A Bayes Decision Rule to Assist Policymakers during a Pandemic.
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ABSTRACT:
SUBMITTER: Cao KH
PROVIDER: S-EPMC8391194 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Background:The number of cases from the coronavirus disease 2019 (COVID-19) global pandemic has overwhelmed existing medical facilities and forced clinicians, patients, and families to make pivotal decisions with limited time and information. Main body:While machine learning (ML) methods have been previously used to augment clinical decisions, there is now a demand for "Emergency ML." Throughout the patient care pathway, there are opportunities for ML-supported decisions based on collected vitals, laboratory results, medication orders, and comorbidities. With rapidly growing datasets, there also remain important considerations when developing and validating ML models. Conclusion:This perspective highlights the utility of evidence-based prediction tools in a number of clinical settings, and how similar models can be deployed during the COVID-19 pandemic to guide hospital frontlines and healthcare administrators to make informed decisions about patient care and managing hospital volume.
| S-EPMC7347420 | biostudies-literature
Project description:Usually, official and survey-based statistics guide policymakers in their choice of response instruments to economic crises. However, in an early phase, after a sudden and unforeseen shock has caused unexpected and fast-changing dynamics, data from traditional statistics are only available with non-negligible time delays. This leaves policymakers uncertain about how to most effectively manage their economic countermeasures to support businesses, especially when they need to respond quickly, as in the COVID-19 pandemic. Given this information deficit, we propose a framework that guided policymakers throughout all stages of this unforeseen economic shock by providing timely and reliable sources of firm-level data as a basis to make informed policy decisions. We do so by combining early stage 'ad hoc' web analyses, 'follow-up' business surveys, and 'retrospective' analyses of firm outcomes. A particular focus of our framework is on assessing the early effects of the pandemic, using highly dynamic and large-scale data from corporate websites. Most notably, we show that textual references to the coronavirus pandemic published on a large sample of company websites and state-of-the-art text analysis methods allowed to capture the heterogeneity of the pandemic's effects at a very early stage and entailed a leading indication on later movements in firm credit ratings. While the proposed framework is specific to the COVID-19 pandemic, the integration of results obtained from real-time online sources in the design of subsequent surveys and their value in forecasting firm-level outcomes typically targeted by policy measures, is a first step towards a more timely and holistic approach for policy guidance in times of economic shocks.
| S-EPMC8843231 | biostudies-literature
Project description:A major challenge in physiology is to exploit the many large-scale data sets available from "-omic" studies to seek answers to key physiological questions. In previous studies, Bayes' theorem has been used for this purpose. This approach requires a means to map continuously distributed experimental data to probabilities (likelihood values) to derive posterior probabilities from the combination of prior probabilities and new data. Here, we introduce the use of minimum Bayes' factors for this purpose and illustrate the approach by addressing a physiological question, "Which deubiquitylating enzymes (DUBs) encoded by mammalian genomes are most likely to regulate plasma membrane transport processes in renal cortical collecting duct principal cells?" To do this, we have created a comprehensive online database of 110 DUBs present in the mammalian genome (https://hpcwebapps.cit.nih.gov/ESBL/Database/DUBs/). We used Bayes' theorem to integrate available information from large-scale data sets derived from proteomic and transcriptomic studies of renal collecting duct cells to rank the 110 known DUBs with regard to likelihood of interacting with and regulating transport processes. The top-ranked DUBs were OTUB1, USP14, PSMD7, PSMD14, USP7, USP9X, OTUD4, USP10, and UCHL5. Among these USP7, USP9X, OTUD4, and USP10 are known to be involved in endosomal trafficking and have potential roles in endosomal recycling of plasma membrane proteins in the mammalian cortical collecting duct.
| S-EPMC5374454 | biostudies-literature
Project description:In this work we propose the adoption of a statistical framework used in the evaluation of forensic evidence as a tool for evaluating and presenting circumstantial "evidence" of a disease outbreak from syndromic surveillance. The basic idea is to exploit the predicted distributions of reported cases to calculate the ratio of the likelihood of observing n cases given an ongoing outbreak over the likelihood of observing n cases given no outbreak. The likelihood ratio defines the Value of Evidence (V). Using Bayes' rule, the prior odds for an ongoing outbreak are multiplied by V to obtain the posterior odds. This approach was applied to time series on the number of horses showing clinical respiratory symptoms or neurological symptoms. The separation between prior beliefs about the probability of an outbreak and the strength of evidence from syndromic surveillance offers a transparent reasoning process suitable for supporting decision makers. The value of evidence can be translated into a verbal statement, as often done in forensics or used for the production of risk maps. Furthermore, a Bayesian approach offers seamless integration of data from syndromic surveillance with results from predictive modeling and with information from other sources such as disease introduction risk assessments.
