A Survey of Plasmas and Their Applications

Plasmas are everywhere and relevant to everyone. We bath in a sea of photons, quanta of electromagnetic radiation, whose sources (natural and artificial) are dominantly plasma-based (stars, fluorescent lights, arc lamps.. .). Plasma surface modification and materials processing contribute increasingly to a wide array of modern artifacts; e.g., tiny plasma discharge elements constitute the pixel arrays of plasma televisions and plasma processing provides roughly one-third of the steps to produce semiconductors, essential elements of our networking and computing infrastructure. Finally, plasmas are central to many cutting edge technologies with high potential (compact high-energy particle accelerators; plasma-enhanced waste processors; high tolerance surface preparation and multifuel preprocessors for transportation systems; fusion for energy production)

spacodiR: structuring of phylogenetic diversity in ecological communities

Motivation: spacodiR is a cross-platform package, written for the R environment, for studying partitioning of diversity among natural communities in space and time. Complementing and extending existing software, spacodiR allows for hypothesis testing and parameter estimation in studying spatial structuring of species-, phylogenetic- and trait diversities. Availability: Integrated with other software in the R environment and with well documented and demonstrated functions, spacodiR is an open-source package and available at http://cran.r-project.org. Contact: [email protected]; [email protected]

A New Algorithm for Supernova Neutrino Transport and Some Applications

We have developed an implicit, multi-group, time-dependent, spherical neutrino transport code based on the Feautrier variables, the tangent-ray method, and accelerated ${\bf \Lambda}$ iteration. The code achieves high angular resolution, is good to O($v/c$), is equivalent to a Boltzmann solver (without gravitational redshifts), and solves the transport equation at all optical depths with precision. In this paper, we present our formulation of the relevant numerics and microphysics and explore protoneutron star atmospheres for snapshot post-bounce models. Our major focus is on spectra, neutrino-matter heating rates, Eddington factors, angular distributions, and phase-space occupancies. In addition, we investigate the influence on neutrino spectra and heating of final-state electron blocking, stimulated absorption, velocity terms in the transport equation, neutrino-nucleon scattering asymmetry, and weak magnetism and recoil effects. Furthermore, we compare the emergent spectra and heating rates obtained using full transport with those obtained using representative flux-limited transport formulations to gauge their accuracy and viability. Finally, we derive useful formulae for the neutrino source strength due to nucleon-nucleon bremsstrahlung and determine bremsstrahlung's influence on the emergent $\nu_{\mu}$ and $\nu_{\tau}$ neutrino spectra.Comment: 58 pages, single-spaced LaTeX, 23 figures, revised title, also available at http://jupiter.as.arizona.edu/~burrows/papers, accepted for publication in the Ap.

Peculiar Type II Supernovae from Blue Supergiants

The vast majority of Type II supernovae (SNe) are produced by red supergiants (RSGs), but SN 1987A revealed that blue supergiants (BSGs) can produce members of this class as well, albeit with some peculiar properties. This best studied event revolutionized our understanding of SNe, and linking it to the bulk of Type II events is essential. We present here optical photometry and spectroscopy gathered for SN 2000cb, which is clearly not a standard Type II SN and yet is not a SN 1987A analog. The light curve of SN 2000cb is reminiscent of that of SN 1987A in shape, with a slow rise to a late optical peak, but on substantially different time scales. Spectroscopically, SN 2000cb resembles a normal SN II but with ejecta velocities that far exceed those measured for SN 1987A or normal SNe II, above 18000 km/s for H-alpha at early times. The red colours, high velocities, late photometric peak, and our modeling of this object all point toward a scenario involving the high-energy explosion of a small-radius star, most likely a BSG, producing 0.1 solar masses of Ni-56. Adding a similar object to the sample, SN 2005ci, we derive a rate of about 2% of the core-collapse rate for this loosely defined class of BSG explosions.Comment: Accepted to MNRAS on March 14, 201

