS: We have used strains that express the bacterial lux operon and therefore do not require exogenous substrate to produce light, as well as strains expressing the firefly luciferase that need luciferin substrate. Results were compared with those obtained using the resazurin reduction assay and cfu plating. RESULTS: Using bioluminescence we were able to reduce the time required to measure the MIC and bactericidal concentrations of antimicrobials to just 3 and 6 days, respectively. Furthermore, antibacterial activity against intracellular mycobacteria was detected within 2 days post-infection. Results were comparable to those obtained by conventional methods. CONCLUSIONS: We have developed a simple and rapid method for screening antimycobacterial drugs in culture and in macrophages. The use of autoluminescent bacteria also facilitates the determination of growth and inhibition kinetics. The method is cost-effective, can easily be adapted to a larger scale and is amenable to automation. Current efforts are directed towards applying this technology to drug screening in vivo

Proton pump inhibitors and dementia risk: Evidence from a cohort study using linked routinely collected national health data in Wales, UK

Objectives: Proton pump inhibitors (PPIs) are commonly prescribed for prevention and treatment of gastrointestinal conditions or for gastroprotection from other drugs. Research suggests they are linked to increased dementia risk. We use linked national health data to examine the association between PPI use and the development of incident dementia. Methods and findings: A population-based study using electronic health-data from the Secure Anonymised Information Linkage (SAIL) Databank, Wales (UK) from 1999 to 2015. Of data available on 3,765,744 individuals, a cohort who had ever been prescribed a PPI was developed (n=183,968) for people aged 55 years and over and compared to non-PPI exposed individuals (131,110). Those with prior dementia, mild-cognitive-impairment or delirium codes were excluded. Confounding factors included comorbidities and/or drugs associated with them. Comorbidities might include head injury and some examples of medications include antidepressants, antiplatelets and anticoagulants. These commonly prescribed drugs were investigated as it was not feasible to explore all drugs in this study. The main outcome was a diagnosis of incident dementia. Cox proportional hazard regression modelling was used to calculate the Hazard ratio (HR) of developing dementia in PPI-exposed compared to unexposed individuals while controlling for potential confounders. The mean age of the PPI exposed individuals was 69.9 years and 39.8% male while the mean age of the unexposed individuals was 72.1 years and 41.1% male. The rate of PPI usage was 58.4% (183,968) and incident dementia rate was 11.8% (37,148/315,078). PPI use was associated with decreased dementia risk (HR: 0.67, 95% CI: 0.65 to 0.67, p<0.01). Conclusions: This study, using large-scale, multi-centre health-data was unable to confirm an association between PPI use and increased dementia risk. Previously reported links may be associated with confounders of people using PPI’s, such as increased risk of cardiovascular disease and/or depression and their associated medications which may be responsible for any increased risk of developing dementia

The Cosmic Ultraviolet Baryon Survey (CUBS) I. Overview and the diverse environments of Lyman limit systems at z<1

We present initial results from the Cosmic Ultraviolet Baryon Survey (CUBS). CUBS is designed to map diffuse baryonic structures at redshift z<~1 using absorption-line spectroscopy of 15 UV-bright QSOs with matching deep galaxy survey data. CUBS QSOs are selected based on their NUV brightness to avoid biases against the presence of intervening Lyman Limit Systems (LLSs) at zabs~ 17.2 over a total redshift survey pathlength of dz=9.3, and a number density of n(z)=0.43 (-0.18, +0.26). Considering all absorbers with log N(HI)/cm^-2 > 16.5 leads to n(z)=1.08 (-0.25, +0.31) at z<1. All LLSs exhibit a multi-component structure and associated metal transitions from multiple ionization states such as CII, CIII, MgII, SiII, SiIII, and OVI absorption. Differential chemical enrichment levels as well as ionization states are directly observed across individual components in three LLSs. We present deep galaxy survey data obtained using the VLT-MUSE integral field spectrograph and the Magellan Telescopes, reaching sensitivities necessary for detecting galaxies fainter than 0.1L* at d<~300 physical kpc (pkpc) in all five fields. A diverse range of galaxy properties is seen around these LLSs, from a low-mass dwarf galaxy pair, a co-rotating gaseous halo/disk, a star-forming galaxy, a massive quiescent galaxy, to a galaxy group. The closest galaxies have projected distances ranging from d=15 to 72 pkpc and intrinsic luminosities from ~0.01L* to ~3L*. Our study shows that LLSs originate in a variety of galaxy environments and trace gaseous structures with a broad range of metallicities.Comment: 26 pages, 14 figures, MNRAS in pres