Scraping the bottom of the barrel: are rare high throughput sequences artifacts?

Metabarcoding data generated using next-generation sequencing (NGS) technologies are overwhelmed with rare taxa and skewed in Operational Taxonomic Unit (OTU) frequencies comprised of few dominant taxa. Low frequency OTUs comprise a rare biosphere of singleton and doubleton OTUs, which may include many artifacts. We present an in-depth analysis of global singletons across sixteen NGS libraries representing different ribosomal RNA gene regions, NGS technologies and chemistries. Our data indicate that many singletons (average of 38 % across gene regions) are likely artifacts or potential artifacts, but a large fraction can be assigned to lower taxonomic levels with very high bootstrap support (~32 % of sequences to genus with ≥90 % bootstrap cutoff). Further, many singletons clustered into rare OTUs from other datasets highlighting their overlap across datasets or the poor performance of clustering algorithms. These data emphasize a need for caution when discarding rare sequence data en masse: such practices may result in throwing the baby out with the bathwater, and underestimating the biodiversity. Yet, the rare sequences are unlikely to greatly affect ecological metrics. As a result, it may be prudent to err on the side of caution and omit rare OTUs prior to downstream analyses

Cell-specific microarray profiling experiments reveal a comprehensive picture of gene expression in the C. elegans nervous system

A novel strategy for profiling Caenorhabditis elegans cells identifies transcripts highly enriched in either the embryonic or larval C. elegans nervous system, including 19 conserved transcripts of unknown function that are also expressed in the mammalian brain

A Madness to the Method: Fixing the Joint Infringement System for Method Patents after Akamai Technologies, Inc. v. Limelight Networks, Inc.

The Federal Circuit’s 2012 joint decision in Akamai Technologies, Inc. v. Limelight Networks, Inc. and McKesson Technologies, Inc. v. Epic Systems Corporation marked a pivotal moment in the federal courts’ development and application of joint patent infringement. In overruling the “single-entity” and “control or direction” rules and establishing a new “inducement-only” rule, the Federal Circuit case destroyed the backbone of joint infringement jurisprudence without a second thought. Surprisingly, the en banc majority avoided several of the primary concerns that were the basis for the en banc rehearing in the first place, including whether or not direct infringement can occur through the joint actions of multiple entities. In contrast, Judge Newman’s dissenting opinion identified the shortcomings of both the previous law as well as the majority’s new rule and proposed an alternative approach which would bring a level of stability to the area of joint patent infringement that has not existed for decades. This Comment will first explain the historical development of joint patent infringement, the major judicial and legislative steps that lead to the present state of the law, including an examination of each of the Akamai Techs., Inc. v. Limelight Networks, Inc. opinions and the newly established “inducement-only” rule. This Comment will then discuss the inadequacies that will result from the adoption of either the majority’s opinion or Judge Linn’s dissenting opinion. Finally, this Comment will propose the implementation of Judge Newman’s recommendations and opinion and the benefits which it will entail in creating clarity and protection for method patent owners