Complex history of the amphibian-killing chytrid fungus revealed with genome resequencing data

Understanding the evolutionary history of microbial pathogens is critical for mitigating the impacts of emerging infectious diseases on economically and ecologically important host species. We used a genome resequencing approach to resolve the evolutionary history of an important microbial pathogen, the chytrid Batrachochytrium dendrobatidis (Bd), which has been implicated in amphibian declines worldwide. We sequenced the genomes of 29 isolates of Bd from around the world, with an emphasis on North, Central, and South America because of the devastating effect that Bd has had on amphibian populations in the New World. We found a substantial amount of evolutionary complexity in Bd with deep phylogenetic diversity that predates observed global amphibian declines. By investigating the entire genome, we found that even the most recently evolved Bd clade (termed the global panzootic lineage) contained more genetic variation than previously reported. We also found dramatic differences among isolates and among genomic regions in chromosomal copy number and patterns of heterozygosity, suggesting complex and heterogeneous genome dynamics. Finally, we report evidence for selection acting on the Bd genome, supporting the hypothesis that protease genes are important in evolutionary transitions in this group. Bd is considered an emerging pathogen because of its recent effects on amphibians, but our data indicate that it has a complex evolutionary history that predates recent disease outbreaks. Therefore, it is important to consider the contemporary effects of Bd in a broader evolutionary context and identify specific mechanisms that may have led to shifts in virulence in this system.Instituto de Botánica "Dr. Carlos Spegazzini

First radial velocity results from the MINiature Exoplanet Radial Velocity Array (MINERVA)

The MINiature Exoplanet Radial Velocity Array (MINERVA) is a dedicated observatory of four 0.7m robotic telescopes fiber-fed to a KiwiSpec spectrograph. The MINERVA mission is to discover super-Earths in the habitable zones of nearby stars. This can be accomplished with MINERVA's unique combination of high precision and high cadence over long time periods. In this work, we detail changes to the MINERVA facility that have occurred since our previous paper. We then describe MINERVA's robotic control software, the process by which we perform 1D spectral extraction, and our forward modeling Doppler pipeline. In the process of improving our forward modeling procedure, we found that our spectrograph's intrinsic instrumental profile is stable for at least nine months. Because of that, we characterized our instrumental profile with a time-independent, cubic spline function based on the profile in the cross dispersion direction, with which we achieved a radial velocity precision similar to using a conventional "sum-of-Gaussians" instrumental profile: 1.8 m s$^{-1}$ over 1.5 months on the RV standard star HD 122064. Therefore, we conclude that the instrumental profile need not be perfectly accurate as long as it is stable. In addition, we observed 51 Peg and our results are consistent with the literature, confirming our spectrograph and Doppler pipeline are producing accurate and precise radial velocities.Comment: 22 pages, 9 figures, submitted to PASP, Peer-Reviewed and Accepte

KELT-25 b and KELT-26 b: A Hot Jupiter and a Substellar Companion Transiting Young A Stars Observed by TESS

We present the discoveries of KELT-25 b (TIC 65412605, TOI-626.01) and KELT-26 b (TIC 160708862, TOI-1337.01), two transiting companions orbiting relatively bright, early A stars. The transit signals were initially detected by the KELT survey and subsequently confirmed by Transiting Exoplanet Survey Satellite (TESS) photometry. KELT-25 b is on a 4.40 day orbit around the V = 9.66 star CD-24 5016 (Teff=8280-180+440 K, M ∗ = 2.18-0.11+0.12 M o˙), while KELT-26 b is on a 3.34 day orbit around the V = 9.95 star HD 134004 (Teff = 8640-240+500 K, M ∗ = 1.93-0.16+0.14 M o˙), which is likely an Am star. We have confirmed the substellar nature of both companions through detailed characterization of each system using ground-based and TESS photometry, radial velocity measurements, Doppler tomography, and high-resolution imaging. For KELT-25, we determine a companion radius of R P = 1.64-0.043+0.039 R J and a 3σ upper limit on the companion\u27s mass of ∼64 M J. For KELT-26 b, we infer a planetary mass and radius of M P = 1.41-0.51+0.43MJ and R P = 1.94-0.058+0.060 R J. From Doppler tomographic observations, we find KELT-26 b to reside in a highly misaligned orbit. This conclusion is weakly corroborated by a subtle asymmetry in the transit light curve from the TESS data. KELT-25 b appears to be in a well-aligned, prograde orbit, and the system is likely a member of the cluster Theia 449

