The ARRIVE guidelines 2019 updated guidelines for reporting animal research, bioRxiv, 2019-07-15
AbstractReproducible science requires transparent reporting. The ARRIVE guidelines were originally developed in 2010 to improve the reporting of animal research. They consist of a checklist of information to include in publications describing in vivo experiments to enable others to scrutinise the work adequately, evaluate its methodological rigour, and reproduce the methods and results. Despite considerable levels of endorsement by funders and journals over the years, adherence to the guidelines has been inconsistent, and the anticipated improvements in the quality of reporting in animal research publications have not been achieved.Here we introduce ARRIVE 2019. The guidelines have been updated and information reorganised to facilitate their use in practice. We used a Delphi exercise to prioritise the items and split the guidelines into two sets, the ARRIVE Essential 10, which constitute the minimum requirement, and the Recommended Set, which describes the research context. This division facilitates improved reporting of animal research by supporting a stepwise approach to implementation. This helps journal editors and reviewers to verify that the most important items are being reported in manuscripts. We have also developed the accompanying Explanation and Elaboration document that serves 1) to explain the rationale behind each item in the guidelines, 2) to clarify key concepts and 3) to provide illustrative examples. We aim through these changes to help ensure that researchers, reviewers and journal editors are better equipped to improve the rigour and transparency of the scientific process and thus reproducibility.
biorxiv scientific-communication-and-education 0-100-users 2019Releasing a preprint is associated with more attention and citations for the peer-reviewed article, bioRxiv, 2019-07-14
AbstractPreprints in biology are gaining popularity, but release of a preprint still precedes only a fraction of peer-reviewed publications. We examined whether having a preprint on bioRxiv was associated with metrics of the corresponding peer-reviewed article. We assembled a dataset of 74,239 articles, 5,405 of which had a preprint, published in 39 journals. Based on log-linear regression and random-effects meta-analysis, articles with a preprint had a 51% higher Altmetric Attention Score and 37% more citations compared to articles without one. These associations were independent of several other article- and author-level variables (e.g., scientific subfield and last author publication age) and unrelated to journal-level variables such as access model and Impact Factor. This observational study can help researchers and publishers make informed decisions about how to incorporate preprints into their work.
biorxiv scientific-communication-and-education 200-500-users 2019souporcell Robust clustering of single cell RNAseq by genotype and ambient RNA inference without reference genotypes, bioRxiv, 2019-07-14
Methods to deconvolve single-cell RNA sequencing (scRNAseq) data are necessary for samples containing a natural mixture of genotypes and for scRNAseq experiments that multiplex cells from different donors1. Multiplexing across donors is a popular experimental design with many benefits including avoiding batch effects2, reducing costs, and improving doublet detection. Using variants detected in the RNAseq reads, it is possible to assign cells to the individuals from which they arose. These variants can also be used to identify and remove cross-genotype doublet cells that may have highly similar transcriptional profiles precluding detection by transcriptional profile. More subtle cross-genotype variant contamination can be used to estimate the amount of ambient RNA in the system. Ambient RNA is caused by cell lysis prior to droplet partitioning and is an important confounder of scRNAseq analysis3. Souporcell is a novel method to cluster cells using only the genetic variants detected within the scRNAseq reads. We show that it achieves high accuracy on genotype clustering, doublet detection, and ambient RNA estimation as demonstrated across a wide range of challenging scenarios.
biorxiv bioinformatics 0-100-users 2019Assembly of hundreds of novel bacterial genomes from the chicken caecum, bioRxiv, 2019-07-12
AbstractChickens are a highly important source of protein for a large proportion of the human population. The caecal microbiota plays a crucial role in chicken nutrition through the production of short chain fatty acids, nitrogen recycling and amino acid production. In this study we sequenced DNA from caecal contents samples taken from 24 chickens belonging to either a fast or slower growing breed consuming either a vegetable-only diet or a diet containing fish meal. We utilised 1.6T of Illumina data to construct 469 draft metagenome-assembled bacterial genomes, including 460 novel strains, 283 novel species and 42 novel genera. We compared our genomes to data from eight EU countries and show that these genomes are abundant within European chicken flocks. We also compared the abundance of our genomes, and the carbohydrate active enzymes they produce, between our chicken groups and demonstrate that there are both breed- and diet-specific microbiomes, as well as an overlapping core microbiome. This data will form the basis for future studies examining the composition and function of the chicken caecal microbiota.
biorxiv microbiology 0-100-users 2019