Seasonal and inter-annual patterns of sediment-water nutrient and oxygen fluxes in Mobile Bay, Alabama (USA): Regulating factors and ecological significance.

Sediment oxygen and nutrient fluxes were measured monthly for 2 yr in Mobile Bay, Alabama, USA. Rates of sediment oxygen consumption (0.1 to 1.25 gO2 m-2 d-1), ammonium flux (-22 to 181 µmol m-2 h-1), nitrate flux (-14 to 67 µmol m-2 h-1), phosphate flux (-2 to 20.4 µmol m-2 h-1), and dissolved silicate flux (-15 to 342 µmol m-2 h-1) were moderate to high compared to values for other estuaries. A step-wise regression analysis revealed that dissolved oxygen concentration and temperature in bottom-waters explained much of the variance in fluxes. This is presumably because of their influence on rates of microbial and physico-chemical processes. Organic matter availability was not found to be an important factor in regulating temporal (month to month) variability of fluxes, possibly because frequent resuspension of the sediments in this shallow system rendered indices of sediment organic matter nearly constant with time. However, warm season-averaged sediment nutrient releases were correlated with sediment chlorophyll a. This relationship in Mobile Bay is in strong agreement with similar relationships found in other estuarine systems, and suggests that the availability of labile organic matter ultimately regulates the maximum rate of nutrient release by the sediments. Annually averaged sediment fluxes supplied 36% of the nitrogen (N) and 25% of the phosphorus (P) required by phytoplankton in Mobile Bay. While this is not particularly high compared to other estuaries, monthly estimates show that the sediments can supply from 0 to 94% of the N, and 0 to 83% of the P required by phytoplankton. In addition, flux ratios show that N and P are released from sediments at N:P ratios that rapidly switch from above (maximum 98) to below (minimum 1.2) that required for phytoplankton growth. This pattern is different from cooler temperate systems, where such switching is seasonally base

Inelastic X-ray Scattering by Electronic Excitations in Solids at High Pressure

Investigating electronic structure and excitations under extreme conditions gives access to a rich variety of phenomena. High pressure typically induces behavior such as magnetic collapse and the insulator-metal transition in 3d transition metals compounds, valence fluctuations or Kondo-like characteristics in $f$-electron systems, and coordination and bonding changes in molecular solids and glasses. This article reviews research concerning electronic excitations in materials under extreme conditions using inelastic x-ray scattering (IXS). IXS is a spectroscopic probe of choice for this study because of its chemical and orbital selectivity and the richness of information it provides. Being an all-photon technique, IXS has a penetration depth compatible with high pressure requirements. Electronic transitions under pressure in 3d transition metals compounds and $f$-electron systems, most of them strongly correlated, are reviewed. Implications for geophysics are mentioned. Since the incident X-ray energy can easily be tuned to absorption edges, resonant IXS, often employed, is discussed at length. Finally studies involving local structure changes and electronic transitions under pressure in materials containing light elements are briefly reviewed.Comment: submitted to Rev. Mod. Phy

A Spitzer Transmission Spectrum for the Exoplanet GJ 436b, Evidence for Stellar Variability, and Constraints on Dayside Flux Variations

In this paper we describe a uniform analysis of eight transits and eleven secondary eclipses of the extrasolar planet GJ 436b obtained in the 3.6, 4.5, and 8.0 micron bands using the IRAC instrument on the Spitzer Space Telescope between UT 2007 June 29 and UT 2009 Feb 4. We find that the best-fit transit depths for visits in the same bandpass can vary by as much as 8% of the total (4.7 sigma significance) from one epoch to the next. Although we cannot entirely rule out residual detector effects or a time-varying, high-altitude cloud layer in the planet's atmosphere as the cause of these variations, we consider the occultation of active regions on the star in a subset of the transit observations to be the most likely explanation. We reconcile the presence of magnetically active regions with the lack of significant visible or infrared flux variations from the star by proposing that the star's spin axis is tilted with respect to our line of sight, and that the planet's orbit is therefore likely to be misaligned. These observations serve to illustrate the challenges associated with transmission spectroscopy of planets orbiting late-type stars; we expect that other systems, such as GJ 1214, may display comparably variable transit depths. Our measured 8 micron secondary eclipse depths are consistent with a constant value, and we place a 1 sigma upper limit of 17% on changes in the planet's dayside flux in this band. Averaging over the eleven visits gives us an improved estimate of 0.0452% +/- 0.0027% for the secondary eclipse depth. We combine timing information from our observations with previously published data to produce a refined orbital ephemeris, and determine that the best-fit transit and eclipse times are consistent with a constant orbital period. [ABRIDGED]Comment: 26 pages, 18 figures, 7 tables in emulateapj format. Accepted for publication in Ap

The gut microbiomes of two Pachysoma MacLeay desert dung beetle species (Coleoptera: Scarabaeidae: Scarabaeinae) feeding on different diets