Antiretroviral Therapy Initiation Before, During, or After Pregnancy in HIV-1-Infected Women: Maternal Virologic, Immunologic, and Clinical Response

Pregnancy has been associated with a decreased risk of HIV disease progression in the highly active antiretroviral therapy (HAART) era. The effect of timing of HAART initiation relative to pregnancy on maternal virologic, immunologic and clinical outcomes has not been assessed.We conducted a retrospective cohort study from 1997–2005 among 112 pregnant HIV-infected women who started HAART before (N = 12), during (N = 70) or after pregnancy (N = 30).0.01). There were no statistical differences in rates of HIV disease progression between groups.HAART initiation during pregnancy was associated with better immunologic and virologic responses than initiation after pregnancy

Complex history of the amphibian-killing chytrid fungus revealed with genome resequencing data

Understanding the evolutionary history of microbial pathogens is critical for mitigating the impacts of emerging infectious diseases on economically and ecologically important host species. We used a genome resequencing approach to resolve the evolutionary history of an important microbial pathogen, the chytrid Batrachochytrium dendrobatidis (Bd), which has been implicated in amphibian declines worldwide. We sequenced the genomes of 29 isolates of Bd from around the world, with an emphasis on North, Central, and South America because of the devastating effect that Bd has had on amphibian populations in the New World. We found a substantial amount of evolutionary complexity in Bd with deep phylogenetic diversity that predates observed global amphibian declines. By investigating the entire genome, we found that even the most recently evolved Bd clade (termed the global panzootic lineage) contained more genetic variation than previously reported. We also found dramatic differences among isolates and among genomic regions in chromosomal copy number and patterns of heterozygosity, suggesting complex and heterogeneous genome dynamics. Finally, we report evidence for selection acting on the Bd genome, supporting the hypothesis that protease genes are important in evolutionary transitions in this group. Bd is considered an emerging pathogen because of its recent effects on amphibians, but our data indicate that it has a complex evolutionary history that predates recent disease outbreaks. Therefore, it is important to consider the contemporary effects of Bd in a broader evolutionary context and identify specific mechanisms that may have led to shifts in virulence in this system.Instituto de Botánica "Dr. Carlos Spegazzini

TESS delivers its first Earth-sized planet and a warm sub-Neptune

The future of exoplanet science is bright, as TESS once again demonstrates with the discovery of its longest-period confirmed planet to date. We hereby present HD 21749b (TOI 186.01), a sub-Neptune in a 36-day orbit around a bright (V = 8.1) nearby (16 pc) K4.5 dwarf. TESS measures HD21749b to be 2.61$^{+0.17}_{-0.16}$ $R_{\oplus}$, and combined archival and follow-up precision radial velocity data put the mass of the planet at $22.7^{+2.2}_{-1.9}$ $M_{\oplus}$. HD 21749b contributes to the TESS Level 1 Science Requirement of providing 50 transiting planets smaller than 4 $R_{\oplus}$ with measured masses. Furthermore, we report the discovery of HD 21749c (TOI 186.02), the first Earth-sized ($R_p = 0.892^{+0.064}_{-0.058} R_{\oplus}$) planet from TESS. The HD21749 system is a prime target for comparative studies of planetary composition and architecture in multi-planet systems.Comment: Published in ApJ Letters; 5 figures, 1 tabl