The microbiome in patients with atopic dermatitis.

As an interface with the environment, the skin is a complex ecosystem colonized by many microorganisms that coexist in an established balance. The cutaneous microbiome inhibits colonization with pathogens, such as Staphylococcus aureus, and is a crucial component for function of the epidermal barrier. Moreover, crosstalk between commensals and the immune system is now recognized because microorganisms can modulate both innate and adaptive immune responses. Host-commensal interactions also have an effect on the developing immune system in infants and, subsequently, the occurrence of diseases, such as asthma and atopic dermatitis (AD). Later in life, the cutaneous microbiome contributes to the development and course of skin disease. Accordingly, in patients with AD, a decrease in microbiome diversity correlates with disease severity and increased colonization with pathogenic bacteria, such as S aureus. Early clinical studies suggest that topical application of commensal organisms (eg, Staphylococcus hominis or Roseomonas mucosa) reduces AD severity, which supports an important role for commensals in decreasing S aureus colonization in patients with AD. Advancing knowledge of the cutaneous microbiome and its function in modulating the course of skin disorders, such as AD, might result in novel therapeutic strategies

VPLanet: The Virtual Planet Simulator

We describe a software package called VPLanet that simulates fundamental aspects of planetary system evolution over Gyr timescales, with a focus on investigating habitable worlds. In this initial release, eleven physics modules are included that model internal, atmospheric, rotational, orbital, stellar, and galactic processes. Many of these modules can be coupled simultaneously to simulate the evolution of terrestrial planets, gaseous planets, and stars. The code is validated by reproducing a selection of observations and past results. VPLanet is written in C and designed so that the user can choose the physics modules to apply to an individual object at runtime without recompiling, i.e., a single executable can simulate the diverse phenomena that are relevant to a wide range of planetary and stellar systems. This feature is enabled by matrices and vectors of function pointers that are dynamically allocated and populated based on user input. The speed and modularity of VPLanet enables large parameter sweeps and the versatility to add/remove physical phenomena to assess their importance. VPLanet is publicly available from a repository that contains extensive documentation, numerous examples, Python scripts for plotting and data management, and infrastructure for community input and future development.Comment: 75 pages, 34 figures, 10 tables, accepted to the Proceedings of the Astronomical Society of the Pacific. Source code, documentation, and examples available at https://github.com/VirtualPlanetaryLaboratory/vplane

eleanor: An open-source tool for extracting light curves from the TESS Full-Frame Images

During its two year prime mission the Transiting Exoplanet Survey Satellite (TESS) will perform a time-series photometric survey covering over 80% of the sky. This survey comprises observations of 26 24 x 96 degree sectors that are each monitored continuously for approximately 27 days. The main goal of TESS is to find transiting planets around 200,000 pre-selected stars for which fixed aperture photometry is recorded every two minutes. However, TESS is also recording and delivering Full-Frame Images (FFIs) of each detector at a 30 minute cadence. We have created an open-source tool, eleanor, to produce light curves for objects in the TESS FFIs. Here, we describe the methods used in eleanor to produce light curves that are optimized for planet searches. The tool performs background subtraction, aperture and PSF photometry, decorrelation of instrument systematics, and cotrending using principal component analysis. We recover known transiting exoplanets in the FFIs to validate the pipeline and perform a limited search for new planet candidates in Sector 1. Our tests indicate that eleanor produces light curves with significantly less scatter than other tools that have been used in the literature. Cadence-stacked images, and raw and detrended eleanor light curves for each analyzed star will be hosted on MAST, with planet candidates on ExoFOP-TESS as Community TESS Objects of Interest (CTOIs). This work confirms the promise that the TESS FFIs will enable the detection of thousands of new exoplanets and a broad range of time domain astrophysics.Comment: 21 pages, 13 figures, 2 tables, Accepted to PAS

Sequence Effects on DNA Entropic Elasticity

DNA stretching experiments are usually interpreted using the worm-like chain model; the persistence length A appearing in the model is then interpreted as the elastic stiffness of the double helix. In fact the persistence length obtained by this method is a combination of bend stiffness and intrinsic bend effects reflecting sequence information, just as at zero stretching force. This observation resolves the discrepancy between the value of A measured in these experiments and the larger ``dynamic persistence length'' measured by other means. On the other hand, the twist persistence length deduced from torsionally-constrained stretching experiments suffers no such correction. Our calculation is very simple and analytic; it applies to DNA and other polymers with weak intrinsic disorder.Comment: LaTeX; postscript available at http://dept.physics.upenn.edu/~nelson/index.shtm

Identifying Planetary Biosignature Impostors: Spectral Features of CO and O4 Resulting from Abiotic O2/O3 Production

O2 and O3 have been long considered the most robust individual biosignature gases in a planetary atmosphere, yet multiple mechanisms that may produce them in the absence of life have been described. However, these abiotic planetary mechanisms modify the environment in potentially identifiable ways. Here we briefly discuss two of the most detectable spectral discriminants for abiotic O2/O3: CO and O4. We produce the first explicit self-consistent simulations of these spectral discriminants as they may be seen by JWST. If JWST-NIRISS and/or NIRSpec observe CO (2.35, 4.6 um) in conjunction with CO2 (1.6, 2.0, 4.3 um) in the transmission spectrum of a terrestrial planet it could indicate robust CO2 photolysis and suggest that a future detection of O2 or O3 might not be biogenic. Strong O4 bands seen in transmission at 1.06 and 1.27 um could be diagnostic of a post-runaway O2-dominated atmosphere from massive H-escape. We find that for these false positive scenarios, CO at 2.35 um, CO2 at 2.0 and 4.3 um, and O4 at 1.27 um are all stronger features in transmission than O2/O3 and could be detected with SNRs $\gtrsim$ 3 for an Earth-size planet orbiting a nearby M dwarf star with as few as 10 transits, assuming photon-limited noise. O4 bands could also be sought in UV/VIS/NIR reflected light (at 0.345, 0.36, 0.38, 0.445, 0.475, 0.53, 0.57, 0.63, 1.06, and 1.27 um) by a next generation direct-imaging telescope such as LUVOIR/HDST or HabEx and would indicate an oxygen atmosphere too massive to be biologically produced.Comment: 7 pages, 4 figures, accepted to the Astrophysical Journal Letter

