Interacting Supernovae: Types IIn and Ibn

Supernovae (SNe) that show evidence of strong shock interaction between their ejecta and pre-existing, slower circumstellar material (CSM) constitute an interesting, diverse, and still poorly understood category of explosive transients. The chief reason that they are extremely interesting is because they tell us that in a subset of stellar deaths, the progenitor star may become wildly unstable in the years, decades, or centuries before explosion. This is something that has not been included in standard stellar evolution models, but may significantly change the end product and yield of that evolution, and complicates our attempts to map SNe to their progenitors. Another reason they are interesting is because CSM interaction is an efficient engine for making bright transients, allowing super-luminous transients to arise from normal SN explosion energies, and allowing transients of normal SN luminosities to arise from sub-energetic explosions or low radioactivity yield. CSM interaction shrouds the fast ejecta in bright shock emission, obscuring our normal view of the underlying explosion, and the radiation hydrodynamics of the interaction is challenging to model. The CSM interaction may also be highly non-spherical, perhaps linked to binary interaction in the progenitor system. In some cases, these complications make it difficult to definitively tell the difference between a core-collapse or thermonuclear explosion, or to discern between a non-terminal eruption, failed SN, or weak SN. Efforts to uncover the physical parameters of individual events and connections to possible progenitor stars make this a rapidly evolving topic that continues to challenge paradigms of stellar evolution.Comment: Final draft of a chapter in the "SN Handbook". Accepted. 25 pages, 3 fig

Large introns in relation to alternative splicing and gene evolution: a case study of Drosophila bruno-3

Background: Alternative splicing (AS) of maturing mRNA can generate structurally and functionally distinct transcripts from the same gene. Recent bioinformatic analyses of available genome databases inferred a positive correlation between intron length and AS. To study the interplay between intron length and AS empirically and in more detail, we analyzed the diversity of alternatively spliced transcripts (ASTs) in the Drosophila RNA-binding Bruno-3 (Bru-3) gene. This gene was known to encode thirteen exons separated by introns of diverse sizes, ranging from 71 to 41,973 nucleotides in D. melanogaster. Although Bru-3's structure is expected to be conducive to AS, only two ASTs of this gene were previously described. Results: Cloning of RT-PCR products of the entire ORF from four species representing three diverged Drosophila lineages provided an evolutionary perspective, high sensitivity, and long-range contiguity of splice choices currently unattainable by high-throughput methods. Consequently, we identified three new exons, a new exon fragment and thirty-three previously unknown ASTs of Bru-3. All exon-skipping events in the gene were mapped to the exons surrounded by introns of at least 800 nucleotides, whereas exons split by introns of less than 250 nucleotides were always spliced contiguously in mRNA. Cases of exon loss and creation during Bru-3 evolution in Drosophila were also localized within large introns. Notably, we identified a true de novo exon gain: exon 8 was created along the lineage of the obscura group from intronic sequence between cryptic splice sites conserved among all Drosophila species surveyed. Exon 8 was included in mature mRNA by the species representing all the major branches of the obscura group. To our knowledge, the origin of exon 8 is the first documented case of exonization of intronic sequence outside vertebrates. Conclusion: We found that large introns can promote AS via exon-skipping and exon turnover during evolution likely due to frequent errors in their removal from maturing mRNA. Large introns could be a reservoir of genetic diversity, because they have a greater number of mutable sites than short introns. Taken together, gene structure can constrain and/or promote gene evolution

New Physics Models of Direct CP Violation in Charm Decays

In view of the recent LHCb measurement of Delta A_CP, the difference between the time-integrated CP asymmetries in D --> K+K- and D --> pi+pi- decays, we perform a comparative study of the possible impact of New Physics degrees of freedom on the direct CP asymmetries in singly Cabibbo suppressed D meson decays. We systematically discuss scenarios with a minimal set of new degrees of freedom that have renormalizable couplings to the SM particles and that are heavy enough such that their effects on the D meson decays can be described by local operators. We take into account both constraints from low energy flavor observables, in particular D0-D0bar mixing, and from direct searches. While models that explain the large measured value for Delta A_CP with chirally enhanced chromomagnetic penguins are least constrained, we identify a few viable models that contribute to the D meson decays at tree level or through loop induced QCD penguins. We emphasize that such models motivate direct searches at the LHC.Comment: 24 pages, 13 figures. v2: typos corrected, reference added, published versio

High-Sensitivity Cardiac Troponin and the Universal Definition of Myocardial Infarction.

