Discovering monogenic patients with a confirmed molecular diagnosis in millions of clinical notes with MonoMiner.

PURPOSE: Cohort building is a powerful foundation for improving clinical care, performing biomedical research, recruiting for clinical trials, and many other applications. We set out to build a cohort of all monogenic patients with a definitive causal gene diagnosis in a 3-million patient hospital system. METHODS: We define a subset (4461) of OMIM diseases that have at least 1 known monogenic causal gene. We then introduce MonoMiner, a natural language processing framework to identify molecularly confirmed monogenic patients from free-text clinical notes. RESULTS: We show that ICD-10-CM codes cover only a fraction of monogenic diseases and that even where available, ICD-10-CM code‒based patient retrieval offers 0.14 precision. Searching by causal gene symbol offers great recall but has an even worse 0.07 precision. MonoMiner achieves 6 to 11 times higher precision (0.80), with 0.87 precision on disease diagnosis alone, tagging 4259 patients with 560 monogenic diseases and 534 causal genes, at 0.48 recall. CONCLUSION: MonoMiner enables the discovery of a large, high-precision cohort of patients with monogenic diseases with an established molecular diagnosis, empowering numerous downstream uses. Because it relies solely on clinical notes, MonoMiner is highly portable, and its approach is adaptable to other domains and languages.

EditABLE: A Simple Web Application for Designing Genome Editing Experiments.

CRISPR-Cas genome editing is transformative; however, there is no simple tool available for determining the optimal genome editing technology to create specific mutations for experimentation or to correct mutations as a curative therapy for specific diseases. We developed editABLE, an online resource (editable-app.stanford.edu) to provide computationally validated CRISPR editors and guide RNAs based on user provided sequence data. We demonstrate the utility of editABLE by applying it to one of the most common monogenic disorders, autosomal dominant polycystic kidney disease (ADPKD), identifying specific editing tools across the landscape of ADPKD mutations.

Coping with Workplace Incivility in Hospital Teams: How Does Team Mindfulness Influence Prevention- and Promotion-Focused Emotional Coping?

Incivility is a growing concern for researchers and practitioners alike, yet we know little about how the team context is related to the way that employees respond to it. In this study, we examined the role of team mindfulness and its direct and buffering effects on individual-level promotion- and prevention-focused emotional coping. We also examined how these forms of coping were related to individual work engagement. In a temporally lagged study of 73 hospital teams (involving 440 team members), multi-level analyses showed that team mindfulness was directly negatively associated with individual-level prevention-focused emotional coping (behavioral disengagement, denial, and venting); however, it was not positively related to individual-level promotion-focused forms of coping (positive reframing and acceptance). In addition, a cross-level interaction effect was identified whereby team mindfulness reduced the positive relationship between incivility and venting, meaning there was less individual-level venting following incivility in the context of higher team mindfulness. These findings may have implications for work engagement, which was shown to be negatively related to venting and behavioral disengagement. Our findings are useful for managers of teams that regularly experience customer incivility as it uncovers how they can develop a team context that discourages ineffective coping responses.