Comparison of classical multi-locus sequence typing software for next-generation sequencing data

Multi-locus sequence typing (MLST) is a widely used method for categorizing bacteria. Increasingly, MLST is being performed using next-generation sequencing (NGS) data by reference laboratories and for clinical diagnostics. Many software applications have been developed to calculate sequence types from NGS data; however, there has been no comprehensive review to date on these methods. We have compared eight of these applications against real and simulated data, and present results on: (1) the accuracy of each method against traditional typing methods, (2) the performance on real outbreak datasets, (3) the impact of contamination and varying depth of coverage, and (4) the computational resource requirements

Black Hole Attractors and the Topological String

A simple relationship of the form Z_BH = |Z_top|^2 is conjectured, where Z_BH is a supersymmetric partition function for a four-dimensional BPS black hole in a Calabi-Yau compactification of Type II superstring theory and Z_top is a second-quantized topological string partition function evaluated at the attractor point in moduli space associated to the black hole charges. Evidence for the conjecture in a perturbation expansion about large graviphoton charge is given. The microcanonical ensemble of BPS black holes can be viewed as the Wigner function associated to the wavefunction defined by the topological string partition function.Comment: 32 pages, harvma

The COS-Dwarfs Survey: The Carbon Reservoir Around sub-L* Galaxies

We report new observations of circumgalactic gas from the COS-Dwarfs survey, a systematic investigation of the gaseous halos around 43 low-mass z $\leq$ 0.1 galaxies using background QSOs observed with the Cosmic Origins Spectrograph. From the projected 1D and 2D distribution of C IV absorption, we find that C IV absorption is detected out to ~ 0.5 R$_{vir}$ of the host galaxies. The C IV absorption strength falls off radially as a power law and beyond 0.5 R$_{vir}$, no C IV absorption is detected above our sensitivity limit of ~ 50-100 m$\AA$. We find a tentative correlation between detected C IV absorption strength and star formation, paralleling the strong correlation seen in highly ionized oxygen for L~L* galaxies by the COS-Halos survey. The data imply a large carbon reservoir in the CGM of these galaxies, corresponding to a minimum carbon mass of $\gtrsim$ 1.2$\times 10^6$ $M_\odot$ out to ~ 110 kpc. This mass is comparable to the carbon mass in the ISM and more than the carbon mass currently in stars of these galaxies. The C IV absorption seen around these sub-L* galaxies can account for almost two-thirds of all $W_r$> 100 m$\AA$ C IV absorption detected at low z. Comparing the C IV covering fraction with hydrodynamical simulations, we find that an energy-driven wind model is consistent with the observations whereas a wind model of constant velocity fails to reproduce the CGM or the galaxy properties.Comment: 18 Pages, 11 Figures, ApJ 796 13

African Bush Viper Envenomation: A Case Report

Atheris squamigera envenomation is an infrequently documented occurrence in the United States (US). Cases of envenomation may induce severe coagulopathies, renal failure, and potentially life-threatening hemorrhage. Currently, there are no antivenoms specific to the Atheris genus, but there have been documented cases of the use of antivenoms for other species. A 26-year-old man presented to the emergency department (ED) complaining of swelling and discomfort in his left foot after being bitten by an Atheris squamigera that he kept as a pet.After performing a physical exam, it was noted that the patient’s envenomation was likely mild. Throughout his hospital stay, he developed lab abnormalities, most notably an elevated D-dimer and low fibrinogen. His clinical symptoms improved after a short stay, and he did not require antivenom treatment. This case highlights a rare, but potentially life-threatening envenomation that may be encountered in the US due to the continued practice of exotic pet ownership and sales. Moreover, procurement of antivenom for non-native species poses a unique challenge to US physicians responsible for treating these patients