Gaussian process nowcasting: application to COVID-19 mortality reporting

Updating observations of a signal due to the delays in the measurement process is a common problem in signal processing, with prominent examples in a wide range of fields. An important example of this problem is the nowcasting of COVID-19 mortality: given a stream of reported counts of daily deaths, can we correct for the delays in reporting to paint an accurate picture of the present, with uncertainty? Without this correction, raw data will often mislead by suggesting an improving situation. We present a flexible approach using a latent Gaussian process that is capable of describing the changing auto-correlation structure present in the reporting time-delay surface. This approach also yields robust estimates of uncertainty for the estimated nowcasted numbers of deaths. We test assumptions in model specification such as the choice of kernel or hyper priors, and evaluate model performance on a challenging real dataset from Brazil. Our experiments show that Gaussian process nowcasting performs favourably against both comparable methods, and against a small sample of expert human predictions. Our approach has substantial practical utility in disease modelling -- by applying our approach to COVID-19 mortality data from Brazil, where reporting delays are large, we can make informative predictions on important epidemiological quantities such as the current effective reproduction number

Plasmas and Controlled Nuclear Fusion

Contains reports on three research projects.U. S. Atomic Energy Commission (Contract AT(30-1)-3980

The association between mechanical ventilator compatible bed occupancy and mortality risk in intensive care patients with COVID-19: a national retrospective cohort study

BACKGROUND: The literature paints a complex picture of the association between mortality risk and ICU strain. In this study, we sought to determine if there is an association between mortality risk in intensive care units (ICU) and occupancy of beds compatible with mechanical ventilation, as a proxy for strain. METHODS: A national retrospective observational cohort study of 89 English hospital trusts (i.e. groups of hospitals functioning as single operational units). Seven thousand one hundred thirty-three adults admitted to an ICU in England between 2 April and 1 December, 2020 (inclusive), with presumed or confirmed COVID-19, for whom data was submitted to the national surveillance programme and met study inclusion criteria. A Bayesian hierarchical approach was used to model the association between hospital trust level (mechanical ventilation compatible), bed occupancy, and in-hospital all-cause mortality. Results were adjusted for unit characteristics (pre-pandemic size), individual patient-level demographic characteristics (age, sex, ethnicity, deprivation index, time-to-ICU admission), and recorded chronic comorbidities (obesity, diabetes, respiratory disease, liver disease, heart disease, hypertension, immunosuppression, neurological disease, renal disease). RESULTS: One hundred thirty-five thousand six hundred patient days were observed, with a mortality rate of 19.4 per 1000 patient days. Adjusting for patient-level factors, mortality was higher for admissions during periods of high occupancy (> 85% occupancy versus the baseline of 45 to 85%) [OR 1.23 (95% posterior credible interval (PCI): 1.08 to 1.39)]. In contrast, mortality was decreased for admissions during periods of low occupancy (< 45% relative to the baseline) [OR 0.83 (95% PCI 0.75 to 0.94)]. CONCLUSIONS: Increasing occupancy of beds compatible with mechanical ventilation, a proxy for operational strain, is associated with a higher mortality risk for individuals admitted to ICU. Further research is required to establish if this is a causal relationship or whether it reflects strain on other operational factors such as staff. If causal, the result highlights the importance of strategies to keep ICU occupancy low to mitigate the impact of this type of resource saturation

Plasmas and Controlled Nuclear Fusion

Contains reports on three research projects.U. S. Atomic Energy Commission (Contract AT(11-1)-3070

Submicron Structure Fabrication and Research

Contains reports on six research projects.Joint Services Electronics Program (Contract DAAG29-78-C-0020)Joint Services Electronics Program (Contract DAAG29-80-C-0104)M.I.T. Sloan Fund for Basic ResearchU.S. Navy - Office of Naval Research (Contract N00014-79-C-0908)Lawrence Livermore Laboratory (Subcontract 206-92-09)U.S. Department of Energy (Contract DE-ACO2-80-E10179)Harkness Foundatio

Plasmas and Controlled Nuclear Fusion

Contains reports on five research projects.U. S. Atomic Energy Commission (Contract AT(30-1)-3980

Plasmas and Controlled Nuclear Fusion

Contains research objectives and reports on six research projects.U. S. Atomic Energy Commission (Contract AT(30-1)-3980

Technical Design Report for the PANDA Solenoid and Dipole Spectrometer Magnets

This document is the Technical Design Report covering the two large spectrometer magnets of the PANDA detector set-up. It shows the conceptual design of the magnets and their anticipated performance. It precedes the tender and procurement of the magnets and, hence, is subject to possible modifications arising during this process.Comment: 10 pages, 14MB, accepted by FAIR STI in May 2009, editors: Inti Lehmann (chair), Andrea Bersani, Yuri Lobanov, Jost Luehning, Jerzy Smyrski, Technical Coordiantor: Lars Schmitt, Bernd Lewandowski (deputy), Spokespersons: Ulrich Wiedner, Paola Gianotti (deputy

Submicron Structures Fabrication and Research

Contains reports on thirteen research projects.Joint Services Electronics Program (Contract DAAG29-83-K-0003)U.S. Navy - Office of Naval Research (Contract N00014-79-C-0908)National Science Foundation (Grant ECS82-05701)I.B.M. (PO No. 90305-QPSA-559)U.S. Department of Energy (Contract DE-AC02-82-ER13019)Lawrence Livermore Laboratory (Contract 2069209

Submicron Structures Fabrication and Research

Contains reports on twelve research projects.Lawrence Livermore Laboratory (Subcontract 2069209)Joint Services Electronics Program (Contract DAAG29-C-0104)U.S. Navy - Office of Naval Research (Contract N00014-79-C-0908)Joint Services Electronics Program (Contract DAAG29-80-C-0104)Harkness FoundationI.B.M.U.S. Department of Energy (Contract DE-ACO2-80-E10179)National Science Foundation (Grant ECS80-17705