Dataset Information

A Bayes Decision Rule to Assist Policymakers during a Pandemic.

ABSTRACT: A new decision rule based on net benefit per capita is proposed and exemplified with the aim of assisting policymakers in deciding whether to lockdown or reopen an economy-fully or partially-amidst a pandemic. Bayesian econometric models using Markov chain Monte Carlo algorithms are used to quantify this rule, which is illustrated via several sensitivity analyses. While we use COVID-19 data from the United States to demonstrate the ideas, our approach is invariant to the choice of pandemic and/or country. The actions suggested by our decision rule are consistent with the closing and reopening of the economies made by policymakers in Florida, Texas, and New York; these states were selected to exemplify the methodology since they capture the broad spectrum of COVID-19 outcomes in the U.S.

SUBMITTER: Cao KH

PROVIDER: S-EPMC8391194 | biostudies-literature | 2021 Aug

REPOSITORIES: biostudies-literature

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A Bayes Decision Rule to Assist Policymakers during a Pandemic.

Cao Kang-Hua KH Damien Paul P Woo Chi-Keung CK Zarnikau Jay J

Healthcare (Basel, Switzerland) 20210809 8

A new decision rule based on net benefit per capita is proposed and exemplified with the aim of assisting policymakers in deciding whether to lockdown or reopen an economy-fully or partially-amidst a pandemic. Bayesian econometric models using Markov chain Monte Carlo algorithms are used to quantify this rule, which is illustrated via several sensitivity analyses. While we use COVID-19 data from the United States to demonstrate the ideas, our approach is invariant to the choice of pandemic and/o ...[more]

PMID: 34442160

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Project description:BackgroundGlobal pandemic influenza preparedness relies heavily on public health surveillance, but it is unclear that current surveillance fully meets pandemic preparedness needs.MethodsWe first developed a conceptual framework to help systematically identify strategies to improve the detection of an early case or cluster of novel human influenza disease during the pre-pandemic period. We then developed a process model (flow diagram) depicting nine major pathways through which a case in the community could be detected and confirmed, and mapped the improvement strategies onto this model. Finally, we developed an interactive decision tool by building quantitative measures of probability and time into each step of the process model and programming it to calculate the net probability and time required for case detection through each detection pathway. Input values for each step can be varied by users to assess the effects of different improvement strategies, alone or in combination. We illustrate application of the tool using hypothetical input data reflecting baseline and 12-month follow-up scenarios, following concurrent implementation of multiple improvement strategies.ResultsWe compared outputs from the tool across detection pathways and across time, at baseline and 12-month follow up. The process model and outputs from the tool suggest that traditional efforts to build epidemiology and laboratory capacity are efficient strategies, as are more focused strategies within these, such as targeted laboratory testing; expedited specimen transport; use of technologies to streamline data flow; and improved reporting compliance. Other promising strategies stem from community detection - better harnessing of electronic data mining and establishment of community-based monitoring.ConclusionOur practical tool allows policymakers to use their own realistic baseline values and program projections to assess the relative impact of different interventions to improve the probability and timeliness of detecting early human cases or clusters caused by a novel influenza virus, a possible harbinger of a new pandemic. Policymakers can use results to target investments to improve their surveillance infrastructure. Multi-national planners can also use the tool to help guide directions in surveillance system improvements more globally. Finally, our systematic approach can also be tailored to help improve surveillance for other diseases.

Project description:MotivationIntrinsically disordered regions of proteins play an essential role in the regulation of various biological processes. Key to their regulatory function is often the binding to globular protein domains via sequence elements known as molecular recognition features (MoRFs). Development of computational tools for the identification of candidate MoRF locations in amino acid sequences is an important task and an area of growing interest. Given the relative sparseness of MoRFs in protein sequences, the accuracy of the available MoRF predictors is often inadequate for practical usage, which leaves a significant need and room for improvement. In this work, we introduce MoRFCHiBi_Web, which predicts MoRF locations in protein sequences with higher accuracy compared to current MoRF predictors.MethodsThree distinct and largely independent property scores are computed with component predictors and then combined to generate the final MoRF propensity scores. The first score reflects the likelihood of sequence windows to harbour MoRFs and is based on amino acid composition and sequence similarity information. It is generated by MoRFCHiBi using small windows of up to 40 residues in size. The second score identifies long stretches of protein disorder and is generated by ESpritz with the DisProt option. Lastly, the third score reflects residue conservation and is assembled from PSSM files generated by PSI-BLAST. These propensity scores are processed and then hierarchically combined using Bayes rule to generate the final MoRFCHiBi_Web predictions.ResultsMoRFCHiBi_Web was tested on three datasets. Results show that MoRFCHiBi_Web outperforms previously developed predictors by generating less than half the false positive rate for the same true positive rate at practical threshold values. This level of accuracy paired with its relatively high processing speed makes MoRFCHiBi_Web a practical tool for MoRF prediction.Availabilityhttp://morf.chibi.ubc.ca:8080/morf/.

Dataset Information

A Bayes Decision Rule to Assist Policymakers during a Pandemic.

Publications

A Bayes Decision Rule to Assist Policymakers during a Pandemic.

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