2,933 research outputs found
Titan solar occultation observations reveal transit spectra of a hazy world
High altitude clouds and hazes are integral to understanding exoplanet
observations, and are proposed to explain observed featureless transit spectra.
However, it is difficult to make inferences from these data because of the need
to disentangle effects of gas absorption from haze extinction. Here, we turn to
the quintessential hazy world -- Titan -- to clarify how high altitude hazes
influence transit spectra. We use solar occultation observations of Titan's
atmosphere from the Visual and Infrared Mapping Spectrometer (VIMS) aboard
NASA's Cassini spacecraft to generate transit spectra. Data span 0.88-5 microns
at a resolution of 12-18 nm, with uncertainties typically smaller than 1%. Our
approach exploits symmetry between occultations and transits, producing transit
radius spectra that inherently include the effects of haze multiple scattering,
refraction, and gas absorption. We use a simple model of haze extinction to
explore how Titan's haze affects its transit spectrum. Our spectra show strong
methane absorption features, and weaker features due to other gases. Most
importantly, the data demonstrate that high altitude hazes can severely limit
the atmospheric depths probed by transit spectra, bounding observations to
pressures smaller than 0.1-10 mbar, depending on wavelength. Unlike the usual
assumption made when modeling and interpreting transit observations of
potentially hazy worlds, the slope set by haze in our spectra is not flat, and
creates a variation in transit height whose magnitude is comparable to those
from the strongest gaseous absorption features. These findings have important
consequences for interpreting future exoplanet observations, including those
from NASA's James Webb Space Telescope.Comment: Updated journal reference; data available via
http://sites.google.com/site/tdrobinsonscience/science/tita
pubassistant.ch: consolidating publication profiles of researchers
Online accounts to keep track of scientific publications, such as Open Researcher and Contributor ID (ORCID) or Google Scholar, can be time consuming to maintain and synchronize. Furthermore, the open access status of publications is often not easily accessible, hindering potential opening of closed publications. To lessen the burden of managing personal profiles, we developed a R shiny app that allows publication lists from multiple platforms to be retrieved and consolidated, as well as interactive exploration and comparison of publication profiles. A live version can be found at pubassistant.ch
A scaling normalization method for differential expression analysis of RNA-seq data
A novel and empirical method for normalization of RNA-seq data is presente
Gapless provides combined scaffolding, gap filling, and assembly correction with long reads
Continuity, correctness, and completeness of genome assemblies are important for many biological projects. Long reads represent a major driver towards delivering high-quality genomes, but not everybody can achieve the necessary coverage for good long read-only assemblies. Therefore, improving existing assemblies with low-coverage long reads is a promising alternative. The improvements include correction, scaffolding, and gap filling. However, most tools perform only one of these tasks and the useful information of reads that supported the scaffolding is lost when running separate programs successively. Therefore, we propose a new tool for combined execution of all three tasks using PacBio or Oxford Nanopore reads. gapless is available at: https://github.com/schmeing/gapless
From RNA-seq reads to differential expression results
Many methods and tools are available for preprocessing high-throughput RNA sequencing data and detecting differential expression
Robustly detecting differential expression in RNA sequencing data using observation weights
A popular approach for comparing gene expression levels between (replicated) conditions of RNA sequencing data relies on counting reads that map to features of interest. Within such count-based methods, many flexible and advanced statistical approaches now exist and offer the ability to adjust for covariates (e.g. batch effects). Often, these methods include some sort of ‘sharing of information' across features to improve inferences in small samples. It is important to achieve an appropriate tradeoff between statistical power and protection against outliers. Here, we study the robustness of existing approaches for count-based differential expression analysis and propose a new strategy based on observation weights that can be used within existing frameworks. The results suggest that outliers can have a global effect on differential analyses. We demonstrate the effectiveness of our new approach with real data and simulated data that reflects properties of real datasets (e.g. dispersion-mean trend) and develop an extensible framework for comprehensive testing of current and future methods. In addition, we explore the origin of such outliers, in some cases highlighting additional biological or technical factors within the experiment. Further details can be downloaded from the project website: http://imlspenticton.uzh.ch/robinson_lab/edgeR_robus
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