Synthetic Light Curves of Shocked Dense Circumstellar Shells

We numerically investigate light curves (LCs) of shocked circumstellar shells which are suggested to reproduce the observed LC of superluminous SN 2006gy analytically. In the previous analytical model, the effects of the recombination and the bolometric correction on LCs are not taken into account. To see the effects, we perform numerical radiation hydrodynamic calculations of shocked shells by using STELLA, which can numerically treat multigroup radiation transfer with realistic opacities. We show that the effects of the recombination and the bolometric correction are significant and the analytical model should be compare to the bolometric LC instead of a single band LC. We find that shocked circumstellar shells have a rapid LC decline initially because of the adiabatic expansion rather than the luminosity increase and the shocked shells fail to explain the LC properties of SN 2006gy. However, our synthetic LCs are qualitatively similar to those of superluminous SN 2003ma and SN 1988Z and they may be related to shocked circumstellar shells.Comment: 7 pages, 7 figures, 1 table, accepted by Monthly Notices of the Royal Astronomical Societ

Electron-capture supernovae exploding within their progenitor wind

The most massive stars on the asymptotic giant branch (AGB), so called super-AGB stars, are thought to produce supernovae (SNe) triggered by electron captures in their degenerate O+Ne+Mg cores. Super-AGB stars are expected to have slow winds with high mass-loss rates, so their wind density is high. The explosions of super-AGB stars are therefore presumed to occur in this dense wind. We provide the first synthetic light curves (LCs) for such events by exploding realistic electron-capture supernova (ecSN) progenitors within their super-AGB winds. We find that the early LC, i.e. before the recombination wave reaches the bottom of the H-rich envelope of SN ejecta (the plateau phase), is not affected by the dense wind. However, after the plateau phase, the luminosity remains higher when the super-AGB wind is taken into account. We compare our results to the historical LC of SN 1054, the progenitor of the Crab Nebula, and show that the explosion of an ecSN within an ordinary super-AGB wind can explain the LC features. We conclude that SN 1054 could have been a Type IIn SN without any extra extreme mass loss which was previously suggested to be necessary to account for its early high luminosity. We also show that our LCs match Type IIn SNe with an early plateau phase (`Type IIn-P') and suggest that they are ecSNe within super-AGB winds. Although some ecSNe can be bright in the optical spectral range due to the large progenitor radius, their X-ray luminosity from the interaction does not necessarily get as bright as other Type IIn SNe whose optical luminosities are also powered by the interaction. Thus, we suggest that optically-bright X-ray-faint Type IIn SNe can emerge from ecSNe. Optically-faint Type IIn SNe, such as SN 2008S, can also originate from ecSNe if their H-rich envelope masses are small. Some of them can be observed as `Type IIn-b' SNe due to the small H-rich envelope mass.Comment: 8 pages, 6 figures, accepted by Astronomy & Astrophysics, abstract abridge

Synaptome.db: A Bioconductor package for synaptic proteomics data

SUMMARY: The neuronal synapse is underpinned by a large and diverse proteome but the molecular evidence is spread across many primary datasets. These data were recently curated into a single dataset describing a landscape of ∼8000 proteins found in studies of mammalian synapses. Here, we describe programmatic access to the dataset via the R/Bioconductor package Synaptome.db, which enables convenient and in-depth data analysis from within the Bioconductor environment. Synaptome.db allows users to obtain the respective gene information, e.g. subcellular localization, brain region, gene ontology, disease association and construct custom protein–protein interaction network models for gene sets and entire subcellular compartments. AVAILABILITY AND IMPLEMENTATION: The package Synaptome.db is part of Bioconductor since release 3.14, https://bioconductor.org/packages/release/data/annotation/html/synaptome.db.html, it is open source and available under the Artistic license 2.0. The development version is maintained on GitHub (https://github.com/lptolik/synaptome.db). Full documentation including examples is provided in the form of vignettes on the package webpage. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online

A Mammalian Homolog of Drosophila melanogaster Transcriptional Coactivator Intersex Is a Subunit of the Mammalian Mediator Complex

The multiprotein Mediator complex is a coactivator required for transcriptional activation of RNA polymerase II transcribed genes by DNA binding transcription factors. We previously partially purified a Med8-containing Mediator complex from rat liver nuclei (Brower, C. S., Sato, S., Tomomori-Sato, C., Kamura, T., Pause, A., Stearman, R., Klausner, R. D., Malik, S., Lane, W. S., Sorokina, I., Roeder, R. G., Conaway, J. W., and Conaway, R. C. (2002) Proc. Natl. Acad. Sci. U. S. A. 99, 10353–10358). Analysis of proteins present in the most highly enriched Mediator fractions by tandem mass spectrometry led to the identification of several new mammalian Mediator subunits, as well as several potential Mediator subunits. Here we identify one of these proteins, encoded by the previously uncharacterized AK000411 open reading frame, as a new subunit of the mammalian Mediator complex. The AK000411 protein, which we designate hIntersex (human Intersex), shares significant sequence similarity with the Drosophila melanogaster intersex protein, which has functional properties expected of a transcriptional coactivator specific for the Drosophila doublesex transactivator. In addition, we show that hIntersex assembles into a subcomplex with Mediator subunits p28b and TRFP. Taken together, our findings identify a new subunit of the mammalian Mediator and shed new light on the architecture of the mammalian Mediator complex

