The relationship between in-hospital location and outcomes of care in patients of a large general medical service

Background: The discrepancy between the number of admissions and the allocation of hospital beds means many patients admitted under the care of a general medical service can be placed in other departments’ wards. These patients are called “outliers” and their outcomes are unknown. Aims: To examine the relation between the proportion of time each patient spent in their “home ward” during an index admission and the outcomes of that hospital stay. Methods: Data from Flinders Medical Centre’s (FMC) patient journey database were extracted and analysed. The analysis was carried out on the patient journeys of patients admitted under the General Medicine units. Results: Outlier patients’ length of stay (LOS) was significantly shorter than that of the inlier patients (110.7 hours cf 141.9 hours; p < 0.001).They had a reduced risk of readmission within 28 days of discharge from hospital. Outlier patients’ discharge summaries were less likely to be completed within a week (64.3% cf 78.0%; p < 0.001). Being an outlier patient increased the risk-adjusted risk of in-hospital mortality by over 40%. 50% of deaths in the outlier group occurred within 48 hours of admission. Outlier patients had spent longer in the Emergency Department (ED) waiting for a bed (6.3 hours cf 5.3 hours; p < 0.001) but duration of ED stay was not an independent predictor of mortality risk. Conclusion: Outlier patients had significantly shorter LOS in hospital, but significantly greater in-patient death rates. Surviving outlier patients had lower rates of readmission but lower rates of discharge summary completion

The Ess/Type VII secretion system of Staphylococcus aureus shows unexpected genetic diversity

We thank the core sequencing and informatics teams at the Sanger Institute for their assistance and The Wellcome Trust for its support of the Sanger Institute Pathogen Genomics and Biology groups. SRH, JP and MTGH were supported by Wellcome Trust grant 098051. Bioinformatics and Computational Biology analyses were supported by the University of St Andrews Bioinformatics Unit that is funded by a Wellcome Trust ISSF award (grant 105621/Z/14/Z). SP is funded by the UKCRC Translational Infection Research Initiative, and the NIHR Cambridge Biomedical Research Centre. CPH is supported by the Wellcome Trust (grant number 104241/z/14/z) TP is a Royal Society/Wolfson Merit Award Holder.BACKGROUND: Type VII protein secretion (T7SS) is a specialised system for excreting extracellular proteins across bacterial cell membranes and has been associated with virulence in Staphylococcus aureus. The genetic diversity of the ess locus, which encodes the T7SS, and the functions of proteins encoded within it are poorly understood. RESULTS: We used whole genome sequence data from 153 isolates representative of the diversity of the species to investigate the genetic variability of T7SS across S. aureus. The ess loci were found to comprise of four distinct modules based on gene content and relative conservation. Modules 1 and 4, comprising of the 5' and 3' modules of the ess locus, contained the most conserved clusters of genes across the species. Module 1 contained genes encoding the secreted protein EsxA, and the EsaAB and EssAB components of the T7SS machinery, and Module 4 contained two functionally uncharacterized conserved membrane proteins. Across the species four variants of Module 2 were identified containing the essC gene, each of which was associated with a specific group of downstream genes. The most diverse module of the ess locus was Module 3 comprising a highly variable arrangement of hypothetical proteins. RNA-Seq was performed on representatives of the four Module 2 variants and demonstrated strain-specific differences in the levels of transcription in the conserved Module 1 components and transcriptional linkage Module 2, and provided evidence of the expression of genes the variable regions of the ess loci. CONCLUSIONS: The ess locus of S. aureus exhibits modularity and organisational variation across the species and transcriptional variation. In silico analysis of ess loci encoded hypothetical proteins identified potential novel secreted substrates for the T7SS. The considerable variety in operon arrangement between otherwise closely related isolates provides strong evidence for recombination at this locus. Comparison of these recombination regions with each other, and with the genomes of other Staphylococcal species, failed to identify evidence of intra- and inter-species recombination, however the analysis identified a novel T7SS in another pathogenic staphylococci, Staphylococcus lugdunensis.Publisher PDFPeer reviewe

P6_1 Bart the Daredevil

This paper examines the feasibility of a planned attempt by Bart Simpson to jump Springfield Gorge on a skateboard. In order to clear the gorge, we have calculated that Bart would need to reach a speed of $22\pm 4.3ms^{-1}$. In order to reach this speed we estimate the drop-in to Springfield Gorge would require an angle of descent $50$ degrees

P6_2 Would the Starkiller Base be able to eat our Sun?

Star Wars: The Force Awakens (2015) includes a large planet-like weapon fuelled by the intake of entire stars. Its diameter is approximated to be 658 km, and the concept of the Schwarzchild Radius is explored - establishing that a black hole would not be created in its core if it were to 'eat' the Sun