Refraction in exoplanet atmospheres: Photometric signatures, implications for transmission spectroscopy, and search in Kepler data

Refraction deflects photons that pass through atmospheres, which affects transit light curves. Refraction thus provides an avenue to probe physical properties of exoplanet atmospheres and to constrain the presence of clouds and hazes. In addition, an effective surface can be imposed by refraction, thereby limiting the pressure levels probed by transmission spectroscopy. The main objective of the paper is to model the effects of refraction on photometric light curves for realistic planets and to explore the dependencies on atmospheric physical parameters. We also explore under which circumstances transmission spectra are significantly affected by refraction. Finally, we search for refraction signatures in photometric residuals in Kepler data. We use the model of Hui & Seager (2002) to compute deflection angles and refraction transit light curves, allowing us to explore the parameter space of atmospheric properties. The observational search is performed by stacking large samples of transit light curves from Kepler. We find that out-of-transit refraction shoulders are the most easily observable features, which can reach peak amplitudes of ~10 parts per million (ppm) for planets around Sun-like stars. More typical amplitudes are a few ppm or less for Jovians and at the sub-ppm level for super-Earths. Interestingly, the signal-to-noise ratio of any refraction residuals for planets orbiting Sun-like hosts are expected to be similar for planets orbiting red dwarfs. We also find that the maximum depth probed by transmission spectroscopy is not limited by refraction for weakly lensing planets, but that the incidence of refraction can vary significantly for strongly lensing planets. We find no signs of refraction features in the stacked Kepler light curves, which is in agreement with our model predictions.Comment: Accepted for publication in A&

Mapping Exoplanets

The varied surfaces and atmospheres of planets make them interesting places to live, explore, and study from afar. Unfortunately, the great distance to exoplanets makes it impossible to resolve their disk with current or near-term technology. It is still possible, however, to deduce spatial inhomogeneities in exoplanets provided that different regions are visible at different times---this can be due to rotation, orbital motion, and occultations by a star, planet, or moon. Astronomers have so far constructed maps of thermal emission and albedo for short period giant planets. These maps constrain atmospheric dynamics and cloud patterns in exotic atmospheres. In the future, exo-cartography could yield surface maps of terrestrial planets, hinting at the geophysical and geochemical processes that shape them.Comment: Updated chapter for Handbook of Exoplanets, eds. Deeg & Belmonte. 17 pages, including 6 figures and 4 pages of reference

The discovery of WASP-151b, WASP-153b, WASP-156b: Insights on giant planet migration and the upper boundary of the Neptunian desert

To investigate the origin of the features discovered in the exoplanet population, the knowledge of exoplanets’ mass and radius with a good precision (≲10%) is essential. To achieve this purpose the discovery of transiting exoplanets around bright stars is of prime interest. In this paper, we report the discovery of three transiting exoplanets by the SuperWASP survey and the SOPHIE spectrograph with mass and radius determined with a precision better than 15%. WASP-151b and WASP-153b are two hot Saturns with masses, radii, densities and equilibrium temperatures of 0.31−0.03+0.04 MJ, 1.13−0.03+0.03 RJ, 0.22−0.02+0.03 ρJ and 1290−10+20 K, and 0.39−0.02+0.02 MJ, 1.55−0.08+0.10 RJ, 0.11−0.02+0.02 ρJ and 1700−40+40 K, respectively. Their host stars are early G type stars (with mag V ~ 13) and their orbital periods are 4.53 and 3.33 days, respectively. WASP-156b is a super-Neptune orbiting a K type star (mag V = 11.6). It has a mass of 0.128−0.009+0.010 MJ, a radius of 0.51−0.02+0.02 RJ, a density of 1.0−0.1+0.1 ρJ, an equilibrium temperature of 970−20+30 K and an orbital period of 3.83 days. The radius of WASP-151b appears to be only slightly inflated, while WASP-153b presents a significant radius anomaly compared to a recently published model. WASP-156b, being one of the few well characterized super-Neptunes, will help to constrain the still debated formation of Neptune size planets and the transition between gas and ice giants. The estimates of the age of these three stars confirms an already observed tendency for some stars to have gyrochronological ages significantly lower than their isochronal ages. We propose that high eccentricity migration could partially explain this behavior for stars hosting a short period planet. Finally, these three planets also lie close to (WASP-151b and WASP-153b) or below (WASP-156b) the upper boundary of the Neptunian desert. Their characteristics support that the ultra-violet irradiation plays an important role in this depletion of planets observed in the exoplanet population

Polymer reptation and nucleosome repositioning

We consider how beads can diffuse along a chain that wraps them, without becoming displaced from the chain; our proposed mechanism is analogous to the reptation of "stored length" in more familiar situations of polymer dynamics. The problem arises in the case of globular aggregates of proteins (histones) that are wound by DNA in the chromosomes of plants and animals; these beads (nucleosomes) are multiply wrapped and yet are able to reposition themselves over long distances, while remaining bound by the DNA chain.Comment: 9 pages, including 2 figures, to be published in Phys. Rev. Let