Near infrared spectroscopy of the type IIn SN 2010jl: evidence for high velocity ejecta

The Type IIn supernova SN 2010jl was relatively nearby and luminous, allowing detailed studies of the near-infrared (NIR) emission. We present 1 - 2.4 micron spectroscopy over the age range of 36 - 565 days from the earliest detection of the supernova. On day 36, the H lines show an unresolved narrow emission component along with a symmetric broad component that can be modeled as the result of electron scattering by a thermal distribution of electrons. Over the next hundreds of days, the broad components of the H lines shift to the blue by 700 km/s, as is also observed in optical lines. The narrow lines do not show a shift, indicating they originate in a different region. He I 1.0830 and 2.0587 micron lines both show an asymmetric broad emission component, with a shoulder on the blue side that varies in prominence and velocity from -5500 km/s on day 108 to -4000 km/s on day 219. This component may be associated with the higher velocity flow indicated by X-ray observations of the supernova. The absence of the feature in the H lines suggests that this is from a He rich ejecta flow. The He I 1.0830 micron feature has a narrow P Cygni line, with absorption extending to ~100 km/s and strengthening over the first 200 days, and an emission component which weakens with time. At day 403, the continuum emission becomes dominated by a blackbody spectrum with a temperature of ~1900 K, suggestive of dust emission.Comment: 17 pages, 18 figure

Hubble Space Telescope WFPC2 Imaging of SN 1979C and Its Environment

The locations of supernovae in the local stellar and gaseous environment in galaxies contain important clues to their progenitor stars. As part of a program to study the environments of supernovae using Hubble Space Telescope (HST) imaging data, we have examined the environment of the Type II-L SN 1979C in NGC 4321 (M100). We place more rigorous constraints on the mass of the SN progenitor, which may have had a mass M \approx 17--18 M_sun. Moreover, we have recovered and measured the brightness of SN 1979C, m=23.37 in F439W (~B; m_B(max) = 11.6), 17 years after explosion. .Comment: 18 pages, 8 figures, submitted to PAS

Aboveground carbon responses to experimental and natural hurricane impacts in a subtropical wet forest in Puerto Rico

Climate change and disturbance make it difficult to project long-term patterns of carbon sequestration in tropical forests, but large ecosystem experiments in these forests can inform predictions. The Canopy Trimming Experiment (CTE) manipulates two key components of hurricane disturbance, canopy openness and detritus deposition, in a tropical forest in Puerto Rico. We documented how the CTE and a real hurricane affected tree recruitment, biomass, and aboveground carbon storage over 15 years. In the CTE treatments, we trimmed branches, but we did not fell trees. We expected that during the 14-year period after initial canopy trimming, regrowth of branches and stems and stem recruitment stimulated by increased light and trimmed debris would help restore biomass and carbon loss due to trimming. Compared to control plots, in the trimmed plots recruitment of palms and dicot trees increased markedly after trimming, and stem diameters of standing trees increased. Data showed that recruitment of small trees adds little to aboveground carbon, compared to the amount in large trees. Nevertheless, this response restored pretreatment biomass and carbon in the experimental period. In particular, the experimental additions of trimmed debris on the forest floor seemed to stimulate increase in aboveground carbon. Toward the end of the experimental period, Hurricane Maria (Category 4 hurricane) trimmed and felled some trees but reduced aboveground carbon less in the plots (including untrimmed plots) than experimental trimming had. Thus, it appears that the amount of regrowth recorded after experimental trimming could also restore aboveground carbon in the forest after a severe hurricane in the same time span. However, Hurricane Maria, unlike the trimming treatments, felled large trees, and it may be that with predicted, more frequent severe hurricanes, that the continued loss of large trees would over the long term decrease aboveground carbon stored in this Puerto Rican forest and likewise in other tropical forests affected by cyclonic storms