Soliton absorption spectroscopy

We analyze optical soliton propagation in the presence of weak absorption lines with much narrower linewidths as compared to the soliton spectrum width using the novel perturbation analysis technique based on an integral representation in the spectral domain. The stable soliton acquires spectral modulation that follows the associated index of refraction of the absorber. The model can be applied to ordinary soliton propagation and to an absorber inside a passively modelocked laser. In the latter case, a comparison with water vapor absorption in a femtosecond Cr:ZnSe laser yields a very good agreement with experiment. Compared to the conventional absorption measurement in a cell of the same length, the signal is increased by an order of magnitude. The obtained analytical expressions allow further improving of the sensitivity and spectroscopic accuracy making the soliton absorption spectroscopy a promising novel measurement technique.Comment: 9 pages, 7 figures

A Mammalian Mediator Subunit that Shares Properties with Saccharomyces cerevisiae Mediator Subunit Cse2

The multiprotein Mediator complex is a coactivator required for activation of RNA polymerase II transcription by DNA bound transcription factors. We previously identified and partially purified a mammalian Mediator complex from rat liver nuclei (Brower, C.S., Sato, S., Tomomori-Sato, C., Kamura, T., Pause, A., Stearman, R., Klausner, R.D., Malik, S., Lane, W.S., Sorokina, I., Roeder, R.G., Conaway, J.W., and Conaway, R.C. (2002) Proc. Natl. Acad. Sci. U. S. A. 99, 10353-10358). Analysis by tandem mass spectrometry of proteins present in the most highly purified rat Mediator fractions led to the identification of a collection of new mammalian Mediator subunits, as well as several potential Mediator subunits including a previously uncharacterized protein encoded by the FLJ10193open reading frame. In this study, we present direct biochemical evidence that the FLJ10193protein, which we designate Med25, is a bona fide subunit of the mammalian Mediator complex. In addition, we present evidence that Med25 shares structural and functional properties with Saccharomyces cerevisiae Mediator subunit Cse2 and may be a mammalian Cse2 ortholog. Taken together, our findings identify a novel mammalian Mediator subunit and shed new light on the architecture of the mammalian Mediator complex

Vertical structure of recent arctic warming from observed data and reanalysis products

The final publication is available at Springer via http://dx.doi.org/10.1007/s10584-011-0192-8Spatiotemporal patterns of recent (1979–2008) air temperature trends are evaluated using three reanalysis datasets and radiosonde data. Our analysis demonstrates large discrepancies between the reanalysis datasets, possibly due to differences in the data assimilation procedures as well as sparseness and inhomogeneity of high-latitude observations. We test the robustness of Arctic tropospheric warming based on the ERA-40 dataset. ERA-40 Arctic atmosphere temperatures tend to be closer to the observed ones in terms of root mean square error compare to other reanalysis products used in the article. However, changes in the ERA-40 data assimilation procedure produce unphysical jumps in atmospheric temperatures, which may be the likely reason for the elevated tropospheric warming trend in 1979-2002. NCEP/NCAR Reanalysis show that the near-surface upward temperature trend over the same period is greater than the tropospheric trend, which is consistent with direct radiosonde observations and inconsistent with ERA-40 results. A change of sign in the winter temperature trend from negative to positive in the late 1980s is documented in the upper troposphere/lower stratosphere with a maximum over the Canadian Arctic, based on radiosonde data. This change from cooling to warming tendency is associated with weakening of the stratospheric polar vortex and shift of its center toward the Siberian coast and possibly can be explained by the changes in the dynamics of the Arctic Oscillation. This temporal pattern is consistent with multi-decadal variations of key Arctic climate parameters like, for example, surface air temperature and oceanic freshwater content. Elucidating the mechanisms behind these changes will be critical to understanding the complex nature of high-latitude variability and its impact on global climate change.acceptedVersio

Identification of Mammalian Mediator Subunits with Similarities to Yeast Mediator Subunits Srb5, Srb6, Med11, and Rox3

The Mediator is a multiprotein coactivator required for activation of RNA polymerase II transcription by DNA binding transactivators. We recently identified a mammalian homologue of yeast Mediator subunit Med8 and partially purified a Med8-containing Mediator complex from rat liver nuclei (Brower, C. S., Sato, S., Tomomori-Sato, C., Kamura, T., Pause, A., Stearman, R., Klausner, R. D., Malik, S., Lane, W. S., Sorokina, I., Roeder, R. G., Conaway, J. W., and Conaway, R. C. (2002) Proc. Natl. Acad. Sci. U. S. A. 99, 10353-10358). Analysis of proteins present in the most highly purified Med8-containing fractions by tandem mass spectrometry led to the identification of many known mammalian Mediator subunits, as well as four potential Mediator subunits exhibiting sequence similarity to yeast Mediator subunits Srb5, Srb6, Med11, and Rox3. Here we present direct biochemical evidence that these four proteins are bona fide mammalian Mediator subunits. In addition, we identify direct pairwise binding partners of these proteins among the known mammalian Mediator subunits. Taken together, our findings identify a collection of novel mammalian Mediator subunits and shed new light on the underlying architecture of the mammalian Mediator complex