The NumPy array: a structure for efficient numerical computation

International audienceIn the Python world, NumPy arrays are the standard representation for numerical data. Here, we show how these arrays enable efficient implementation of numerical computations in a high-level language. Overall, three techniques are applied to improve performance: vectorizing calculations, avoiding copying data in memory, and minimizing operation counts. We first present the NumPy array structure, then show how to use it for efficient computation, and finally how to share array data with other libraries

The Nature of Optically Dull Active Galactic Nuclei in COSMOS

We present infrared, optical, and X-ray data of 48 X-ray bright, optically dull AGNs in the COSMOS field. These objects exhibit the X-ray luminosity of an active galactic nucleus (AGN) but lack broad and narrow emission lines in their optical spectrum. We show that despite the lack of optical emission lines, most of these optically dull AGNs are not well-described by a typical passive red galaxy spectrum: instead they exhibit weak but significant blue emission like an unobscured AGN. Photometric observations over several years additionally show significant variability in the blue emission of four optically dull AGNs. The nature of the blue and infrared emission suggest that the optically inactive appearance of these AGNs cannot be caused by obscuration intrinsic to the AGNs. Instead, up to ~70% of optically dull AGNs are diluted by their hosts, with bright or simply edge-on hosts lying preferentially within the spectroscopic aperture. The remaining ~30% of optically dull AGNs have anomalously high f_x/f_o ratios and are intrinsically weak, not obscured, in the optical. These optically dull AGNs are best described as a weakly accreting AGN with a truncated accretion disk from a radiatively inefficient accretion flow.Comment: 12 pages, 10 figures. Accepted for publication in the Ap

Identification of immunodominant T cell epitopes induced by natural Zika virus infection

Zika virus (ZIKV) is a flavivirus primarily transmitted by Aedes species mosquitoes, first discovered in Africa in 1947, that disseminated through Southeast Asia and the Pacific Islands in the 2000s. The first ZIKV infections in the Americas were identified in 2014, and infections exploded through populations in Brazil and other countries in 2015/16. ZIKV infection during pregnancy can cause severe brain and eye defects in offspring, and infection in adults has been associated with higher risks of Guillain-Barré syndrome. We initiated a study to describe the natural history of Zika (the disease) and the immune response to infection, for which some results have been reported. In this paper, we identify ZIKV-specific CD4+ and CD8+ T cell epitopes that induce responses during infection. Two screening approaches were utilized: an untargeted approach with overlapping peptide arrays spanning the entire viral genome, and a targeted approach utilizing peptides predicted to bind human MHC molecules. Immunoinformatic tools were used to identify conserved MHC class I supertype binders and promiscuous class II binding peptide clusters predicted to bind 9 common class II alleles. T cell responses were evaluated in overnight IFN-γ ELISPOT assays. We found that MHC supertype binding predictions outperformed the bulk overlapping peptide approach. Diverse CD4+ T cell responses were observed in most ZIKV-infected participants, while responses to CD8+ T cell epitopes were more limited. Most individuals developed a robust T cell response against epitopes restricted to a single MHC class I supertype and only a single or few CD8+ T cell epitopes overall, suggesting a strong immunodominance phenomenon. Noteworthy is that many epitopes were commonly immunodominant across persons expressing the same class I supertype. Nearly all of the identified epitopes are unique to ZIKV and are not present in Dengue viruses. Collectively, we identified 31 immunogenic peptides restricted by the 6 major class I supertypes and 27 promiscuous class II epitopes. These sequences are highly relevant for design of T cell-targeted ZIKV vaccines and monitoring T cell responses to Zika virus infection and vaccination

Emotion aside or emotional side?:Crafting an ‘experience of involvement’ in the news

In relation to journalism, the concept of ‘emotion’ is consistently undertheorized. Employed with commonsensical discernment, it is conflated with tabloid practices, sensationalism, bias, commercialization, and the like. Consequently, when discussed, emotion is often treated dismissively; a marker of unprincipled and flawed journalism. Yet hard, self-styled objective, ‘just the facts’ journalism is not unemotional, just as soft, so-called tabloid news is not irrational. As authors who study the sociology of emotions note, emotion has a social component and can more broadly be conceptualized as the experience of involvement. This article utilizes this understanding to interrogate traditional news dichotomies before applying this perspective to consider non-valorized news alternatives. One significant change over the past few decades is not that the news has become emotional (indeed, it has always been); rather, the diversity of emotional styles, the acceptability of journalistic involvement, and attempts to involve the audience have become more explicit