Background: COVID-19 has infected millions of people worldwide and is responsible for several hundred thousand fatalities. The COVID-19 pandemic has necessitated thoughtful resource allocation and early identification of high-risk patients. However, effective methods to meet these needs are lacking. Objective: The aims of this study were to analyze the electronic health records (EHRs) of patients who tested positive for COVID-19 and were admitted to hospitals in the Mount Sinai Health System in New York City; to develop machine learning models for making predictions about the hospital course of the patients over clinically meaningful time horizons based on patient characteristics at admission; and to assess the performance of these models at multiple hospitals and time points. Methods: We used Extreme Gradient Boosting (XGBoost) and baseline comparator models to predict in-hospital mortality and critical events at time windows of 3, 5, 7, and 10 days from admission. Our study population included harmonized EHR data from five hospitals in New York City for 4098 COVID-19–positive patients admitted from March 15 to May 22, 2020. The models were first trained on patients from a single hospital (n=1514) before or on May 1, externally validated on patients from four other hospitals (n=2201) before or on May 1, and prospectively validated on all patients after May 1 (n=383). Finally, we established model interpretability to identify and rank variables that drive model predictions. Results: Upon cross-validation, the XGBoost classifier outperformed baseline models, with an area under the receiver operating characteristic curve (AUC-ROC) for mortality of 0.89 at 3 days, 0.85 at 5 and 7 days, and 0.84 at 10 days. XGBoost also performed well for critical event prediction, with an AUC-ROC of 0.80 at 3 days, 0.79 at 5 days, 0.80 at 7 days, and 0.81 at 10 days. In external validation, XGBoost achieved an AUC-ROC of 0.88 at 3 days, 0.86 at 5 days, 0.86 at 7 days, and 0.84 at 10 days for mortality prediction. Similarly, the unimputed XGBoost model achieved an AUC-ROC of 0.78 at 3 days, 0.79 at 5 days, 0.80 at 7 days, and 0.81 at 10 days. Trends in performance on prospective validation sets were similar. At 7 days, acute kidney injury on admission, elevated LDH, tachypnea, and hyperglycemia were the strongest drivers of critical event prediction, while higher age, anion gap, and C-reactive protein were the strongest drivers of mortality prediction. Conclusions: We externally and prospectively trained and validated machine learning models for mortality and critical events for patients with COVID-19 at different time horizons. These models identified at-risk patients and uncovered underlying relationships that predicted outcomes.

Sleep quality has been directly linked to cognitive function, quality of life, and a variety of serious diseases across many clinical domains. Standard methods for assessing sleep involve overnight studies in hospital settings, which are uncomfortable, expensive, not representative of real sleep, and difficult to conduct on a large scale. Recently, numerous commercial digital devices have been developed that record physiological data, such as movement, heart rate, and respiratory rate, which can act as a proxy for sleep quality in lieu of standard electroencephalogram recording equipment. The sleep-related output metrics from these devices include sleep staging and total sleep duration and are derived via proprietary algorithms that utilize a variety of these physiological recordings. Each device company makes different claims of accuracy and measures different features of sleep quality, and it is still unknown how well these devices correlate with one another and perform in a research setting. In this pilot study of 21 participants, we investigated whether sleep metric outputs from self-reported sleep metrics (SRSMs) and four sensors, specifically Fitbit Surge (a smart watch), Withings Aura (a sensor pad that is placed under a mattress), Hexoskin (a smart shirt), and Oura Ring (a smart ring), were related to known cognitive and psychological metrics, including the n-back test and Pittsburgh Sleep Quality Index (PSQI). We analyzed correlation between multiple device-related sleep metrics. Furthermore, we investigated relationships between these sleep metrics and cognitive scores across different timepoints and SRSM through univariate linear regressions. We found that correlations for sleep metrics between the devices across the sleep cycle were almost uniformly low, but still significant (p < 0.05). For cognitive scores, we found the Withings latency was statistically significant for afternoon and evening timepoints at p = 0.016 and p = 0.013. We did not find any significant associations between SRSMs and PSQI or cognitive scores. Additionally, Oura Ring’s total sleep duration and efficiency in relation to the PSQI measure was statistically significant at p = 0.004 and p = 0.033, respectively. These findings can hopefully be used to guide future sensor-based sleep research.

Coronavirus 2019 (COVID-19), caused by the SARS-CoV-2 virus, has become the deadliest pandemic in modern history, reaching nearly every country worldwide and overwhelming healthcare institutions. As of April 20, there have been more than 2.4 million confirmed cases with over 160,000 deaths. Extreme case surges coupled with challenges in forecasting the clinical course of affected patients have necessitated thoughtful resource allocation and early identification of high-risk patients. However, effective methods for achieving this are lacking. In this paper, we use electronic health records from over 3,055 New York City confirmed COVID-19 positive patients across five hospitals in the Mount Sinai Health System and present a decision tree-based machine learning model for predicting in-hospital mortality and critical events. This model is first trained on patients from a single hospital and then externally validated on patients from four other hospitals. We achieve strong performance, notably predicting mortality at 1 week with an AUC-ROC of 0.84. Finally, we establish model interpretability by calculating SHAP scores to identify decisive features, including age, inflammatory markers (procalcitonin and LDH), and coagulation parameters (PT, PTT, D-Dimer). To our knowledge, this is one of the first models with external validation to both predict outcomes in COVID-19 patients with strong validation performance and identify key contributors in outcome prediction that may assist clinicians in making effective patient management decisions. One-Sentence Summary: We identify clinical features that robustly predict mortality and critical events in a large cohort of COVID-19 positive patients in New York City.

