ggplot2: Elegant Graphics for Data Analysis

Abstracts not available for BookReview

Optimization of insect odorant receptor trafficking and functional expression via transient transfection in HEK293 cells

Insect odorant receptors show a limited functional expression in various heterologous expression systems including insect and mammalian cells. This may be in part due to the absence of key components driving the release of these proteins from the endoplasmic reticulum and directing them to the plasma membrane. In order to mitigate this problem we took advantage of small export signals within the human HCN1 and Rhodopsin that have been shown to promote protein release from the endoplasmic reticulum and the trafficking of post-Golgi vesicles, respectively. Moreover, we designed a new vector based on a bidirectional expression cassette to drive the functional expression of the insect odorant receptor co-receptor (Orco) and an odor-binding odorant receptor, simultaneously. We show that this new method can be used to reliably express insect odorant receptors in HEK293 cells via transient transfection and that is highly suitable for downstream applications using automated and high-throughput imaging platforms

Overlapping: a R package for Estimating Overlapping in Empirical Distributions

overlapping is an R package for estimating the overlapping area of two or more kernel density estimations from empirical data. The main idea of the package is to offer an easy way to quantify the similarity (or the difference) between two or more empirical distributions

The Computer as Filter Machine: A Clustering Approach to Categorize Artworks Based on a Social Tagging Network

Image catalogs containing several million reproductions of artworks still pose a costly or computationally intensive challenge if one tries to categorize them adequately, either in a manual or automatic way. Using crowdsourced annotations assigned by laypersons, this article proposes the application of a clustering algorithm to segment artworks into groups. It is shown that the resulting clusters allow for a consistent reclassification extending the traditional categories (history, genre, portrait, still life, landscape), and thus enable a finely-grained differentiation which can be used to search in and filter image inventories, among other things

Boulder Bands on Lobate Debris Aprons: Does Spatial Clustering Reveal Accumulation History for Martian Glaciations?

Glacial landforms such as lobate debris aprons (LDA) and Concentric Crater Fill (CCF) are the dominant debris-covered glacial landforms on Mars. These landforms represent a volumetrically significant component of the Amazonian water ice budget, however, because small craters (diameter D 0.5-1 km) are poorly retained glacial brain terrain surfaces, and, since the glacial landforms are geologically young, it is challenging to reliably constrain either individual glacial deposit ages or formational sequences in order to determine how quickly the glaciers accumulated. A fundamental question remaining is whether ice deposition and flow that formed LDA occurred episodically during a few, short instances, or whether glacial flow was quasi-continuous over a long period (~108 yr). Because glaciation is thought to be controlled largely by obliquity excursions, a larger question is whether glacial deposits on Mars exhibit regional to global characteristics that can be used to infer synchronicity of flow or degradation

Keep Me Around: Intron Retention Detection and Analysis

We present a tool, keep me around (kma), a suite of python scripts and an R package that finds retained introns in RNA-Seq experiments and incorporates biological replicates to reduce the number of false positives when detecting retention events. kma uses the results of existing quantification tools that probabilistically assign multi-mapping reads, thus interfacing easily with transcript quantification pipelines. The data is represented in a convenient, database style format that allows for easy aggregation across introns, genes, samples, and conditions to allow for further exploratory analysis

Comparing long-term crop yields of a short rotation alley cropping agroforestry system and of a standard agricultural field in northern Germany

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