A Synthetic Genetic Edge Detection Program

SummaryEdge detection is a signal processing algorithm common in artificial intelligence and image recognition programs. We have constructed a genetically encoded edge detection algorithm that programs an isogenic community of E. coli to sense an image of light, communicate to identify the light-dark edges, and visually present the result of the computation. The algorithm is implemented using multiple genetic circuits. An engineered light sensor enables cells to distinguish between light and dark regions. In the dark, cells produce a diffusible chemical signal that diffuses into light regions. Genetic logic gates are used so that only cells that sense light and the diffusible signal produce a positive output. A mathematical model constructed from first principles and parameterized with experimental measurements of the component circuits predicts the performance of the complete program. Quantitatively accurate models will facilitate the engineering of more complex biological behaviors and inform bottom-up studies of natural genetic regulatory networks

Photometric Observations of Three High Mass X-Ray Binaries and a Search for Variations Induced by Orbital Motion

We searched for long period variation in V-band, Ic-band and RXTE X-ray light curves of the High Mass X-ray Binaries (HMXBs) LS 1698 / RX J1037.5-5647, HD 110432 / 1H 1249-637 and HD 161103 / RX J1744.7-2713 in an attempt to discover orbitally induced variation. Data were obtained primarily from the ASAS database and were supplemented by shorter term observations made with the 24- and 40-inch ANU telescopes and one of the robotic PROMPT telescopes. Fourier periodograms suggested the existence of long period variation in the V-band light curves of all three HMXBs, however folding the data at those periods did not reveal convincing periodic variation. At this point we cannot rule out the existence of long term V-band variation for these three sources and hints of longer term variation may be seen in the higher precision PROMPT data. Long term V-band observations, on the order of several years, taken at a frequency of at least once per week and with a precision of 0.01 mag, therefore still have a chance of revealing long term variation in these three HMXBs.Comment: Accepted, RAA, May, 201

Biogenesis of Influenza A Virus Hemagglutinin Cross-Protective Stem Epitopes

Antigenic variation in the globular domain of influenza A virus (IAV) hemagglutinin (HA) precludes effective immunity to this major human pathogen. Although the HA stem is highly conserved between influenza virus strains, HA stem-reactive antibodies (StRAbs) were long considered biologically inert. It is now clear, however, that StRAbs reduce viral replication in animal models and protect against pathogenicity and death, supporting the potential of HA stem-based immunogens as drift-resistant vaccines. Optimally designing StRAb-inducing immunogens and understanding StRAb effector functions require thorough comprehension of HA stem structure and antigenicity. Here, we study the biogenesis of HA stem epitopes recognized in cells infected with various drifted IAV H1N1 strains using mouse and human StRAbs. Using a novel immunofluorescence (IF)-based assay, we find that human StRAbs bind monomeric HA in the endoplasmic reticulum (ER) and trimerized HA in the Golgi complex (GC) with similar high avidity, potentially good news for producing effective monomeric HA stem immunogens. Though HA stem epitopes are nestled among several N-linked oligosaccharides, glycosylation is not required for full antigenicity. Rather, as N-linked glycans increase in size during intracellular transport of HA through the GC, StRAb binding becomes temperature-sensitive, binding poorly to HA at 4°C and well at 37°C. A de novo designed, 65-residue protein binds the mature HA stem independently of temperature, consistent with a lack of N-linked oligosaccharide steric hindrance due to its small size. Likewise, StRAbs bind recombinant HA carrying simple N-linked glycans in a temperature-independent manner. Chemical cross-linking experiments show that N-linked oligosaccharides likely influence StRAb binding by direct local effects rather than by globally modifying the conformational flexibility of HA. Our findings indicate that StRAb binding to HA is precarious, raising the possibility that sufficient immune pressure on the HA stem region could select for viral escape mutants with increased steric hindrance from N-linked glycans.</p

Optical and Ultraviolet Spectroscopy of SN 1995N: Evidence for Strong Circumstellar Interaction