| S-EPMC4218722 | biostudies-literature
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.
| S-EPMC2430963 | biostudies-literature
Project description:Clinical decision support systems (CDSS) are data aggregation tools based on computer technology that assist clinicians to promote healthy weight management and prevention of cardiovascular diseases. We carried out a randomised controlled 3-month trial to implement lifestyle modifications in breast cancer (BC) patients by means of CDSS during the COVID-19 pandemic. In total, 55 BC women at stages I-IIIA were enrolled. They were randomly assigned either to Control group, receiving general lifestyle advice (n = 28) or the CDSS group (n = 27), to whom the CDSS provided personalised dietary plans based on the Mediterranean diet (MD) together with physical activity guidelines. Food data, anthropometry, blood markers and quality of life were evaluated. At 3 months, higher adherence to MD was recorded in the CDSS group, accompanied by lower body weight (kg) and body fat mass percentage compared to control (p < 0.001). In the CDSS arm, global health/quality of life was significantly improved at the trial endpoint (p < 0.05). Fasting blood glucose and lipid levels (i.e., cholesterol, LDL, triacylglycerols) of the CDSS arm remained unchanged (p > 0.05) but were elevated in the control arm at 3 months (p < 0.05). In conclusion, CDSS could be a promising tool to assist BC patients with lifestyle modifications during the COVID-19 pandemic.
| S-EPMC8235424 | biostudies-literature
Project description: Not available
| S-EPMC7435509 | biostudies-literature
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/.
| S-EPMC4627796 | biostudies-literature
Project description:Hamilton’s rule [W. D. Hamilton, Am. Nat. 97, 354–356 (1963); W. D. Hamilton, J. Theor. Biol. 7, 17–52 (1964)] quantifies the central evolutionary ideas of inclusive fitness and kin selection into a simple algebraic relationship. Evidence consistent with Hamilton’s rule is found in many animal species. A drawback of investigating Hamilton’s rule in these species is that one can estimate whether a given behavior is consistent with the rule, but a direct examination of the exact cutoff for altruistic behavior predicted by Hamilton is almost impossible. However, to the degree that economic resources confer survival benefits in modern society, Hamilton’s rule may be applicable to economic decision-making, in which case techniques from experimental economics offer a way to determine this cutoff. We employ these techniques to examine whether Hamilton’s rule holds in human decision-making, by measuring the dependence between an experimental subject’s maximal willingness to pay for a gift of $50 to be given to someone else and the genetic relatedness of the subject to the gift’s recipient. We find good agreement with the predictions of Hamilton’s rule. Moreover, regression analysis of the willingness to pay versus genetic relatedness, the number of years living in the same residence, age, and sex shows that almost all the variation is explained by genetic relatedness. Similar but weaker results are obtained from hypothetical questions regarding the maximal risk to her own life that the subject is willing to take in order to save the recipient’s life.
| S-EPMC9169854 | biostudies-literature
Project description:BackgroundMathematical modeling of infectious diseases is an important decision-making tool for outbreak control. However, in Africa, limited expertise reduces the use and impact of these tools on policy. Therefore, there is a need to build capacity in Africa for the use of mathematical modeling to inform policy. Here we describe our experience implementing a mathematical modeling training program for public health professionals in East Africa.MethodsWe used a deliverable-driven and learning-by-doing model to introduce trainees to the mathematical modeling of infectious diseases. The training comprised two two-week in-person sessions and a practicum where trainees received intensive mentorship. Trainees evaluated the content and structure of the course at the end of each week, and this feedback informed the strategy for subsequent weeks.FindingsOut of 875 applications from 38 countries, we selected ten trainees from three countries - Rwanda (6), Kenya (2), and Uganda (2) - with guidance from an advisory committee. Nine trainees were based at government institutions and one at an academic organization. Participants gained skills in developing models to answer questions of interest and critically appraising modeling studies. At the end of the training, trainees prepared policy briefs summarizing their modeling study findings. These were presented at a dissemination event to policymakers, researchers, and program managers. All trainees indicated they would recommend the course to colleagues and rated the quality of the training with a median score of 9/10.ConclusionsMathematical modeling training programs for public health professionals in Africa can be an effective tool for research capacity building and policy support to mitigate infectious disease burden and forecast resources. Overall, the course was successful, owing to a combination of factors, including institutional support, trainees' commitment, intensive mentorship, a diverse trainee pool, and regular evaluations.
| S-EPMC10959131 | biostudies-literature