The Molecular Hydrogen Deficit in Gamma-Ray Burst Afterglows

Recent analysis of five gamma-ray burst (GRB) afterglow spectra reveal the absence of molecular hydrogen absorption lines, a surprising result in light of their large neutral hydrogen column densities and the detection of H$_2$ in similar, more local star-forming regions like 30 Doradus in the Large Magellanic Cloud (LMC). Observational evidence further indicates that the bulk of the neutral hydrogen column in these sight lines lies 100 pc beyond the progenitor and that H$_2$ was absent prior to the burst, suggesting that direct flux from the star, FUV background fields, or both suppressed its formation. We present one-dimensional radiation hydrodynamical models of GRB host galaxy environments, including self-consistent radiative transfer of both ionizing and Lyman-Werner photons, nine-species primordial chemistry with dust formation of H$_2$, and dust extinction of UV photons. We find that a single GRB progenitor is sufficient to ionize neutral hydrogen to distances of 50 - 100 pc but that a galactic Lyman-Werner background is required to dissociate the molecular hydrogen in the ambient ISM. Intensities of 0.1 - 100 times the Galactic mean are necessary to destroy H$_2$ in the cloud, depending on its density and metallicity. The minimum radii at which neutral hydrogen will be found in afterglow spectra is insensitive to the mass of the progenitor or the initial mass function (IMF) of its cluster, if present.Comment: 12 pages, 7 figures, accepted for Ap

A method for continuous monitoring of the Ground Reaction Force during daily activity

Theoretical models and experimental studies of bone remodeling have identified peak cyclic force levels (or cyclic tissue strain energy density), number of daily loading cycles, and load (strain) rate as possible contributors to bone modeling and remodeling stimulus. To test our theoretical model and further investigate the influence of mechanical forces on bone density, we have focused on the calcaneus as a model site loaded by calcaneal surface tractions which are predominantly determined by the magnitude of the external ground reaction force (GRF)

Helping System Engineers Bridge the Peaks

In our experience at NASA, system engineers generally follow the Twin Peaks approach when developing safety-critical systems. However, iterations between the peaks require considerable manual, and in some cases duplicate, effort. A significant part of the manual effort stems from the fact that requirements are written in English natural language rather than a formal notation. In this work, we propose an approach that enables system engineers to leverage formal requirements and automated test generation to streamline iterations, effectively "bridging the peaks". The key to the approach is a formal language notation that a) system engineers are comfortable with, b) is supported by a family of automated V&V tools, and c) is semantically rich enough to describe the requirements of interest. We believe the combination of formalizing requirements and providing tool support to automate the iterations will lead to a more efficient Twin Peaks implementation at NASA

The Health Halo Trend in UK Television Food Advertising Viewed by Children: The Rise of Implicit and Explicit Health Messaging in the Promotion of Unhealthy Foods

Monitoring the creative content within food marketing to children is strongly advocated by public health authorities, but few studies address the prevalence of health-related messaging in television adverts. Food and beverage adverts (n = 18,888 in 2008, n = 6664 in 2010) from UK television channels popular with children were coded and analyzed. Physical-activity depiction displayed an 18.8 percentage point increase from 2008 (4.4%) to 2010 (23.2%). Of the food adverts containing physical-activity depiction in 2010, 81.1% were for non-core foods. The appearance of health claims in food adverts in 2010 increased 4.1 percentage points from 2008 levels (20.7% to 24.8%) where the majority of food adverts featuring health and nutrition claims were for non-core foods (58.3%). Health-related (e.g., health/nutrition, weight loss/diet) appeals were used in 17.1% of food adverts during peak child-viewing times, rising to 33.0% of adverts shown on dedicated children’s channels in 2010. Implicit (physical activity) and explicit (health claims) health messages are increasingly prevalent in UK television food advertising viewed by children, and are frequently used to promote unhealthy foods. Policy makers in the UK should consider amendments to the existing statutory approach in order to address this issue

High-Redshift Starbursting Dwarf Galaxies Revealed by GRB Afterglows

We present a study of 15 long-duration gamma-ray burst (GRB) host galaxies at z>2. The GRBs are selected with available early-time afterglow spectra in order to compare interstellar medium (ISM) absorption-line properties with stellar properties of the host galaxies. In addition to five previously studied hosts, we consider new detections for the host galaxies of GRB050820 and GRB060206 and place 2-sigma upper limits to the luminosities of the remaining unidentified hosts. We examine the nature of the host galaxy population and find that (1) the UV luminosity distribution of GRB host galaxies is consistent with expectations from a UV luminosity weighted random galaxy population with a median luminosity of =0.1 L*; (2) there exists a moderate correlation between UV luminosity and SiII 1526 absorption width, which together with the observed large line widths of W(1526)>1.5 Ang for a large fraction of the objects suggests a galactic outflow driven velocity field in the host galaxies; (3) there is tentative evidence for a trend of declining ISM metallicity with decreasing galaxy luminosity in the star-forming galaxy population at z=2-4; (4) the interstellar UV radiation field is found ~ 35-350 times higher in GRB hosts than the Galactic mean value; and (5) additional galaxies are found at < 2" from the GRB host in all fields with known presence of strong MgII absorbers, but no additional faint galaxies are found at < 2" in fields without strong MgII absorbers. Our study confirms that the GRB host galaxies (with known optical afterglows) are representative of unobscured star-forming galaxies at z>2, and demonstrates that high spatial resolution images are necessary for an accurate identification of GRB host galaxies in the presence of strong intervening absorbers.Comment: 24 emulateapj pages, 24 figures, ApJ in press; full-resolution version available at http://lambda.uchicago.edu/public/tmp/ghost.pd

