A dedicated caller for DUX4 rearrangements from whole-genome sequencing data.

Rearrangements involving the DUX4 gene (DUX4-r) define a subtype of paediatric and adult acute lymphoblastic leukaemia (ALL) with a favourable outcome. Currently, there is no 'standard of care' diagnostic method for their confident identification. Here, we present an open-source software tool designed to detect DUX4-r from short-read, whole-genome sequencing (WGS) data.

A comprehensive allele specific expression resource for the equine transcriptome.

Background: Allele-specific expression (ASE) analysis provides a nuanced view of cis-regulatory mechanisms affecting gene expression.

Results: An equine ASE analysis was performed, using integrated Iso-seq and short-read RNA sequencing data from four healthy Thoroughbreds (2 mares and 2 stallions) across 9 tissues from the Functional Annotation of Animal Genomes (FAANG) project. Allele expression was quantified by haplotypes from long-read data, with 42,900 allele expression events compared.

How Often Is Rifampin Therapy Initiated and Completed in Patients With Periprosthetic Joint Infections?

Background: Rifampin therapy is indicated for the treatment of staphylococcal periprosthetic joint infection (PJI) in patients who have undergone debridement, antibiotics, and implant retention (DAIR) or one-stage revision as per the Infectious Diseases Society of America (IDSA) guideline. Given the well-established effectiveness of rifampin as adjunctive therapy in staphylococcal PJI, it is crucial to evaluate its utilization in practice and identify factors that contribute to its underuse or incomplete administration, as these deviations may undermine treatment efficacy and patient outcomes.

Questions/purposes: Among patients who met clear indications for rifampin use having undergone DAIR or one-stage revision for staphylococcal PJI, (1) what proportion of patients did not receive it? (2) What proportion of patients started it but did not complete the planned course? (3) Where documented in the medical record, what were the common reasons for not using it or prematurely discontinuing it, and in what percentage of the patients' charts was no reason given? (4) What proportion of patients were taking a medication that put them at risk for a drug-drug interaction (DDI)?

Methods: Using an institutional database, patients who underwent DAIR or revision arthroplasty for PJI from January 2013 to April 2023 were identified (n = 935).

Scoping review of the societal impacts of compound climate events.

Unlabelled: Climatic extremes have historically been seen as univariate; however, recent international reports have highlighted the potential for an increase in compound climate events (e.g., hot and dry events, recurrent flooding).