Background: The introduction of more sensitive cardiac troponin assays has led to increased recognition of myocardial injury in acute illnesses other than acute coronary syndrome. The Universal Definition of Myocardial Infarction recommends high-sensitivity cardiac troponin (hs-cTn) testing and classification of patients with myocardial injury based on aetiology, but the clinical implications of implementing this guideline are not well understood. Methods: In a stepped-wedge cluster randomized controlled trial, we implemented a hs-cTn assay and the recommendations of the Universal Definition in 48,282 consecutive patients with suspected acute coronary syndrome. In a pre-specified secondary analysis, we compared the primary outcome of myocardial infarction or cardiovascular death and secondary outcome of non-cardiovascular death at one year across diagnostic categories. Results: Implementation increased the diagnosis of type 1 myocardial infarction by 11% (510/4,471), type 2 myocardial infarction by 22% (205/916), and acute and chronic myocardial injury by 36% (443/1,233) and 43% (389/898), respectively. Compared to those without myocardial injury, the rate of the primary outcome was highest in those with type 1 myocardial infarction (cause-specific hazard ratio [csHR] 5.64, 95% confidence interval [CI] 5.12 to 6.22), but was similar across diagnostic categories, whereas non-cardiovascular deaths were highest in those with acute myocardial injury (csHR 2.65, 95%CI 2.33 to 3.01). Despite modest increases in anti-platelet therapy and coronary revascularization after implementation in patients with type 1 myocardial infarction, the primary outcome was unchanged (csHR 1.00, 95%CI 0.82 to 1.21). Increased recognition of type 2 myocardial infarction and myocardial injury did not lead to changes in investigation, treatment or outcomes. Conclusions: Implementation of high-sensitivity cardiac troponin and the recommendations of the Universal Definition of Myocardial Infarction identified patients at high-risk of cardiovascular and non-cardiovascular events, but was not associated with consistent increases in treatment or improved outcomes. Trials of secondary prevention are urgently required to determine whether this risk is modifiable in patients without type 1 myocardial infarction. Clinical Trial Registration: URL: https://clinicaltrials.gov Unique Identifier: NCT0185212

Massive stars as thermonuclear reactors and their explosions following core collapse

Nuclear reactions transform atomic nuclei inside stars. This is the process of stellar nucleosynthesis. The basic concepts of determining nuclear reaction rates inside stars are reviewed. How stars manage to burn their fuel so slowly most of the time are also considered. Stellar thermonuclear reactions involving protons in hydrostatic burning are discussed first. Then I discuss triple alpha reactions in the helium burning stage. Carbon and oxygen survive in red giant stars because of the nuclear structure of oxygen and neon. Further nuclear burning of carbon, neon, oxygen and silicon in quiescent conditions are discussed next. In the subsequent core-collapse phase, neutronization due to electron capture from the top of the Fermi sea in a degenerate core takes place. The expected signal of neutrinos from a nearby supernova is calculated. The supernova often explodes inside a dense circumstellar medium, which is established due to the progenitor star losing its outermost envelope in a stellar wind or mass transfer in a binary system. The nature of the circumstellar medium and the ejecta of the supernova and their dynamics are revealed by observations in the optical, IR, radio, and X-ray bands, and I discuss some of these observations and their interpretations.Comment: To be published in " Principles and Perspectives in Cosmochemistry" Lecture Notes on Kodai School on Synthesis of Elements in Stars; ed. by Aruna Goswami & Eswar Reddy, Springer Verlag, 2009. Contains 21 figure