The Atacama Cosmology Telescope: Data Characterization and Map Making

We present a description of the data reduction and mapmaking pipeline used for the 2008 observing season of the Atacama Cosmology Telescope (ACT). The data presented here at 148 GHz represent 12% of the 90 TB collected by ACT from 2007 to 2010. In 2008 we observed for 136 days, producing a total of 1423 hours of data (11 TB for the 148 GHz band only), with a daily average of 10.5 hours of observation. From these, 1085 hours were devoted to a 850 deg^2 stripe (11.2 hours by 9.1 deg) centered on a declination of -52.7 deg, while 175 hours were devoted to a 280 deg^2 stripe (4.5 hours by 4.8 deg) centered at the celestial equator. We discuss sources of statistical and systematic noise, calibration, telescope pointing, and data selection. Out of 1260 survey hours and 1024 detectors per array, 816 hours and 593 effective detectors remain after data selection for this frequency band, yielding a 38% survey efficiency. The total sensitivity in 2008, determined from the noise level between 5 Hz and 20 Hz in the time-ordered data stream (TOD), is 32 micro-Kelvin sqrt{s} in CMB units. Atmospheric brightness fluctuations constitute the main contaminant in the data and dominate the detector noise covariance at low frequencies in the TOD. The maps were made by solving the least-squares problem using the Preconditioned Conjugate Gradient method, incorporating the details of the detector and noise correlations. Cross-correlation with WMAP sky maps, as well as analysis from simulations, reveal that our maps are unbiased at multipoles ell > 300. This paper accompanies the public release of the 148 GHz southern stripe maps from 2008. The techniques described here will be applied to future maps and data releases.Comment: 20 pages, 18 figures, 6 tables, an ACT Collaboration pape

The Atacama Cosmology Telescope: A Measurement of the Cosmic Microwave Background Power Spectrum at 148 and 218 GHz from the 2008 Southern Survey

We present measurements of the cosmic microwave background (CMB) power spectrum made by the Atacama Cosmology Telescope at 148 GHz and 218 GHz, as well as the cross-frequency spectrum between the two channels. Our results clearly show the second through the seventh acoustic peaks in the CMB power spectrum. The measurements of these higher-order peaks provide an additional test of the {\Lambda}CDM cosmological model. At l > 3000, we detect power in excess of the primary anisotropy spectrum of the CMB. At lower multipoles 500 < l < 3000, we find evidence for gravitational lensing of the CMB in the power spectrum at the 2.8{\sigma} level. We also detect a low level of Galactic dust in our maps, which demonstrates that we can recover known faint, diffuse signals.Comment: 19 pages, 13 figures. Submitted to ApJ. This paper is a companion to Hajian et al. (2010) and Dunkley et al. (2010

Evaluating the Sensitivity and Specificity of Siemens Clinitest Lateral Flow Test and the Simple AMplification-Based Assay (SAMBA)-2 PCR Test for SARS-CoV-2 Infection.

Introduction Accurate point-of-care testing for SARS-CoV-2 could quickly identify which patients need to be isolated and improve flow for patients being admitted as an emergency to the hospital. We evaluated two diagnostic tests with shorter turnaround times, the Siemens Clinitest Lateral Flow (Siemens Healthineers AG, Erlangen, Germany) and the Simple AMplification-Based Assay (SAMBA)-2 PCR test against a standard laboratory PCR test. Methods We conducted a prospective diagnostic cohort study in a single English emergency department. Adult participants underwent three swabs: the Siemens Clinitest Lateral Flow Test, the SAMBA-2 and a standard laboratory PCR test. Results A total of 212 participants were recruited. The sensitivity and specificity of the Siemens Clinitest Lateral Flow Test against the laboratory PCR test was 55.6% (95% CI 30.8-78.5) and 100% (95% CI 98.1-100) respectively. The sensitivity and specificity of the SAMBA-2 PCR test against the laboratory PCR test was 60.0% (95% CI 32.3-83.7) and 100% (95% CI 97.9-100) respectively. Conclusion Neither the Siemens Clinitest Lateral Flow Test nor the SAMBA-2 PCR test demonstrated sufficient sensitivity to rule out active SARS-CoV-2 infection. Both tests demonstrated high specificity

High-Content Imaging to Phenotype Antimicrobial Effects on Individual Bacteria at Scale.

High-content imaging (HCI) is a technique for screening multiple cells in high resolution to detect subtle morphological and phenotypic variation. The method has been commonly deployed on model eukaryotic cellular systems, often for screening new drugs and targets. HCI is not commonly utilized for studying bacterial populations but may be a powerful tool in understanding and combatting antimicrobial resistance. Consequently, we developed a high-throughput method for phenotyping bacteria under antimicrobial exposure at the scale of individual bacterial cells. Imaging conditions were optimized on an Opera Phenix confocal microscope (Perkin Elmer), and novel analysis pipelines were established for both Gram-negative bacilli and Gram-positive cocci. The potential of this approach was illustrated using isolates of Klebsiella pneumoniae, Salmonella enterica serovar Typhimurium, and Staphylococcus aureus HCI enabled the detection and assessment of subtle morphological characteristics, undetectable through conventional phenotypical methods, that could reproducibly distinguish between bacteria exposed to different classes of antimicrobials with distinct modes of action (MOAs). In addition, distinctive responses were observed between susceptible and resistant isolates. By phenotyping single bacterial cells, we observed intrapopulation differences, which may be critical in identifying persistence or emerging resistance during antimicrobial treatment. The work presented here outlines a comprehensive method for investigating morphological changes at scale in bacterial populations under specific perturbation.IMPORTANCE High-content imaging (HCI) is a microscopy technique that permits the screening of multiple cells simultaneously in high resolution to detect subtle morphological and phenotypic variation. The power of this methodology is that it can generate large data sets comprised of multiple parameters taken from individual cells subjected to a range of different conditions. We aimed to develop novel methods for using HCI to study bacterial cells exposed to a range of different antibiotic classes. Using an Opera Phenix confocal microscope (Perkin Elmer) and novel analysis pipelines, we created a method to study the morphological characteristics of Klebsiella pneumoniae, Salmonella enterica serovar Typhimurium, and Staphylococcus aureus when exposed to antibacterial drugs with differing modes of action. By imaging individual bacterial cells at high resolution and scale, we observed intrapopulation differences associated with different antibiotics. The outlined methods are highly relevant for how we begin to better understand and combat antimicrobial resistance