Search

Correct annotation metadata is critical for reproducible and accurate RNA-seq analysis. When files are shared publicly or among collaborators with incorrect or missing annotation metadata, it becomes difficult or impossible to reproduce bioinformatic analyses from raw data. It also makes it more difficult to locate the transcriptomic features, such as transcripts or genes, in their proper genomic context, which is necessary for overlapping expression data with other datasets. We provide a solution in the form of an R/Bioconductor package tximeta that performs numerous annotation and metadata gathering tasks automatically on behalf of users during the import of transcript quantification files. The correct reference transcriptome is identified via a hashed checksum stored in the quantification output, and key transcript databases are downloaded and cached locally. The computational paradigm of automatically adding annotation metadata based on reference sequence checksums can greatly facilitate genomic workflows, by helping to reduce overhead during bioinformatic analyses, preventing costly bioinformatic mistakes, and promoting computational reproducibility. The tximeta package is available at https://bioconductor.org/packages/tximeta.

Infection with the larval stage of the cestode, Echinococcus granulosus sensu lato (s.l.), causes hydatid disease (hydatidosis) in a range of hosts, including macropods and other marsupials, cattle, and humans. Wild macropods are an important sylvatic reservoir for the life cycle of E. granulosus (s.l.) in Australia, and so provide a conduit for transmission of hydatid disease to domestic animals and humans. Two Lumholtz's tree-kangaroos (Dendrolagus lumholtzi) from the Atherton Tablelands of Far North Queensland were recently found to have hydatid cysts in both liver and lung tissues. Tree-kangaroos may travel across the ground between patches of forest but are primarily arboreal leaf-eating macropods. The finding of hydatid cysts in an arboreal folivore may indicate that the area has a high level of contamination with eggs of E. granulosus (s.l.). This finding may be of significance to human health as well as indicating the need for further investigation into the prevalence of hydatid disease in domestic stock, wildlife and humans living in this rapidly urbanizing region.

Understanding nutrient intake of anorexia nervosa (AN) patients is essential for the treatment. Therefore, estimates of total energy and nutrient consumption were made in a group of young women (19 to 30 years) with restricting and binge purge subtypes of

Understanding nutrient intake of anorexia nervosa (AN) patients is essential for the treatment. Therefore, estimates of total energy and nutrient consumption were made in a group of young women (19 to 30 years) with restricting and binge purge subtypes of