PTF12os and iPTF13bvn: Two stripped-envelope supernovae from low-mass progenitors in NGC 5806

© ESO, 2016.Context. We investigate two stripped-envelope supernovae (SNe) discovered in the nearby galaxy NGC 5806 by the (intermediate) Palomar Transient Factory [(i)PTF]. These SNe, designated PTF12os/SN 2012P and iPTF13bvn, exploded within ∼520 days of one another at a similar distance from the host-galaxy center. We classify PTF12os as a Type IIb SN based on our spectral sequence; iPTF13bvn has previously been classified as Type Ib having a likely progenitor with zero age main sequence (ZAMS) mass below ∼17 M⊙. Because of the shared and nearby host, we are presented with a unique opportunity to compare these two SNe. Aims. Our main objective is to constrain the explosion parameters of iPTF12os and iPTF13bvn, and to put constraints on the SN progenitors. We also aim to spatially map the metallicity in the host galaxy, and to investigate the presence of hydrogen in early-time spectra of both SNe. Methods. We present comprehensive datasets collected on PTF12os and iPTF13bvn, and introduce a new automatic reference-subtraction photometry pipeline (FPipe) currently in use by the iPTF. We perform a detailed study of the light curves (LCs) and spectral evolution of the SNe. The bolometric LCs are modeled using the hydrodynamical code hyde. We analyze early spectra of both SNe to investigate the presence of hydrogen; for iPTF13bvn we also investigate the regions of the Paschen lines in infrared spectra. We perform spectral line analysis of helium and iron lines to map the ejecta structure of both SNe. We use nebular models and late-time spectroscopy to constrain the ZAMS mass of the progenitors. We also perform image registration of ground-based images of PTF12os to archival HST images of NGC 5806 to identify a potential progenitor candidate. Results. We find that our nebular spectroscopy of iPTF13bvn remains consistent with a low-mass progenitor, likely having a ZAMS mass of ∼12M⊙. Our late-time spectroscopy of PTF12os is consistent with a ZAMS mass of ∼15M⊙. We successfully identify a source in pre-explosion HST images coincident with PTF12os. The colors and absolute magnitude of this object are consistent between pre-explosion and late-time HST images, implying it is a cluster of massive stars. Our hydrodynamical modeling suggests that the progenitor of PTF12os had a compact He core with a mass of 3.25+ 0.77-0.56M⊙ at the time of the explosion, which had a total kinetic energy of 0.54+ 0.41-0.25 × 1051 erg and synthesized 0.063+ 0.020-0.011M⊙ of strongly mixed 56Ni. Spectral comparisons to the Type IIb SN 2011dh indicate that the progenitor of PTF12os was surrounded by a thin hydrogen envelope with a mass lower than 0.02M⊙. We also find tentative evidence that the progenitor of iPTF13bvn could have been surrounded by a small amount of hydrogen prior to the explosion. This result is supported by possible weak signals of hydrogen in both optical and infrared spectra

Inactivation of SAM-methyltransferase is the mechanism of attenuation of a historic louse borne typhus vaccine strain

Louse borne typhus (also called epidemic typhus) was one of man's major scourges, and epidemics of the disease can be reignited when social, economic, or political systems are disrupted. The fear of a bioterrorist attack using the etiologic agent of typhus, Rickettsia prowazekii, was a reality. An attenuated typhus vaccine, R. prowazekii Madrid E strain, was observed to revert to virulence as demonstrated by isolation of the virulent revertant Evir strain from animals which were inoculated with Madrid E strain. The mechanism of the mutation in R. prowazekii that affects the virulence of the vaccine was not known. We sequenced the genome of the virulent revertant Evir strain and compared its genome sequence with the genome sequences of its parental strain, Madrid E. We found that only a single nucleotide in the entire genome was different between the vaccine strain Madrid E and its virulent revertant strain Evir. The mutation is a single nucleotide insertion in the methyltransferase gene (also known as PR028) in the vaccine strain that inactivated the gene. We also confirmed that the vaccine strain E did not cause fever in guinea pigs and the virulent revertant strain Evir caused fever in guinea pigs. We concluded that a single nucleotide insertion in the methyltransferase gene of R. prowazekii attenuated the R. prowazekii vaccine strain E. This suggested that an irreversible insertion or deletion mutation in the methyl transferase gene of R. prowazekii is required for Madrid E to be considered a safe vaccine

