Steric-blocking oligonucleotides (SBOs) are short, single-stranded nucleic acids designed to modulate gene expression by binding to RNA transcripts and blocking access from cellular machinery such as splicing factors. SBOs have the potential to bind to near-complementary sites in the transcriptome, causing off-target effects. In this study, we used RNA-seq to evaluate the off-target differential splicing events of 81 SBOs and differential expression events of 46 SBOs. Our results suggest that differential splicing events are predominantly hybridization driven, whereas differential expression events are more common and driven by other mechanisms (including spurious experimental variation). We further evaluated the performance of in silico screens for offtarget splicing events, and found an edit distance cutoff of three to result in a sensitivity of 14% and false discovery rate (FDR) of 99%. A machine learning model incorporating splicing predictions substantially improved the ability to prioritize low edit distance hits, increasing sensitivity from 4% to 26% at a fixed FDR of 90%. Despite these large improvements in performance, this approach does not detect the majority of events at an FDR <99%. Our results suggest that in silico methods are currently of limited use for predicting the off-target effects of SBOs, and experimental screening by RNA-seq should be the preferred approach.

ObjectiveLaboratory tests are an important contributor to treatment decisions in the emergency department (ED). Rapid turnaround of laboratory tests can optimize ED throughout by reducing the length of stay (LOS) and improving patient outcomes. Despite evidence supporting the effect of shorter turnaround time (TAT) on LOS and outcomes, there is still a lack of large retrospective studies examining these associations. Here, we evaluated the effect of a reduction in laboratory TAT on ED LOS using retrospective analysis of Electronic Health Records (EHR).Materials and methodsRetrospective analysis of ED encounters from a large, US-based, de-identified EHR database and a separate analysis of ED encounters from the EHR of an ED at a top-tier tertiary care center were performed. Additionally, an efficiency model calculating the cumulative potential LOS time savings and resulting financial opportunity due to laboratory TAT reduction was created, assuming other factors affecting LOS are constant.ResultsMultivariate regression analysis of patients from the multisite study showed that a 1-minute decrease in laboratory TAT was associated with 0.50 minutes of decrease in LOS. The single-site analysis confirmed our findings from the multisite analysis that a positive correlation between laboratory TAT and ED LOS exists in the ED population as a whole, as well as across different patient acuity levels. In addition, based on the calculations from the efficiency model, for a 5-, 10- and 15-minute TAT reduction, the single-site ED can potentially admit a total of 127, 256 and 386 additional patients, respectively, annually.ConclusionA positive correlation between laboratory TAT and ED LOS was observed in a broad patient population and across distinct acuity levels.

Steric-blocking oligonucleotides (SBOs) are short, single-stranded nucleic acids designed to modulate gene expression by binding to mRNA and blocking access from cellular machinery such as splicing factors. SBOs have the potential to bind to near-complementary sites in the transcriptome, causing off-target effects. In this study, we used RNA-seq to evaluate the off-target differential splicing events of 81 SBOs and differential expression events of 46 SBOs. Our results suggest that differential splicing events are predominantly hybridization-driven, while differential expression events are more common and driven by other mechanisms. We further evaluated the performance of in silico screens for off-target events, and found an edit distance cutoff of three to result in a sensitivity of 14% and false discovery rate of 99%. A machine learning model incorporating splicing predictions substantially improved the ability to prioritize low edit distance hits, increasing sensitivity from 4% to 26% at a fixed FDR. Despite these large improvements in performance, the approach does not detect the majority of events at a false discovery rate below 99%. Our results suggest that in silico methods are currently of limited use for predicting the off-target effects of SBOs.

Introduction: Characterize the burden of illness in pediatric patients with congen ital athymia who were receiving supportive care. Methods: This cross-sectional study of adult caregivers of patients with congenital athymia used both a quantitative survey and qualitative

To assess the correspondence between ideal and actual monitoring for disease-modifying anti-rheumatic drugs and the reasons for protocol failure, and the sharing of this task between primary and secondary care, we studied 249 patients with rheumatoid arthritis in a single district general hospital. Ideal monitoring protocols were derived from data sheets and from the rheumatological literature. Overall the ideal protocol was followed in 65% of cases: this ranged from 93% for methotrexate to 26% for sodium aurothiromalate. Most of the monitoring was done in general practice (e.g. 67% of all blood tests) and, with some exceptions, general practitioners (GPs) were willing to perform this task. However, many GPs reported logistic differences with specimen transfer and expressed the need for more information and support. Poor communication between hospital, patient and GP was also found to be a cause of protocol failure.