Leveraging artificial intelligence for pandemic preparedness and response: a scoping review to identify key use cases

Strengthening disease surveillance capacity at national level across five countries: a qualitative study

OBJECTIVES

Disease surveillance is an essential component of public health and a core function of National Public Health Institutes (NPHIs), including to better prepare and respond to infectious diseases outbreaks. Strengthening NPHIs in their efforts to establish and maintain efficient surveillance systems is an opportunity to ensure future outbreak preparedness and response; yet, guidance on how to increase and prioritise capacity building efforts is limited. This study sought to investigate approaches to capacity building and training for disease surveillance at national level and understand the potential role of NPHIs.

STUDY DESIGN

Qualitative study.

METHODS

This is a qualitative study, based on a literature review and interviews undertaken between June and November 2022. Fifty seven in-depth interviews were conducted in five countries: Côte d'Ivoire, Ecuador, Madagascar, Namibia, and the Kingdom of Saudi Arabia. Participants included a range of professionals from government, NPHIs, academic institutions and the private sector. Interviews were thematically analysed.

RESULTS

Selected countries varied in terms of their disease surveillance capacities, as well as in the structure of their surveillance systems and decision-making. Research identified shared priority areas for action at national level, identifying common challenges and opportunities: 1) capacity building, here specifically the need for a training agenda at national level to ensure sustainability and guide donor funded training offers; 2) data tools and technology-to help decision-makers select the best software tool to address countries' identified need; 3) data sharing-the need for clear data sharing standards and norms for national to international data sharing; and 4) genomic sequencing-the need for national genomic surveillance strategies and reporting guidelines.

CONCLUSION

Addressing challenges and using opportunities to strengthen disease surveillance at national level is an important step to build capacity in this area and to help prevent future epidemic and pandemics globally. The findings of this study help decision-makers to identify priority areas for capacity building and understand the potential role and significance of NPHIs.

Forensic Microbiology: When, Where and How

Forensic microbiology is a relatively new discipline, born in part thanks to the development of advanced methodologies for the detection, identification and characterization of microorganisms, and also in relation to the growing impact of infectious diseases of iatrogenic origin. Indeed, the increased application of medical practices, such as transplants, which require immunosuppressive treatments, and the growing demand for prosthetic installations, associated with an increasing threat of antimicrobial resistance, have led to a rise in the number of infections of iatrogenic origin, which entails important medico-legal issues. On the other hand, the possibility of detecting minimal amounts of microorganisms, even in the form of residual traces (e.g., their nucleic acids), and of obtaining gene and genomic sequences at contained costs, has made it possible to ask new questions of whether cases of death or illness might have a microbiological origin, with the possibility of also tracing the origin of the microorganisms involved and reconstructing the chain of contagion. In addition to the more obvious applications, such as those mentioned above related to the origin of iatrogenic infections, or to possible cases of infections not properly diagnosed and treated, a less obvious application of forensic microbiology concerns its use in cases of violence or violent death, where the characterization of the microorganisms can contribute to the reconstruction of the case. Finally, paleomicrobiology, e.g., the reconstruction and characterization of microorganisms in historical or even archaeological remnants, can be considered as a sister discipline of forensic microbiology. In this article, we will review these different aspects and applications of forensic microbiology.

A scoping review of methodologies for applying artificial intelligence to physical activity interventions

PURPOSE

This scoping review aimed to offer researchers and practitioners an understanding of artificial intelligence (AI) applications in physical activity (PA) interventions; introduce them to prevalent machine learning (ML), deep learning (DL), and reinforcement learning (RL) algorithms; and encourage the adoption of AI methodologies.

METHODS

A scoping review was performed in PubMed, Web of Science, Cochrane Library, and EBSCO focusing on AI applications for promoting PA or predicting related behavioral or health outcomes. AI methodologies were summarized and categorized to identify synergies, patterns, and trends informing future research. Additionally, a concise primer on predominant AI methodologies within the realm of PA was provided to bolster understanding and broader application.