Micro-organisms inhabiting animal guts benefit from a protected and nutrient-rich environment while assisting the host with digestion and nutrition. In this study we compare, for the first time, the bacterial and fungal gut communities of two species of the small desert dung beetle genus Pachysoma feeding on different diets: the detritivorous P. endroedyi and the dry-dung-feeding P. striatum. Whole-gut microbial communities from 5 individuals of each species were assessed using 454 pyrosequencing of the bacterial 16S rRNA gene and fungal ITS gene regions. The two bacterial communities were significantly different, with only 3.7% of operational taxonomic units shared, and displayed intra-specific variation. The number of bacterial phyla present within the guts of P. endroedyi and P. striatum individuals ranged from 6–11 and 4–7, respectively. Fungal phylotypes could only be detected within the gut of P. striatum. Although the role of host phylogeny in Pachysoma microbiome assembly remains unknown, evidence presented in this study suggests that host diet may be a deterministic factor.S1 Fig. Rarefactions curves showing gut microbial community richness of all Pachysoma individuals for bacterial 16S rRNA gene amplicon data of: a) P. endroedyi, b) P. striatum; and c) fungal ITS gene region amplicon data of P. striatum.S2 Fig. Photographs of P. endroedyi (a) and P. striatum (b) in their natural environment before collection (courtesy of Hennie de Klerk).http://www.plosone.orgam2016Genetic

Protocol for the development of a core outcome set and reporting guidelines for locoregional treatment in neoadjuvant systemic breast cancer treatment trials: the PRECEDENT project

Introduction: Neoadjuvant systemic anticancer therapy (neoSACT) is increasingly used in the treatment of early breast cancer. Response to therapy is prognostic and allows locoregional and adjuvant systemic treatments to be tailored to minimise morbidity and optimise oncological outcomes and quality of life. Accurate information about locoregional treatments following neoSACT is vital to allow the translation of downstaging benefits into practice and facilitate meaningful interpretation of oncological outcomes, particularly locoregional recurrence. Reporting of locoregional treatments in neoSACT studies, however, is currently poor. The development of a core outcome set (COS) and reporting guidelines is one strategy by which this may be improved. Methods and analysis: A COS for reporting locoregional treatment (surgery and radiotherapy) in neoSACT trials will be developed in accordance with Core Outcome Measures in Effectiveness Trials (COMET) and Core Outcome Set-Standards for Development guidelines. Reporting guidance will be developed concurrently. The project will have three phases: (1) generation of a long list of relevant outcome domains and reporting items from a systematic review of published neoSACT studies and interviews with key stakeholders. Identified items and domains will be categorised and formatted into Delphi consensus questionnaire items. (2) At least two rounds of an international online Delphi survey in which at least 250 key stakeholders (surgeons/oncologists/radiologists/pathologists/trialists/methodologists) will score the importance of reporting each outcome. (3) A consensus meeting with key stakeholders to discuss and agree the final COS and reporting guidance. Ethics and dissemination: Ethical approval for the consensus process will be obtained from the Queen’s University Belfast Faculty Ethics Committee. The COS/reporting guidelines will be presented at international meetings and published in peer-reviewed journals. Dissemination materials will be produced in collaboration with our steering group and patient advocates so the results can be shared widely. Registration: The study has been prospectively registered on the COMET website (https://www.comet-initiative.org/Studies/Details/2854)

Transiting Exoplanet Studies and Community Targets for JWST's Early Release Science Program

The James Webb Space Telescope will revolutionize transiting exoplanet atmospheric science due to its capability for continuous, long-duration observations and its larger collecting area, spectral coverage, and spectral resolution compared to existing space-based facilities. However, it is unclear precisely how well JWST will perform and which of its myriad instruments and observing modes will be best suited for transiting exoplanet studies. In this article, we describe a prefatory JWST Early Release Science (ERS) program that focuses on testing specific observing modes to quickly give the community the data and experience it needs to plan more efficient and successful future transiting exoplanet characterization programs. We propose a multi-pronged approach wherein one aspect of the program focuses on observing transits of a single target with all of the recommended observing modes to identify and understand potential systematics, compare transmission spectra at overlapping and neighboring wavelength regions, confirm throughputs, and determine overall performances. In our search for transiting exoplanets that are well suited to achieving these goals, we identify 12 objects (dubbed "community targets") that meet our defined criteria. Currently, the most favorable target is WASP-62b because of its large predicted signal size, relatively bright host star, and location in JWST's continuous viewing zone. Since most of the community targets do not have well-characterized atmospheres, we recommend initiating preparatory observing programs to determine the presence of obscuring clouds/hazes within their atmospheres. Measurable spectroscopic features are needed to establish the optimal resolution and wavelength regions for exoplanet characterization. Other initiatives from our proposed ERS program include testing the instrument brightness limits and performing phase-curve observations.(Abridged)Comment: This is a white paper that originated from an open discussion at the Enabling Transiting Exoplanet Science with JWST workshop held November 16 - 18, 2015 at STScI (http://www.stsci.edu/jwst/science/exoplanets). Accepted for publication in PAS