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the associated Coronavirus Disease 2019 (COVID-19) is a public health emergency. Acute kidney injury (AKI) is a common complication in hospitalized patients with COVID-19 although mechanisms underlying AKI are yet unclear. There may be a direct effect of SARS-CoV-2 virus on the kidney; however, there is currently no data linking SARS-CoV-2 viral load (VL) to AKI. We explored the association of SARS-CoV-2 VL at admission to AKI in a large diverse cohort of hospitalized patients with COVID-19. Methods and findings: We included patients hospitalized between March 13^th and May 19^th, 2020 with SARS-CoV-2 in a large academic healthcare system in New York City (N = 1,049) with available VL at admission quantified by real-time RT-PCR. We extracted clinical and outcome data from our institutional electronic health records (EHRs). AKI was defined by KDIGO guidelines. We fit a Fine-Gray competing risks model (with death as a competing risk) using demographics, comorbidities, admission severity scores, and log₁₀ transformed VL as covariates and generated adjusted hazard ratios (aHR) and 95% Confidence Intervals (CIs). VL was associated with an increased risk of AKI (aHR = 1.04, 95% CI: 1.01–1.08, p = 0.02) with a 4% increased hazard for each log₁₀ VL change. Patients with a viral load in the top 50^th percentile had an increased adjusted hazard of 1.27 (95% CI: 1.02–1.58, p = 0.03) for AKI as compared to those in the bottom 50^th percentile. Conclusions: VL is weakly but significantly associated with in-hospital AKI after adjusting for confounders. This may indicate the role of VL in COVID-19 associated AKI. This data may inform future studies to discover the mechanistic basis of COVID-19 associated AKI.

While clinical trials of human pluripotent stem cell–derived midbrain dopamine (mDA) neuron precursor grafts for Parkinson’s disease (PD) are ongoing, current protocols remain suboptimal. In particular, the yield of TH+ mDA neurons after in vivo grafting and the expression of certain mDA neuron and subtype-specific markers require improvement. Single-cell transcriptomic analyses of grafts have revealed low proportions of mDA neurons and substantial off-target contamination. Here, we present an optimized mDA neuron differentiation strategy that builds on our clinical-grade (“Boost”) protocol by adding FGF18 and IWP2 treatment (“Boost+”) at the neurogenesis stage. Boost+ mDA neurons show higher expression of EN1, PITX3, and ALDH1A1. Improvements in mDA neuron yield and transcriptional similarity to primary mDA neurons are observed in vitro and following transplantation. Single-nucleus RNA sequencing demonstrates enrichment of A9 mDA neurons within Boost+ grafts. Functional studies in vitro demonstrate increased dopamine production and release and improved electrophysiological properties. In vivo analyses show higher percentages of TH+ mDA neurons, resulting in efficient rescue of amphetamine-induced rotation behavior in the 6-OHDA rat model and rescue of deficits in some nondrug-induced assays, including the ladder rung assay, which are not improved by Boost mDA neurons. The Boost+ conditions present an optimized differentiation protocol with advantages for disease modeling and mDA neuron grafting paradigms. This study introduces a refined method for producing dopamine neurons in vitro, providing a new protocol for applications in cell therapy for Parkinson's disease.

Sleep quality has been directly linked to cognitive function, quality of life, and a variety of serious diseases across many clinical domains such as psychiatry and cardiology. Standard methods for assessing sleep involve overnight studies in hospital settings, which are uncomfortable, expensive, not representative of real sleep, and difficult to conduct on a large scale. Recently, a number of commercial digital devices have been developed that record physiological data which can act as a proxy for sleep quality in lieu of standard electroencephalogram recording equipment. Each device company makes different claims of accuracy and measures different features of sleep quality, and it is still unknown how well these devices correlate with one another and perform in a research setting. In this pilot study of 21 participants, we investigated whether outputs from four sensors, specifically FitBit, Withings Aura, Hexoskin, and Oura Ring, were related to known cognitive and psychological metrics, including the PSQI and N-back test. We found that sleep metrics extracted from these devices did not predict cognitive and psychological metrics well in our pilot data. However, we did identify certain signification associations, specifically the Oura Ring’s total sleep duration and efficiency in relation to the PSQI measure with p=0.004 and p=0.033, respectively. Additionally, correlation of various sleep features among the devices across the sleep cycle was almost uniformly low. These findings can hopefully be used to guide future sensor-based sleep research.