High throughput method for analysis of repeat number for 28 phase variable loci of C. jejuni strain NCTC11168

Mutations in simple sequence repeat tracts are a major mechanism of phase variation in several bacterial species including Campylobacter jejuni. Changes in repeat number of tracts located within the reading frame can produce a high frequency of reversible switches in gene expression between ON and OFF states. The genome of C. jejuni strain NCTC11168 contains 29 loci with polyG/polyC tracts of seven or more repeats. This protocol outlines a method for rapidly determining ON/OFF states of these 28 phase-variable loci in a large number of individual colonies. The method combines a series of multiplex PCR assays with a GeneScan assay and automated extraction of tract length, repeat number and expression state. This high throughput, multiplex assay has utility for detecting shifts in phase variation states within and between populations over time and for exploring the effects of phase variation on adaptation to differing selective pressures. An important output of this assay is combinatorial expression states that cannot be determined by other methods. This method can be adapted to analysis of phase variation in other C. jejuni strains and in a diverse range of bacterial species

Impacts of organic and conventional crop management on diversity and activity of free-living nitrogen fixing bacteria and total bacteria are subsidiary to temporal effects

A three year field study (2007-2009) of the diversity and numbers of the total and metabolically active free-living diazotophic bacteria and total bacterial communities in organic and conventionally managed agricultural soil was conducted at the Nafferton Factorial Systems Comparison (NFSC) study, in northeast England. The result demonstrated that there was no consistent effect of either organic or conventional soil management across the three years on the diversity or quantity of either diazotrophic or total bacterial communities. However, ordination analyses carried out on data from each individual year showed that factors associated with the different fertility management measures including availability of nitrogen species, organic carbon and pH, did exert significant effects on the structure of both diazotrophic and total bacterial communities. It appeared that the dominant drivers of qualitative and quantitative changes in both communities were annual and seasonal effects. Moreover, regression analyses showed activity of both communities was significantly affected by soil temperature and climatic conditions. The diazotrophic community showed no significant change in diversity across the three years, however, the total bacterial community significantly increased in diversity year on year. Diversity was always greatest during March for both diazotrophic and total bacterial communities. Quantitative analyses using qPCR of each community indicated that metabolically active diazotrophs were highest in year 1 but the population significantly declined in year 2 before recovering somewhat in the final year. The total bacterial population in contrast increased significantly each year. Seasonal effects were less consistent in this quantitative study

Light dark matter and Z′Z' dark force at colliders

Light Dark Matter, $<10$ GeV, with sizable direct detection rate is an interesting and less explored scenario. Collider searches can be very powerful, such as through the channel in which a pair of dark matter particle are produced in association with a jet. It is a generic possibility that the mediator of the interaction between DM and the nucleus will also be accessible at the Tevatron and the LHC. Therefore, collider search of the mediator can provide a more comprehensive probe of the dark matter and its interactions. In this article, to demonstrate the complementarity of these two approaches, we focus on the possibility of the mediator being a new $U(1)'$ gauge boson, which is probably the simplest model which allows a large direct detection cross section for a light dark matter candidate. We combine searches in the monojet+MET channel and dijet resonance search for the mediator. We find that for the mass of $Z'$ between 250 GeV and 4 TeV, resonance searches at the colliders provide stronger constraints on this model than the monojet+MET searches.Comment: 23 pages and 14 figure