RESULTS

The review included 24 studies that met the predetermined eligibility criteria. AI models were found effective in detecting significant patterns of PA behavior and associations between specific factors and intervention outcomes. Most studies comparing AI models to traditional statistical approaches reported higher prediction accuracy for AI models on test data. Comparisons of different AI models yielded mixed results, likely due to model performance being highly dependent on the dataset and task. An increasing trend of adopting state-of-the-art DL and RL models over standard ML was observed, addressing complex human-machine communication, behavior modification, and decision-making tasks. Six key areas for future AI adoption in PA interventions emerged: personalized PA interventions, real-time monitoring and adaptation, integration of multimodal data sources, evaluation of intervention effectiveness, expanding access to PA interventions, and predicting and preventing injuries.

CONCLUSION

The scoping review highlights the potential of AI methodologies for advancing PA interventions. As the field progresses, staying informed and exploring emerging AI-driven strategies is essential for achieving significant improvements in PA interventions and fostering overall well-being.

Enhanced SARS-CoV-2 case prediction using public health data and machine learning models

Objectives

The goal of this study is to propose and test a scalable framework for machine learning (ML) algorithms to predict near-term severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cases by incorporating and evaluating the impact of real-time dynamic public health data.

Materials and Methods

Data used in this study include patient-level results, procurement, and location information of all SARS-CoV-2 tests reported in West Virginia as part of their mandatory reporting system from January 2021 to March 2022. We propose a method for incorporating and comparing widely available public health metrics inside of a ML framework, specifically a long-short-term memory network, to forecast SARS-CoV-2 cases across various feature sets.

Results

Our approach provides better prediction of localized case counts and indicates the impact of the dynamic elements of the pandemic on predictions, such as the influence of the mixture of viral variants in the population and variable testing and vaccination rates during various eras of the pandemic.

Discussion

Utilizing real-time public health metrics, including estimated Rt from multiple SARS-CoV-2 variants, vaccination rates, and testing information, provided a significant increase in the accuracy of the model during the Omicron and Delta period, thus providing more precise forecasting of daily case counts at the county level. This work provides insights on the influence of various features on predictive performance in rural and non-rural areas.

Conclusion

Our proposed framework incorporates available public health metrics with operational data on the impact of testing, vaccination, and current viral variant mixtures in the population to provide a foundation for combining dynamic public health metrics and ML models to deliver forecasting and insights in healthcare domains. It also shows the importance of developing and deploying ML frameworks in rural settings.

Natural language processing of multi-hospital electronic health records for public health surveillance of suicidality

There is an urgent need to monitor the mental health of large populations, especially during crises such as the COVID-19 pandemic, to timely identify the most at-risk subgroups and to design targeted prevention campaigns. We therefore developed and validated surveillance indicators related to suicidality: the monthly number of hospitalisations caused by suicide attempts and the prevalence among them of five known risks factors. They were automatically computed analysing the electronic health records of fifteen university hospitals of the Paris area, France, using natural language processing algorithms based on artificial intelligence. We evaluated the relevance of these indicators conducting a retrospective cohort study. Considering 2,911,920 records contained in a common data warehouse, we tested for changes after the pandemic outbreak in the slope of the monthly number of suicide attempts by conducting an interrupted time-series analysis. We segmented the assessment time in two sub-periods: before (August 1, 2017, to February 29, 2020) and during (March 1, 2020, to June 31, 2022) the COVID-19 pandemic. We detected 14,023 hospitalisations caused by suicide attempts. Their monthly number accelerated after the COVID-19 outbreak with an estimated trend variation reaching 3.7 (95%CI 2.1-5.3), mainly driven by an increase among girls aged 8-17 (trend variation 1.8, 95%CI 1.2-2.5). After the pandemic outbreak, acts of domestic, physical and sexual violence were more often reported (prevalence ratios: 1.3, 95%CI 1.16-1.48; 1.3, 95%CI 1.10-1.64 and 1.7, 95%CI 1.48-1.98), fewer patients died (p = 0.007) and stays were shorter (p < 0.001). Our study demonstrates that textual clinical data collected in multiple hospitals can be jointly analysed to compute timely indicators describing mental health conditions of populations. Our findings also highlight the need to better take into account the violence imposed on women, especially at early ages and in the aftermath of the COVID-19 pandemic.