Optical and ultraviolet observations of the Type IIn supernova SN 1995N at epochs between 321 and 1799 days after the explosion show three distinct velocity components. The narrow lines come from circumstellar gas and show both low and high ionization. This component has a low filling factor and is photoionized by X-rays from the shock. The intermediate component, which is dominated by newly processed oxygen, originates in a shell with velocity of 2500-5000 km s-1 and most likely comes from the ejecta. The hydrogen- and helium-dominated gas has a low ionization, a high density, and velocities that extend out to 10,000 km s-1. Strong signatures of Lyα-pumped fluorescence lines of Fe II are seen in the near-infrared and ultraviolet. The He/H ratio, ~0.3 by number, and the nitrogen overabundance provide strong evidence for CNO-burning products. The fluxes of the broad hydrogen and helium lines decrease considerably faster than the oxygen lines. The Hα line profile shows strong evolution, with the red wing decreasing faster than the blue. Possible scenarios, involving either a clumpy circumstellar medium or an aspherical distribution of the surrounding gas, are discussed based on the line profiles and physical conditions. Finally, we propose that Type IIn supernovae have their origin in red supergiants in a superwind phase

The Mutational signature comprehensive analysis toolkit (musicatk) for the discovery, prediction, and exploration of mutational signatures

Mutational signatures are patterns of somatic alterations in the genome caused by carcinogenic exposures or aberrant cellular processes. To provide a comprehensive workflow for preprocessing, analysis, and visualization of mutational signatures, we created the Mutational Signature Comprehensive Analysis Toolkit (musicatk) package. musicatk enables users to select different schemas for counting mutation types and to easily combine count tables from different schemas. Multiple distinct methods are available to deconvolute signatures and exposures or to predict exposures in individual samples given a pre-existing set of signatures. Additional exploratory features include the ability to compare signatures to the Catalogue Of Somatic Mutations In Cancer (COSMIC) database, embed tumors in two dimensions with uniform manifold approximation and projection, cluster tumors into subgroups based on exposure frequencies, identify differentially active exposures between tumor subgroups, and plot exposure distributions across user-defined annotations such as tumor type. Overall, musicatk will enable users to gain novel insights into the patterns of mutational signatures observed in cancer cohorts. SIGNIFICANCE: The musicatk package empowers researchers to characterize mutational signatures and tumor heterogeneity with a comprehensive set of preprocessing utilities, discovery and prediction tools, and multiple functions for downstream analysis and visualization.R21 CA226188 - NCI NIH HHS; T32 GM100842 - NIGMS NIH HHShttps://cancerres.aacrjournals.org/content/81/23/5813.full-text.pd

Detailed Analysis of Early to Late-Time Spectra of Supernova 1993J

We present a detailed study of line structure in early to late-time spectra of Supernova (SN) 1993J. Spectra during the nebular phase, but within the first two years after explosion, exhibit small-scale structure in the emission lines of some species, notably oxygen and magnesium, showing that the ejecta of SN 1993J are clumpy. On the other hand, a lack of structure in emission lines of calcium implies that the source of calcium emission is uniformly distributed throughout the ejecta. These results are interpreted as evidence that oxygen emission originates in clumpy, newly synthesized material, while calcium emission arises from material pre-existing in the atmosphere of the progenitor. Spectra spanning the range 433-2454 days after the explosion show box-like profiles for the emission lines, clearly indicating circumstellar interaction in a roughly spherical shell. This is interpreted within the Chevalier & Fransson (1994) model for SNe interacting with mass lost during prior stellar winds. At very late times, the emission lines have a two-horned profile, implying the formation of a somewhat flattened or disk-like structure that is a significant source of emission. The very high signal-to-noise ratio spectra are used to demonstrate the potential significance of misinterpretation of telluric absorption lines in the spectra of bright SNe.Comment: 34 pages, 16 figures, AASTeX V5.0. Accepted for publication in A