Structural Basis of PP2A Inhibition by Small t Antigen

The SV40 small t antigen (ST) is a potent oncoprotein that perturbs the function of protein phosphatase 2A (PP2A). ST directly interacts with the PP2A scaffolding A subunit and alters PP2A activity by displacing regulatory B subunits from the A subunit. We have determined the crystal structure of full-length ST in complex with PP2A A subunit at 3.1 Å resolution. ST consists of an N-terminal J domain and a C-terminal unique domain that contains two zinc-binding motifs. Both the J domain and second zinc-binding motif interact with the intra-HEAT-repeat loops of HEAT repeats 3–7 of the A subunit, which overlaps with the binding site of the PP2A B56 subunit. Intriguingly, the first zinc-binding motif is in a position that may allow it to directly interact with and inhibit the phosphatase activity of the PP2A catalytic C subunit. These observations provide a structural basis for understanding the oncogenic functions of ST

Whole Genome Resequencing Reveals Natural Target Site Preferences of Transposable Elements in Drosophila melanogaster

Transposable elements are mobile DNA sequences that integrate into host genomes using diverse mechanisms with varying degrees of target site specificity. While the target site preferences of some engineered transposable elements are well studied, the natural target preferences of most transposable elements are poorly characterized. Using population genomic resequencing data from 166 strains of Drosophila melanogaster, we identified over 8,000 new insertion sites not present in the reference genome sequence that we used to decode the natural target preferences of 22 families of transposable element in this species. We found that terminal inverted repeat transposon and long terminal repeat retrotransposon families present clade-specific target site duplications and target site sequence motifs. Additionally, we found that the sequence motifs at transposable element target sites are always palindromes that extend beyond the target site duplication. Our results demonstrate the utility of population genomics data for high-throughput inference of transposable element targeting preferences in the wild and establish general rules for terminal inverted repeat transposon and long terminal repeat retrotransposon target site selection in eukaryotic genomes

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals &lt;1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Infant BCG vaccination and risk of pulmonary and extrapulmonary tuberculosis throughout the life course: a systematic review and individual participant data meta-analysis.

BACKGROUND: BCG vaccines are given to more than 100 million children every year, but there is considerable debate regarding the effectiveness of BCG vaccination in preventing tuberculosis and death, particularly among older children and adults. We therefore aimed to investigate the age-specific impact of infant BCG vaccination on tuberculosis (pulmonary and extrapulmonary) development and mortality. METHODS: In this systematic review and individual participant data meta-analysis, we searched MEDLINE, Web of Science, BIOSIS, and Embase without language restrictions for case-contact cohort studies of tuberculosis contacts published between Jan 1, 1998, and April 7, 2018. Search terms included "mycobacterium tuberculosis", "TB", "tuberculosis", and "contact". We excluded cohort studies that did not provide information on BCG vaccination or were done in countries that did not recommend BCG vaccination at birth. Individual-level participant data for a prespecified list of variables, including the characteristics of the exposed participant (contact), the index case, and the environment, were requested from authors of all eligible studies. Our primary outcome was a composite of prevalent (diagnosed at or within 90 days of baseline) and incident (diagnosed more than 90 days after baseline) tuberculosis in contacts exposed to tuberculosis. Secondary outcomes were pulmonary tuberculosis, extrapulmonary tuberculosis, and mortality. We derived adjusted odds ratios (aORs) using mixed-effects, binary, multivariable logistic regression analyses with study-level random effects, adjusting for the variable of interest, baseline age, sex, previous tuberculosis, and whether data were collected prospectively or retrospectively. We stratified our results by contact age and Mycobacterium tuberculosis infection status. This study is registered with PROSPERO, CRD42020180512. FINDINGS: We identified 14 927 original records from our database searches. We included participant-level data from 26 cohort studies done in 17 countries in our meta-analysis. Among 68 552 participants, 1782 (2·6%) developed tuberculosis (1309 [2·6%] of 49 686 BCG-vaccinated participants vs 473 [2·5%] of 18 866 unvaccinated participants). The overall effectiveness of BCG vaccination against all tuberculosis was 18% (aOR 0·82, 95% CI 0·74-0·91). When stratified by age, BCG vaccination only significantly protected against all tuberculosis in children younger than 5 years (aOR 0·63, 95% CI 0·49-0·81). Among contacts with a positive tuberculin skin test or IFNγ release assay, BCG vaccination significantly protected against tuberculosis among all participants (aOR 0·81, 95% CI 0·69-0·96), participants younger than 5 years (0·68, 0·47-0·97), and participants aged 5-9 years (0·62, 0·38-0·99). There was no protective effect among those with negative tests, unless they were younger than 5 years (0·54, 0·32-0·90). 14 cohorts reported on whether tuberculosis was pulmonary or extrapulmonary (n=57 421). BCG vaccination significantly protected against pulmonary tuberculosis among all participants (916 [2·2%] in 41 119 vaccinated participants vs 334 [2·1%] in 16 161 unvaccinated participants; aOR 0·81, 0·70-0·94) but not against extrapulmonary tuberculosis (106 [0·3%] in 40 318 vaccinated participants vs 38 [0·2%] in 15 865 unvaccinated participants; 0·96, 0·65-1·41). In the four studies with mortality data, BCG vaccination was significantly protective against death (0·25, 0·13-0·49). INTERPRETATION: Our results suggest that BCG vaccination at birth is effective at preventing tuberculosis in young children but is ineffective in adolescents and adults. Immunoprotection therefore needs to be boosted in older populations. FUNDING: National Institutes of Health