Deep learning prediction of hospital readmissions for asthma and COPD.

QUESTION: Severe asthma and COPD exacerbations requiring hospitalization are linked to increased disease morbidity and healthcare costs. We sought to identify Electronic Health Record (EHR) features of severe asthma and COPD exacerbations and evaluate the performance of four machine learning (ML) and one deep learning (DL) model in predicting readmissions using EHR data. STUDY DESIGN AND METHODS: Observational study between September 30, 2012, and December 31, 2017, of patients hospitalized with asthma and COPD exacerbations. RESULTS: This study included 5,794 patients, 1,893 with asthma and 3,901 with COPD. Patients with asthma were predominantly female (n = 1288 [68%]), 35% were Black (n = 669), and 25% (n = 479) were Hispanic. Black (44 vs. 33%, p = 0.01) and Hispanic patients (30 vs. 24%, p = 0.02) were more likely to be readmitted for asthma. Similarly, patients with COPD readmissions included a large percentage of Blacks (18 vs. 10%, p < 0.01) and Hispanics (8 vs. 5%, p < 0.01). To identify patients at high risk of readmission index hospitalization data of a subset of 2,682 patients, 777 with asthma and 1,905 with COPD, was analyzed with four ML models, and one DL model. We found that multilayer perceptron, the DL method, had the best sensitivity and specificity compared to the four ML methods implemented in the same dataset. INTERPRETATION: Multilayer perceptron, a deep learning method, had the best performance in predicting asthma and COPD readmissions, demonstrating that EHR and deep learning integration can improve high-risk patient detection.

Limited Health Literacy Is Associated With Worse Patient-Reported Outcomes in Inflammatory Bowel Disease.

Background: Patients with inflammatory bowel disease (IBD) face complex health tasks and decisions. Limited health literacy is a risk factor for poor health outcomes, but this has not been examined in IBD. This study aims to assess the role of health literacy for patients with IBD. Methods: We prospectively enrolled adults with IBD receiving care from the Section of Gastroenterology at the Boston Medical Center. In-person, standardized questionnaires were administered to measure health literacy with the Newest Vital Sign, self-efficacy with the Medication Use and Self-Efficacy Scale, quality of life with the 10-question Short Inflammatory Bowel Disease Questionnaire, depression with the Patient-Reported Outcomes Measurement System Short Form, and clinical disease activity for patients with Crohn's disease with the Harvey-Bradshaw Index and for patients with ulcerative colitis with the Simple Clinical Colitis Activity Index (SCCAI). The relationships between health literacy and these variables were subsequently examined. Results: Of 112 patients invited to participate, 99 enrolled and completed the interview. Limited health literacy was identified in 40% (n = 40) of patients. Patients with limited health literacy reported significantly worse overall health (P = 0.03) and more depressive symptoms (P = 0.01). Of the 56 patients with Crohn's disease, those with adequate health literacy were more likely to be in clinical remission (mean Harvey-Bradshaw Index score < 5), compared with those with limited health literacy (odds ratio, 4.15; 95% confidence interval, 1.37 to 13.45; P = 0.01). There was no significant association between health literacy and clinical disease activity (SCCAI) in patients with ulcerative colitis. Conclusions: Limited health literacy is associated with lower ratings of subjective health and depression in IBD and more symptoms of active disease in patients with Crohn's disease.

Multifocal Synchronous Granular Cell Tumors of the Gastrointestinal Tract.

Granular cell tumors (GCT) are rare and unusual tumors, which are usually benign and asymptomatic. Only 5-10% of cases involve the gastrointestinal tract, most commonly as singular, non-cancerous lesions in the esophagus. We report a rare case of symptomatic, multifocal, synchronous GCT involving the esophagus, stomach, and cecum.

Sgs1 and exo1 redundantly inhibit break-induced replication and de novo telomere addition at broken chromosome ends.

In budding yeast, an HO endonuclease-inducible double-strand break (DSB) is efficiently repaired by several homologous recombination (HR) pathways. In contrast to gene conversion (GC), where both ends of the DSB can recombine with the same template, break-induced replication (BIR) occurs when only the centromere-proximal end of the DSB can locate homologous sequences. Whereas GC results in a small patch of new DNA synthesis, BIR leads to a nonreciprocal translocation. The requirements for completing BIR are significantly different from those of GC, but both processes require 5' to 3' resection of DSB ends to create single-stranded DNA that leads to formation of a Rad51 filament required to initiate HR. Resection proceeds by two pathways dependent on Exo1 or the BLM homolog, Sgs1. We report that Exo1 and Sgs1 each inhibit BIR but have little effect on GC, while overexpression of either protein severely inhibits BIR. In contrast, overexpression of Rad51 markedly increases the efficiency of BIR, again with little effect on GC. In sgs1Delta exo1Delta strains, where there is little 5' to 3' resection, the level of BIR is not different from either single mutant; surprisingly, there is a two-fold increase in cell viability after HO induction whereby 40% of all cells survive by formation of a new telomere within a few kb of the site of DNA cleavage. De novo telomere addition is rare in wild-type, sgs1Delta, or exo1Delta cells. In sgs1Delta exo1Delta, repair by GC is severely inhibited, but cell viability remains high because of new telomere formation. These data suggest that the extensive 5' to 3' resection that occurs before the initiation of new DNA synthesis in BIR may prevent efficient maintenance of a Rad51 filament near the DSB end. The severe constraint on 5' to 3' resection, which also abrogates activation of the Mec1-dependent DNA damage checkpoint, permits an unprecedented level of new telomere addition.

Break-induced replication requires all essential DNA replication factors except those specific for pre-RC assembly.

Break-induced replication (BIR) is an efficient homologous recombination (HR) pathway employed to repair a DNA double-strand break (DSB) when homology is restricted to one end. All three major replicative DNA polymerases are required for BIR, including the otherwise nonessential Pol32 subunit. Here we show that BIR requires the replicative DNA helicase (Cdc45, the GINS, and Mcm2-7 proteins) as well as Cdt1. In contrast, both subunits of origin recognition complex (ORC) and Cdc6, which are required to create a prereplication complex (pre-RC), are dispensable. The Cdc7 kinase, required for both initiation of DNA replication and post-replication repair (PRR), is also required for BIR. Ubiquitination and sumoylation of the DNA processivity clamp PCNA play modest roles; in contrast, PCNA alleles that suppress pol32Delta's cold sensitivity fail to suppress its role in BIR, and are by themselves dominant inhibitors of BIR. These results suggest that origin-independent BIR involves cross-talk between normal DNA replication factors and PRR.