Signs of strong Na and K absorption in the transmission spectrum of WASP-103b

Context: Transmission spectroscopy has become a prominent tool for characterizing the atmospheric properties on close-in transiting planets. Recent observations have revealed a remarkable diversity in exoplanet spectra, which show absorption signatures of Na, K and $\mathrm{H_2O}$, in some cases partially or fully attenuated by atmospheric aerosols. Aerosols (clouds and hazes) themselves have been detected in the transmission spectra of several planets thanks to wavelength-dependent slopes caused by the particles' scattering properties. Aims: We present an optical 550 - 960 nm transmission spectrum of the extremely irradiated hot Jupiter WASP-103b, one of the hottest (2500 K) and most massive (1.5 $M_J$) planets yet to be studied with this technique. WASP-103b orbits its star at a separation of less than 1.2 times the Roche limit and is predicted to be strongly tidally distorted. Methods: We have used Gemini/GMOS to obtain multi-object spectroscopy hroughout three transits of WASP-103b. We used relative spectrophotometry and bin sizes between 20 and 2 nm to infer the planet's transmission spectrum. Results: We find that WASP-103b shows increased absorption in the cores of the alkali (Na, K) line features. We do not confirm the presence of any strong scattering slope as previously suggested, pointing towards a clear atmosphere for the highly irradiated, massive exoplanet WASP-103b. We constrain the upper boundary of any potential cloud deck to reside at pressure levels above 0.01 bar. This finding is in line with previous studies on cloud occurrence on exoplanets which find that clouds dominate the transmission spectra of cool, low surface gravity planets while hot, high surface gravity planets are either cloud-free, or possess clouds located below the altitudes probed by transmission spectra.Comment: Accepted for publication in A&

PyTranSpot\texttt{PyTranSpot} - A tool for multiband light curve modeling of planetary transits and stellar spots

Several studies have shown that stellar activity features, such as occulted and non-occulted starspots, can affect the measurement of transit parameters biasing studies of transit timing variations and transmission spectra. We present $\texttt{PyTranSpot}$, which we designed to model multiband transit light curves showing starspot anomalies, inferring both transit and spot parameters. The code follows a pixellation approach to model the star with its corresponding limb darkening, spots, and transiting planet on a two dimensional Cartesian coordinate grid. We combine $\texttt{PyTranSpot}$ with an MCMC framework to study and derive exoplanet transmission spectra, which provides statistically robust values for the physical properties and uncertainties of a transiting star-planet system. We validate $\texttt{PyTranSpot}$'s performance by analyzing eleven synthetic light curves of four different star-planet systems and 20 transit light curves of the well-studied WASP-41b system. We also investigate the impact of starspots on transit parameters and derive wavelength dependent transit depth values for WASP-41b covering a range of 6200-9200 $\AA$, indicating a flat transmission spectrum.Comment: 17 pages, 22 figures; accepted for publication in Astronomy & Astrophysic

Topological Designs

We give an exponential upper and a quadratic lower bound on the number of pairwise non-isotopic simple closed curves can be placed on a closed surface of genus g such that any two of the curves intersects at most once. Although the gap is large, both bounds are the best known for large genus. In genus one and two, we solve the problem exactly. Our methods generalize to variants in which the allowed number of pairwise intersections is odd, even, or bounded, and to surfaces with boundary components.Comment: 14 p., 4 Figures. To appear in Geometriae Dedicat

Crossing and weighted crossing number of near-planar graphs

A nonplanar graph G is near-planar if it contains an edge e such that G − e is planar. The problem of determining the crossing number of a near-planar graph is exhibited from different combinatorial viewpoints. On the one hand, we develop min-max formulas involving efficiently computable lower and upper bounds. These min-max results are the first of their kind in the study of crossing numbers and improve the approximation factor for the approximation algorithm given by Hliněny and Salazar (Graph Drawing GD’06). On the other hand, we show that it is NP-hard to compute a weighted version of the crossing number for near-planar graphs

RNAmotifs : Prediction of multivalent RNA motifs that control alternative splicing

RNA-binding proteins (RBPs) regulate splicing according to position-dependent principles, which can be exploited for analysis of regulatory motifs. Here we present RNAmotifs, a method that evaluates the sequence around differentially regulated alternative exons to identify clusters of short and degenerate sequences, referred to as multivalent RNA motifs. We show that diverse RBPs share basic positional principles, but differ in their propensity to enhance or repress exon inclusion. We assess exons differentially spliced between brain and heart, identifying known and new regulatory motifs, and predict the expression pattern of RBPs that bind these motifs

Tools and data services registry: a community effort to document bioinformatics resources.

Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.Here we present a community-driven curation effort, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners.As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools

The Sterolgene v0 cDNA microarray: a systemic approach to studies of cholesterol homeostasis and drug metabolism

<p>Abstract</p> <p>Background</p> <p>Cholesterol homeostasis and xenobiotic metabolism are complex biological processes, which are difficult to study with traditional methods. Deciphering complex regulation and response of these two processes to different factors is crucial also for understanding of disease development. Systems biology tools as are microarrays can importantly contribute to this knowledge and can also discover novel interactions between the two processes.</p> <p>Results</p> <p>We have developed a low density Sterolgene v0 cDNA microarray dedicated to studies of cholesterol homeostasis and drug metabolism in the mouse. To illustrate its performance, we have analyzed mouse liver samples from studies focused on regulation of cholesterol homeostasis and drug metabolism by diet, drugs and inflammation. We observed down-regulation of cholesterol biosynthesis during fasting and high-cholesterol diet and subsequent up-regulation by inflammation. Drug metabolism was down-regulated by fasting and inflammation, but up-regulated by phenobarbital treatment and high-cholesterol diet. Additionally, the performance of the Sterolgene v0 was compared to the two commercial high density microarray platforms: the Agilent cDNA (G4104A) and the Affymetrix MOE430A GeneChip. We hybridized identical RNA samples to the commercial microarrays and showed that the performance of Sterolgene is comparable to commercial arrays in terms of detection of changes in cholesterol homeostasis and drug metabolism.</p> <p>Conclusion</p> <p>Using the Sterolgene v0 microarray we were able to detect important changes in cholesterol homeostasis and drug metabolism caused by diet, drugs and inflammation. Together with its next generations the Sterolgene microarrays represent original and dedicated tools enabling focused and cost effective studies of cholesterol homeostasis and drug metabolism. These microarrays have the potential of being further developed into screening or diagnostic tools.</p

High precision ground-based CCD photometry from the Next Generation Transit Survey

The Next Generation Transit Survey (NGTS) has now been operating for six years, discovering and characterizing transiting exoplanets around bright stars. We outline the NGTS project, including the Andor CCD cameras used to perform high-precision time-series photometry. We quantify the photometric precision for a sample of over 20,000 bright star observations. We find for single NGTS telescope observations we achieve a 30-minute photometric precision of 400 ppm at low airmass. This is in good agreement with the photometric noise predicted using a four-component noise model. We find that the photometric noise for bright stars (G < 12) is dominated by atmospheric scintillation. We also present details of the NGTS multi-telescope observing mode, whereby 12 telescopes can be used simultaneously on a single target star to achieve a 30-minute photometric precision of 100 ppm. Finally, we describe a new generation scientific CMOS camera that we will be testing on-sky at the NGTS facility to determine if it can compete with state-of-the-art CCD cameras used for high precision bright star photometry