In resource-limited settings-where a massive scale up of HIV services has occurred in the last 5 years-both understanding the extent of and improving retention in care presents special challenges. First, retention in care within the decentralizing network of services is likely higher than existing estimates that account only for retention in clinic, and therefore antiretroviral therapy services may be more effective than currently believed. Second, both magnitude and determinants of patient retention vary substantially and therefore encouraging the conduct of locally relevant epidemiology is needed to inform programmatic decisions. Third, socio-structural factors such as program characteristics, transportation, poverty, work/child care responsibilities, and social relations are the major determinants of retention in care, and therefore interventions to improve retention in care should focus on implementation strategies. Research to assess and improve retention in care for HIV-infected patients can be strengthened by incorporating novel methods such as sampling-based approaches and a causal analytic framework.

Background Improved mortality prediction for patients in intensive care units (ICU) remains an important challenge. Many severity scores have been proposed but validation studies have concluded that they are not adequately calibrated. Many flexible algorithms are available, yet none of these individually outperform all others regardless of context. In contrast, the Super Learner (SL), an ensemble machine learning technique that leverages on multiple learning algorithms to obtain better prediction performance, has been shown to perform at least as well as the optimal member of its library. It might provide an ideal opportunity to construct a novel severity score with an improved performance profile. The aim of the present study was to provide a new mortality prediction algorithm for ICU patients using an implementation of the Super Learner, and to assess its performance relative to prediction based on the SAPS II, APACHE II and SOFA scores. Methods We used the Multiparameter Intelligent Monitoring in Intensive Care II (MIMIC-II) database (v26) including all patients admitted to an ICU at Boston’s Beth Israel Deaconess Medical Center from 2001 to 2008. The calibration, discrimination and risk classification of predicted hospital mortality based on SAPS II, on APACHE II, on SOFA and on our Super Learned-based proposal were evaluated. Performance measures were calculated using cross-validation to avoid making biased assessments. Our proposed score was then externally validated on a dataset of 200 randomly selected patients admitted at the ICU of Hôpital Européen Georges-Pompidou in Paris, France between September 2013 and June 2014. The primary outcome was hospital mortality. The explanatory variables were the same as those included in the SAPS II score. Results 24,508 patients were included, with median SAPS II 38 (IQR: 27–51), median SOFA 5 (IQR: 2–8). A total of 3,002/24,508(12.2%) patients died in the hospital. The two versions of our Super Learner-based proposal yielded average predicted probabilities of death of 0.12 (IQR: 0.02–0.16) and 0.13 (IQR: 0.01–0.19), whereas the corresponding values for the SOFA and SAPS II scores were, respectively, 0.12 (IQR: 0.05–0.15) and 0.30 (IQR: 0.08–0.48). The cross-validated area under the receiver operating characteristics curve (AUROC) for SAPS II and SOFA were 0.78(95%CI: 0.77–0.78) and 0.71 (95%CI: 0.71–0.72), respectively. Our proposal reached an AUROC of 0.85 (95%CI: 0.84–0.85) when the explanatory variables were categorized as in SAPS II, and of 0.88 (95%CI: 0.87–0.89) when the same explanatory variables were included without any transformation. In addition, it exhibited better calibration properties than previous score systems. On the external validation dataset, the AUROC was 0.94 (95%CI: 0.90–0.98) and calibration properties were good. Interpretation As compared to conventional severity scores, our Super Learner-based proposal offers improved performance for predicting hospital mortality in ICU patients. A user-friendly implementation is available online an...

ObjectiveTo understand the epidemiology and burden of severe coronavirus disease 2019 (covid-19) during the first epidemic wave on the west coast of the United States.DesignProspective cohort study.SettingKaiser Permanente integrated healthcare delivery systems serving populations in northern California, southern California, and Washington state.Participants1840 people with a first acute hospital admission for confirmed covid-19 by 22 April 2020, among 9 596 321 healthcare plan enrollees. Analyses of hospital length of stay and clinical outcomes included 1328 people admitted by 9 April 2020 (534 in northern California, 711 in southern California, and 83 in Washington).Main outcome measuresCumulative incidence of first acute hospital admission for confirmed covid-19, and subsequent probabilities of admission to an intensive care unit (ICU) and mortality, as well as duration of hospital stay and ICU stay. The effective reproduction number (RE) describing transmission dynamics was estimated for each region.ResultsAs of 22 April 2020, cumulative incidences of a first acute hospital admission for covid-19 were 15.6 per 100 000 cohort members in northern California, 23.3 per 100 000 in southern California, and 14.7 per 100 000 in Washington. Accounting for censoring of incomplete hospital stays among those admitted by 9 April 2020, the estimated median duration of stay among survivors was 9.3 days (with 95% staying 0.8 to 32.9 days) and among non-survivors was 12.7 days (1.6 to 37.7 days). The censoring adjusted probability of ICU admission for male patients was 48.5% (95% confidence interval 41.8% to 56.3%) and for female patients was 32.0% (26.6% to 38.4%). For patients requiring critical care, the median duration of ICU stay was 10.6 days (with 95% staying 1.3 to 30.8 days). The censoring adjusted case fatality ratio was 23.5% (95% confidence interval 19.6% to 28.2%) among male inpatients and 14.9% (11.8% to 18.6%) among female inpatients; mortality risk increased with age for both male and female patients. Reductions in RE were identified over the study period within each region.ConclusionsAmong residents of California and Washington state enrolled in Kaiser Permanente healthcare plans who were admitted to hospital with covid-19, the probabilities of ICU admission, of long hospital stay, and of mortality were identified to be high. Incidence rates of new hospital admissions have stabilized or declined in conjunction with implementation of social distancing interventions.