Asymmetry of Early Endosome Distribution in C. elegans Embryos

development, we examined the distribution and dynamics of early endosomes (EEs) in embryos.EEs are primarily found at the cell periphery with an initially uniform distribution after fertilization. Strikingly, we find that during the first cell cycle, EEA-1 positive EEs become enriched at the anterior cortex. In contrast, the Golgi compartment shows no asymmetry in distribution. Asymmetric enrichment of EEs depends on acto-myosin contractility and embryonic PAR polarity. In addition to their localization at the cortex, EEs are also found around the centrosome. These EEs move rapidly (1.3um/s) from the cortex directly to the centrosome, a speed comparable to that of the minus end directed motor dynein.We speculate that the asymmetry of early endosomes might play a role in cell asymmetries or fate decisions

The Roasting Marshmallows Program with IGRINS on Gemini South I: Composition and Climate of the Ultra Hot Jupiter WASP-18 b

We present high-resolution dayside thermal emission observations of the exoplanet WASP-18b using IGRINS on Gemini South. We remove stellar and telluric signatures using standard algorithms, and we extract the planet signal via cross correlation with model spectra. We detect the atmosphere of WASP-18b at a signal-to-noise ratio (SNR) of 5.9 using a full chemistry model, measure H2O (SNR=3.3), CO (SNR=4.0), and OH (SNR=4.8) individually, and confirm previous claims of a thermal inversion layer. The three species are confidently detected (>4$\sigma$) with a Bayesian inference framework, which we also use to retrieve abundance, temperature, and velocity information. For this ultra-hot Jupiter (UHJ), thermal dissociation processes likely play an important role. Retrieving abundances constant with altitude and allowing the temperature-pressure profile to freely adjust results in a moderately super-stellar carbon to oxygen ratio (C/O=0.75^{+0.14}_{-0.17}) and metallicity ([M/H]=1.03^{+0.65}_{-1.01}). Accounting for undetectable oxygen produced by thermal dissociation leads to C/O=0.45^{+0.08}_{-0.10} and [M/H]=1.17^{+0.66}_{-1.01}. A retrieval that assumes radiative-convective-thermochemical-equilibrium and naturally accounts for thermal dissociation constrains C/O<0.34 (2$\sigma$) and [M/H]=0.48^{+0.33}_{-0.29}, in line with the chemistry of the parent star. Looking at the velocity information, we see a tantalising signature of different Doppler shifts at the level of a few km/s for different molecules, which might probe dynamics as a function of altitude and location on the planet disk. Our results demonstrate that ground-based, high-resolution spectroscopy at infrared wavelengths can provide meaningful constraints on the compositions and climate of highly irradiated planets. This work also elucidates potential pitfalls with commonly employed retrieval assumptions when applied to UHJ spectra.Comment: 27 pages, 18 figures, submitted to AAS Journals. Community feedback welcom

Smaller than expected bright-spot offsets in Spitzer phase curves of the hot Jupiter Qatar-1b

We present \textit{Spitzer} full-orbit thermal phase curves of the hot Jupiter Qatar-1b, a planet with the same equilibrium temperature---and intermediate surface gravity and orbital period---as the well-studied planets HD 209458b and WASP-43b. We measure secondary eclipse of $0.21 \pm 0.02 \%$ at $3.6~\mu$m and $0.30 \pm 0.02 \%$ at $4.5~\mu$m, corresponding to dayside brightness temperatures of $1542^{+32}_{-31}$~K and $1557^{+35}_{-36}$~K, respectively, consistent with a vertically isothermal dayside. The respective nightside brightness temperatures are $1117^{+76}_{-71}$~K and $1167^{+69}_{-74}$~K, in line with a trend that hot Jupiters all have similar nightside temperatures. We infer a Bond albedo of $0.12_{-0.16}^{+0.14}$ and a moderate day-night heat recirculation efficiency, similar to HD 209458b. General circulation models for HD 209458b and WASP-43b predict that their bright-spots should be shifted east of the substellar point by tens of degrees, and these predictions were previously confirmed with \textit{Spitzer} full-orbit phase curve observations. The phase curves of Qatar-1b are likewise expected to exhibit eastward offsets. Instead, the observed phase curves are consistent with no offset: $11^{\circ}\pm 7^{\circ}$ at $3.6~\mu$m and $-4^{\circ}\pm 7^{\circ}$ at $4.5~\mu$m. The discrepancy in circulation patterns between these three otherwise similar planets points to the importance of secondary parameters like rotation rate and surface gravity, and the presence or absence of clouds, in determining atmospheric conditions on hot Jupiters.Comment: 14 pages, 8 figures. Accepted for publication in A