Changes to Public Health Surveillance Methods Due to the COVID-19 Pandemic: Scoping Review

BACKGROUND

Public health surveillance plays a vital role in informing public health decision-making. The onset of the COVID-19 pandemic in early 2020 caused a widespread shift in public health priorities. Global efforts focused on COVID-19 monitoring and contact tracing. Existing public health programs were interrupted due to physical distancing measures and reallocation of resources. The onset of the COVID-19 pandemic intersected with advancements in technologies that have the potential to support public health surveillance efforts.

OBJECTIVE

This scoping review aims to explore emergent public health surveillance methods during the early COVID-19 pandemic to characterize the impact of the pandemic on surveillance methods.

METHODS

A scoping search was conducted in multiple databases and by scanning key government and public health organization websites from March 2020 to January 2022. Published papers and gray literature that described the application of new or revised approaches to public health surveillance were included. Papers that discussed the implications of novel public health surveillance approaches from ethical, legal, security, and equity perspectives were also included. The surveillance subject, method, location, and setting were extracted from each paper to identify trends in surveillance practices. Two public health epidemiologists were invited to provide their perspectives as peer reviewers.

RESULTS

Of the 14,238 unique papers, a total of 241 papers describing novel surveillance methods and changes to surveillance methods are included. Eighty papers were review papers and 161 were single studies. Overall, the literature heavily featured papers detailing surveillance of COVID-19 transmission (n=187). Surveillance of other infectious diseases was also described, including other pathogens (n=12). Other public health topics included vaccines (n=9), mental health (n=11), substance use (n=4), healthy nutrition (n=1), maternal and child health (n=3), antimicrobial resistance (n=2), and misinformation (n=6). The literature was dominated by applications of digital surveillance, for example, by using big data through mobility tracking and infodemiology (n=163). Wastewater surveillance was also heavily represented (n=48). Other papers described adaptations to programs or methods that existed prior to the COVID-19 pandemic (n=9). The scoping search also found 109 papers that discuss the ethical, legal, security, and equity implications of emerging surveillance methods. The peer reviewer public health epidemiologists noted that additional changes likely exist, beyond what has been reported and available for evidence syntheses.

CONCLUSIONS

The COVID-19 pandemic accelerated advancements in surveillance and the adoption of new technologies, especially for digital and wastewater surveillance methods. Given the investments in these systems, further applications for public health surveillance are likely. The literature for surveillance methods was dominated by surveillance of infectious diseases, particularly COVID-19. A substantial amount of literature on the ethical, legal, security, and equity implications of these emerging surveillance methods also points to a need for cautious consideration of potential harm.

Artificial intelligence, ChatGPT, and other large language models for social determinants of health: Current state and future directions

This perspective highlights the importance of addressing social determinants of health (SDOH) in patient health outcomes and health inequity, a global problem exacerbated by the COVID-19 pandemic. We provide a broad discussion on current developments in digital health and artificial intelligence (AI), including large language models (LLMs), as transformative tools in addressing SDOH factors, offering new capabilities for disease surveillance and patient care. Simultaneously, we bring attention to challenges, such as data standardization, infrastructure limitations, digital literacy, and algorithmic bias, that could hinder equitable access to AI benefits. For LLMs, we highlight potential unique challenges and risks including environmental impact, unfair labor practices, inadvertent disinformation or "hallucinations," proliferation of bias, and infringement of copyrights. We propose the need for a multitiered approach to digital inclusion as an SDOH and the development of ethical and responsible AI practice frameworks globally and provide suggestions on bridging the gap from development to implementation of equitable AI technologies.

Mapping the Bibliometrics Landscape of AI in Medicine: Methodological Study

BACKGROUND

Artificial intelligence (AI), conceived in the 1950s, has permeated numerous industries, intensifying in tandem with advancements in computing power. Despite the widespread adoption of AI, its integration into medicine trails other sectors. However, medical AI research has experienced substantial growth, attracting considerable attention from researchers and practitioners.

OBJECTIVE

In the absence of an existing framework, this study aims to outline the current landscape of medical AI research and provide insights into its future developments by examining all AI-related studies within PubMed over the past 2 decades. We also propose potential data acquisition and analysis methods, developed using Python (version 3.11) and to be executed in Spyder IDE (version 5.4.3), for future analogous research.

