Pandemetrics: systematically assessing, monitoring, and controlling the evolution of a pandemic

The still ongoing pandemic of SARS-CoV-2 virus and COVID-19 disease, affecting the population worldwide, has demonstrated the need of more accurate methodologies for assessing, monitoring, and controlling an outbreak of such devastating proportions. Authoritative attempts have been made in traditional fields of medicine (epidemiology, virology, infectiology) to address these shortcomings, mainly by relying on mathematical and statistical modeling. However, here, we propose approaching the methodological work from a different, and to some extent alternative, standpoint. Applied systematically, the concepts and tools of statistical engineering and quality management, developed not only in healthcare settings, but also in other scientific contexts, can be very useful in assessing, monitoring, and controlling pandemic events. We propose a methodology based on a set of tools and techniques, formulas, graphs, and tables to support the decision-making concerning the management of a pandemic like COVID-19. This methodological body is hereby named Pandemetrics. This name intends to emphasize the peculiarity of our approach to measuring, and graphically presenting the unique context of the COVID-19 pandemic

A standardized analytics pipeline for reliable and rapid development and validation of prediction models using observational health data

Background and objective: As a response to the ongoing COVID-19 pandemic, several prediction models in the existing literature were rapidly developed, with the aim of providing evidence-based guidance. However, none of these COVID-19 prediction models have been found to be reliable. Models are commonly assessed to have a risk of bias, often due to insufficient reporting, use of non-representative data, and lack of large-scale external validation. In this paper, we present the Observational Health Data Sciences and Informatics (OHDSI) analytics pipeline for patient-level prediction modeling as a standardized approach for rapid yet reliable development and validation of prediction models. We demonstrate how our analytics pipeline and open-source software tools can be used to answer important prediction questions while limiting potential causes of bias (e.g., by validating phenotypes, specifying the target population, performing large-scale external validation, and publicly providing all analytical source code). Methods: We show step-by-step how to implement the analytics pipeline for the question: ‘In patients hospitalized with COVID-19, what is the risk of death 0 to 30 days after hospitalization?’. We develop models using six different machine learning methods in a USA claims database containing over 20,000 COVID-19 hospitalizations and externally validate the models using data containing over 45,000 COVID-19 hospitalizations from South Korea, Spain, and the USA. Results: Our open-source software tools enabled us to efficiently go end-to-end from problem design to reliable Model Development and evaluation. When predicting death in patients hospitalized with COVID-19, AdaBoost, random forest, gradient boosting machine, and decision tree yielded similar or lower internal and external validation discrimination performance compared to L1-regularized logistic regression, whereas the MLP neural network consistently resulted in lower discrimination. L1-regularized logistic regression models were well calibrated. Conclusion: Our results show that following the OHDSI analytics pipeline for patient-level prediction modelling can enable the rapid development towards reliable prediction models. The OHDSI software tools and pipeline are open source and available to researchers from all around the world.</p

A Cross-Domain Approach to Analyzing the Short-Run Impact of COVID-19 on the U.S. Electricity Sector

The novel coronavirus disease (COVID-19) has rapidly spread around the globe in 2020, with the U.S. becoming the epicenter of COVID-19 cases since late March. As the U.S. begins to gradually resume economic activity, it is imperative for policymakers and power system operators to take a scientific approach to understanding and predicting the impact on the electricity sector. Here, we release a first-of-its-kind cross-domain open-access data hub, integrating data from across all existing U.S. wholesale electricity markets with COVID-19 case, weather, cellular location, and satellite imaging data. Leveraging cross-domain insights from public health and mobility data, we uncover a significant reduction in electricity consumption across that is strongly correlated with the rise in the number of COVID-19 cases, degree of social distancing, and level of commercial activity.Comment: This paper has been accepted for publication by Joule. The manuscript can also be accessed from EnerarXiv: http://www.enerarxiv.org/page/thesis.html?id=198

Digital early warning scores in cardiac care settings: Mixed-methods research

The broad adoption of the National Early Warning Score (NEWS2) was formally endorsed for prediction of early deterioration across all settings. With current digitalisation of the Early Warning Score (EWS) through electronic health records (EHR) and automated patient monitoring, there is an excellent opportunity for facilitating and evaluating NEWS2 implementation. However, no evidence yet shows the success of such standardisation or digitalisation of EWS in cardiac care settings. Individuals with cardiovascular disease (CVD) have a significant risk of developing critical events, and CVD-related morbidity is a critical burden for health and social care. However, there is a gap in research evaluating the performance and implementation of EWS in cardiac settings and the role of digital solutions in the implementation and performance of EWS and clinicians' practice. This PhD aims to provide high-quality evidence on the effectiveness of NEWS2 in predicting worsening events in patients with CVD, the implementation of the digital NEWS2 in two healthcare settings, the experience of escalation of care during the COVID-19 pandemic, and the evaluation of EHR-integrated dashboard for auditing NEWS2 and clinicians' performance

