BACKGROUND: Plasmids and viruses are two types of mobile genetic elements (ME), that rely on host cells to reproduce and propagate themselves. Recently, metagenomics has greatly facilitated the discovery and characterization of new plasmids and viruses, which relies on accurate identification of these reads in metagenomes. Some state-of-the-art tools can identify plasmid or viral reads, while others are able to identify the probable host or source species of these reads. Since the Minimizer-based Naïve Bayes Classifier (MNBC) tool accurately classifies chromosomal and viral reads to the species level, we extended it to develop the MNBC-ME tool that can also identify plasmid reads and their putative host species. RESULTS: A standard reference- and test-sequence framework using simulated variable-length reads was used to benchmark MNBC-ME with eleven other state-of-the-art tools for ME identification: DeepMicroClass, geNomad, PPR-Meta, viralVerify, Plasmer, PlasClass, PlasX, VIBRANT, DeepVirFinder, HOTSPOT, and MOSTPLAS. MNBC-ME was the most consistent tool at classifying chromosomal, viral and plasmid reads of variable lengths, in contrast to the other tools whose precision or recall dropped below 50% in some circumstances. MNBC-ME also exceeded 65% and 70% performance in predicting host genus and family of plasmid reads, respectively. CONCLUSIONS: MNBC-ME is tool for identification of both short and long viral- and plasmid-originated reads across a wide variety of read types. It also identifies potential low-level host taxa for plasmid reads, and source taxa for chromosomal and viral reads. It is freely available at https://github.com/ComputationalPathogens/MNBC-ME and can be found as the 'mnbc-me' package in bioconda.

MOTIVATION: State-of-the-art tools for classifying metagenomic sequencing reads provide both rapid and accurate options, although the combination of both in a single tool is a constantly improving area of research. The machine learning-based Naïve Bayes Classifier (NBC) approach provides a theoretical basis for accurate classification of all reads in a sample. RESULTS: We developed the multithreaded Minimizer-based Naïve Bayes Classifier (MNBC) tool to improve the NBC approach by applying minimizers, as well as plurality voting for closely related classification scores. A standard reference- and test-sequence framework using simulated variable-length reads benchmarked MNBC with six other state-of-the-art tools: MetaMaps, Ganon, Kraken2, KrakenUniq, CLARK, and Centrifuge. We also applied MNBC to the "marine" and "strain-madness" short-read metagenomic datasets in the Critical Assessment of Metagenome Interpretation (CAMI) II challenge using a corresponding database from the time. MNBC efficiently identified reads from unknown microorganisms, and exhibited the highest species- and genus-level precision and recall on short reads, as well as the highest species-level precision on long reads. It also achieved the highest accuracy on the "strain-madness" dataset. AVAILABILITY AND IMPLEMENTATION: MNBC is freely available at: https://github.com/ComputationalPathogens/MNBC.

Pneumatic, non-contact end effectors for robotic pick-and-place applications use compressed air to provide an adhesion force based on the Bernoulli principle, which creates a low pressure region near the surface of the end effector. However, consideration of the influence of the Bernoulli principle alone gives an inadequate account of the performance of some end effector designs. In fact, end effector geometry can be constructed in such a way that the Bernoulli principle provides only a small contribution to the overall adhesion force. This paper investigates the role of viscous flow entrainment in improving adhesion efficiency. Both simulation and experimental results show a significant improvement of adhesion force by nearly five times over a commercially available Bernoulli gripper, which makes the improved adhesion mechanism suitable for more demanding wall climbing robotic applications.

Requirements is too often seen as a "stenographer's task", one where the requirements engineer passively listens and records while the stakeholders state their needs. However, this approach relies on stakeholders knowing what they need, and what they want. Experience tells us that except for rare visionaries, people do not know what they want until they see it. Many of the useful products that we take for granted today, did not come about from the stakeholders' imagination, but from an invention. In this tutorial we explain and illustrate how to use creative techniques to invent requirements that result in more useful, usable and competitive products. We provide a guide for invention, and show participants how to use this guide to invent innovative requirements for a familiar system.