Estimating population exposure to particulate matter during wildfires can be difficult because of insufficient monitoring data to capture the spatiotemporal variability of smoke plumes. Chemical transport models (CTMs) and satellite retrievals provide spatiotemporal data that may be useful in predicting PM2.5 during wildfires. We estimated PM2.5 concentrations during the 2008 northern California wildfires using 10-fold cross-validation (CV) to select an optimal prediction model from a set of 11 statistical algorithms and 29 predictor variables. The variables included CTM output, three measures of satellite aerosol optical depth, distance to the nearest fires, meteorological data, and land use, traffic, spatial location, and temporal characteristics. The generalized boosting model (GBM) with 29 predictor variables had the lowest CV root mean squared error and a CV-R2 of 0.803. The most important predictor variable was the Geostationary Operational Environmental Satellite Aerosol/Smoke Product (GASP) Aerosol Optical Depth (AOD), followed by the CTM output and distance to the nearest fire cluster. Parsimonious models with various combinations of fewer variables also predicted PM2.5 well. Using machine learning algorithms to combine spatiotemporal data from satellites and CTMs can reliably predict PM2.5 concentrations during a major wildfire event.

Among 3,302 persons tested for SARS-CoV-2 by BinaxNOW TM and RT-PCR in a community setting, rapid assay sensitivity was 100%/98.5%/89% using RT-PCR Ct thresholds of 30, 35 and none. The specificity was 99.9%. Performance was high across ages and those with and without symptoms. Rapid resulting permitted immediate public health action.

The consistency of propensity score (PS) estimators relies on correct specification of the PS model. The PS is frequently estimated using main-effects logistic regression. However, the underlying model assumptions may not hold. Machine learning methods provide an alternative nonparametric approach to PS estimation. In this simulation study, we evaluated the benefit of using Super Learner (SL) for PS estimation. We created 1,000 simulated data sets (n = 500) under 4 different scenarios characterized by various degrees of deviance from the usual main-term logistic regression model for the true PS. We estimated the average treatment effect using PS matching and inverse probability of treatment weighting. The estimators' performance was evaluated in terms of PS prediction accuracy, covariate balance achieved, bias, standard error, coverage, and mean squared error. All methods exhibited adequate overall balancing properties, but in the case of model misspecification, SL performed better for highly unbalanced variables. The SL-based estimators were associated with the smallest bias in cases of severe model misspecification. Our results suggest that use of SL to estimate the PS can improve covariate balance and reduce bias in a meaningful manner in cases of serious model misspecification for treatment assignment.

We evaluated the performance of the Abbott BinaxNOW rapid antigen test for coronavirus disease 2019 (Binax-CoV2) to detect virus among persons, regardless of symptoms, at a public plaza site of ongoing community transmission. Titration with cultured severe acute respiratory syndrome coronavirus 2 yielded a human observable threshold between 1.6 × 104-4.3 × 104 viral RNA copies (cycle threshold [Ct], 30.3–28.8). Among 878 subjects tested, 3% (26 of 878) were positive by reverse-transcription polymerase chain reaction, of whom 15 of 26 had a Ct <30, indicating high viral load; of these, 40% (6 of 15) were asymptomatic. Using this Ct threshold (<30) for Binax-CoV2 evaluation, the sensitivity of Binax-CoV2 was 93.3% (95% confidence interval, 68.1%–99.8%) (14 of 15) and the specificity was 99.9% (99.4%–99.9%) (855 of 856).

Background There is urgent need to understand the dynamics and risk factors driving ongoing SARS-CoV-2 transmission during shelter-in-place mandates. Methods We offered SARS-CoV-2 reverse transcription-PCR and antibody (Abbott ARCHITECT IgG) testing, regardless of symptoms, to all residents (≥4 years) and workers in a San Francisco census tract (population: 5,174) at outdoor, community-mobilized events over four days. We estimated SARS-CoV-2 point prevalence (PCR-positive) and cumulative incidence (antibody or PCR-positive) in the census tract and evaluated risk factors for recent (PCR-positive/antibody-negative) versus prior infection (antibody-positive/PCR-negative). SARS-CoV-2 genome recovery and phylogenetics were used to measure viral strain diversity, establish viral lineages present, and estimate number of introductions. Results We tested 3,953 persons: 40% Latinx; 41% White; 9% Asian/Pacific Islander; and 2% Black. Overall, 2.1% (83/3,871) tested PCR-positive: 95% were Latinx and 52% asymptomatic when tested. 1.7% of census tract residents and 6.0% of workers (non-census tract residents) were PCR-positive. Among 2,598 tract residents, estimated point prevalence of PCR-positives was 2.3% (95%CI: 1.2-3.8%): 3.9% (95%CI: 2.0-6.4%) among Latinx vs. 0.2% (95%CI: 0.0-0.4%) among non-Latinx persons. Estimated cumulative incidence among residents was 6.1% (95%CI: 4.0-8.6%). Prior infections were 67% Latinx, 16% White, and 17% other ethnicities. Among recent infections, 96% were Latinx. Risk factors for recent infection were Latinx ethnicity, inability to shelter-in-place and maintain income, frontline service work, unemployment, and household income &$50,000/year. Five SARS-CoV-2 phylogenetic lineages were detected. Conclusion SARS-CoV-2 infections from diverse lineages continued circulating among low-income, Latinx persons unable to work from home and maintain income during San Francisco’s shelter-in-place ordinance.