Using the data quality dashboard to improve the ehden network

Federated networks of observational health databases have the potential to be a rich resource to inform clinical practice and regulatory decision making. However, the lack of standard data quality processes makes it difficult to know if these data are research ready. The EHDEN COVID-19 Rapid Collaboration Call presented the opportunity to assess how the newly developed open-source tool Data Quality Dashboard (DQD) informs the quality of data in a federated network. Fifteen Data Partners (DPs) from 10 different countries worked with the EHDEN taskforce to map their data to the OMOP CDM. Throughout the process at least two DQD results were collected and compared for each DP. All DPs showed an improvement in their data quality between the first and last run of the DQD. The DQD excelled at helping DPs identify and fix conformance issues but showed less of an impact on completeness and plausibility checks. This is the first study to apply the DQD on multiple, disparate databases across a network. While study-specific checks should still be run, we recommend that all data holders converting their data to the OMOP CDM use the DQD as it ensures conformance to the model specifications and that a database meets a baseline level of completeness and plausibility for use in research.</p

Comprehensive public health evaluation of lockdown as a non-pharmaceutical intervention on COVID-19 spread in India: national trends masking state-level variations

Objectives To evaluate the effect of four-phase national lockdown from March 25 to May 31 in response to the COVID-19 pandemic in India and unmask the state-wise variations in terms of multiple public health metrics. Design Cohort study (daily time series of case counts). Setting Observational and population based. Participants Confirmed COVID-19 cases nationally and across 20 states that accounted for \u3e99% of the current cumulative case counts in India until 31 May 2020. Exposure Lockdown (non-medical intervention). Main outcomes and measures We illustrate the masking of state-level trends and highlight the variations across states by presenting evaluative evidence on some aspects of the COVID-19 outbreak: case fatality rates, doubling times of cases, effective reproduction numbers and the scale of testing. Results The estimated effective reproduction number R for India was 3.36 (95% CI 3.03 to 3.71) on 24 March, whereas the average of estimates from 25 May to 31 May stands at 1.27 (95% CI 1.26 to 1.28). Similarly, the estimated doubling time across India was at 3.56 days on 24 March, and the past 7-day average for the same on 31 May is 14.37 days. The average daily number of tests increased from 1717 (19–25 March) to 113 372 (25–31 May) while the test positivity rate increased from 2.1% to 4.2%, respectively. However, various states exhibit substantial departures from these national patterns. Conclusions Patterns of change over lockdown periods indicate the lockdown has been partly effective in slowing the spread of the virus nationally. However, there exist large state-level variations and identifying these variations can help in both understanding the dynamics of the pandemic and formulating effective public health interventions. Our framework offers a holistic assessment of the pandemic across Indian states and union territories along with a set of interactive visualisation tools that are daily updated at covind19.org

Dashboard COMPRIME_COMPRI_MOv: Multiscalar Spatio-Temporal Monitoring of the COVID-19 Pandemic in Portugal

Due to its novelty, the recent pandemic of the coronavirus disease (COVID-19), which is associated with the spread of the new severe acute respiratory syndrome coronavirus (SARS-CoV-2), triggered the public’s interest in accessing information, demonstrating the importance of obtaining and analyzing credible and updated information from an epidemiological surveillance context. For this purpose, health authorities, international organizations, and university institutions have published online various graphic and cartographic representations of the evolution of the pandemic with daily updates that allow the almost real-time monitoring of the evolutionary behavior of the spread, lethality, and territorial distribution of the disease. The purpose of this article is to describe the technical solution and the main results associated with the publication of the COMPRIME_COMPRI_MOv dashboard for the dissemination of information and multi-scale knowledge of COVID-19. Under two rapidly implementing research projects for innovative solutions to respond to the COVID-19 pandemic, promoted in Portugal by the FCT (Foundation for Science and Technology), a website was created. That website brings together a diverse set of variables and indicators in a dynamic and interactive way that reflects the evolutionary behavior of the pandemic from a multi-scale perspective, in Portugal, constituting itself as a system for monitoring the evolution of the pandemic. In the current situation, this type of exploratory solutions proves to be crucial to guarantee everyone’s access to information while simultaneously emerging as an epidemiological surveillance tool that is capable of assisting decision-making by public authorities with competence in defining control policies and fight the spread of the new coronavirusinfo:eu-repo/semantics/publishedVersio

Software Engineers Response to Public Crisis: Lessons Learnt from Spontaneously Building an Informative COVID-19 Dashboard

The Coronavirus disease 2019 (COVID-19) outbreak quickly spread around the world, resulting in over 240 million infections and 4 million deaths by Oct 2021. While the virus is spreading from person to person silently, fear has also been spreading around the globe. The COVID-19 information from the Australian Government is convincing but not timely or detailed, and there is much information on social networks with both facts and rumors. As software engineers, we have spontaneously and rapidly constructed a COVID-19 information dashboard aggregating reliable information semi-automatically checked from different sources for providing one-stop information sharing site about the latest status in Australia. Inspired by the John Hopkins University COVID-19 Map, our dashboard contains the case statistics, case distribution, government policy, latest news, with interactive visualization. In this paper, we present a participant's in-person observations in which the authors acted as founders of https://covid-19-au.com/ serving more than 830K users with 14M page views since March 2020. According to our first-hand experience, we summarize 9 lessons for developers, researchers and instructors. These lessons may inspire the development, research and teaching in software engineer aspects for coping with similar public crises in the future