METHODS

Our dual-pronged approach involved (1) retrieving publication metadata related to AI from PubMed (spanning 2000-2022) via Python, including titles, abstracts, authors, journals, country, and publishing years, followed by keyword frequency analysis and (2) classifying relevant topics using latent Dirichlet allocation, an unsupervised machine learning approach, and defining the research scope of AI in medicine. In the absence of a universal medical AI taxonomy, we used an AI dictionary based on the European Commission Joint Research Centre AI Watch report, which emphasizes 8 domains: reasoning, planning, learning, perception, communication, integration and interaction, service, and AI ethics and philosophy.

RESULTS

From 2000 to 2022, a comprehensive analysis of 307,701 AI-related publications from PubMed highlighted a 36-fold increase. The United States emerged as a clear frontrunner, producing 68,502 of these articles. Despite its substantial contribution in terms of volume, China lagged in terms of citation impact. Diving into specific AI domains, as the Joint Research Centre AI Watch report categorized, the learning domain emerged dominant. Our classification analysis meticulously traced the nuanced research trajectories across each domain, revealing the multifaceted and evolving nature of AI's application in the realm of medicine.

CONCLUSIONS

The research topics have evolved as the volume of AI studies increases annually. Machine learning remains central to medical AI research, with deep learning expected to maintain its fundamental role. Empowered by predictive algorithms, pattern recognition, and imaging analysis capabilities, the future of AI research in medicine is anticipated to concentrate on medical diagnosis, robotic intervention, and disease management. Our topic modeling outcomes provide a clear insight into the focus of AI research in medicine over the past decades and lay the groundwork for predicting future directions. The domains that have attracted considerable research attention, primarily the learning domain, will continue to shape the trajectory of AI in medicine. Given the observed growing interest, the domain of AI ethics and philosophy also stands out as a prospective area of increased focus.

Unsupervised natural language processing in the identification of patients with suspected COVID-19 infection

Patients with post-COVID-19 syndrome benefit from health promotion programs. Their rapid identification is important for the cost-effective use of these programs. Traditional identification techniques perform poorly especially in pandemics. A descriptive observational study was carried out using 105,008 prior authorizations paid by a private health care provider with the application of an unsupervised natural language processing method by topic modeling to identify patients suspected of being infected by COVID-19. A total of 6 models were generated: 3 using the BERTopic algorithm and 3 Word2Vec models. The BERTopic model automatically creates disease groups. In the Word2Vec model, manual analysis of the first 100 cases of each topic was necessary to define the topics related to COVID-19. The BERTopic model with more than 1,000 authorizations per topic without word treatment selected more severe patients - average cost per prior authorizations paid of BRL 10,206 and total expenditure of BRL 20.3 million (5.4%) in 1,987 prior authorizations (1.9%). It had 70% accuracy compared to human analysis and 20% of cases with potential interest, all subject to analysis for inclusion in a health promotion program. It had an important loss of cases when compared to the traditional research model with structured language and identified other groups of diseases - orthopedic, mental and cancer. The BERTopic model served as an exploratory method to be used in case labeling and subsequent application in supervised models. The automatic identification of other diseases raises ethical questions about the treatment of health information by machine learning.

Capturing Emerging Experiential Knowledge for Vaccination Guidelines Through Natural Language Processing: Proof-of-Concept Study

BACKGROUND

Experience-based knowledge and value considerations of health professionals, citizens, and patients are essential to formulate public health and clinical guidelines that are relevant and applicable to medical practice. Conventional methods for incorporating such knowledge into guideline development often involve a limited number of representatives and are considered to be time-consuming. Including experiential knowledge can be crucial during rapid guidance production in response to a pandemic but it is difficult to accomplish.

OBJECTIVE

This proof-of-concept study explored the potential of artificial intelligence (AI)-based methods to capture experiential knowledge and value considerations from existing data channels to make these insights available for public health guideline development.

METHODS

We developed and examined AI-based methods in relation to the COVID-19 vaccination guideline development in the Netherlands. We analyzed Dutch messages shared between December 2020 and June 2021 on social media and on 2 databases from the Dutch National Institute for Public Health and the Environment (RIVM), where experiences and questions regarding COVID-19 vaccination are reported. First, natural language processing (NLP) filtering techniques and an initial supervised machine learning model were developed to identify this type of knowledge in a large data set. Subsequently, structural topic modeling was performed to discern thematic patterns related to experiences with COVID-19 vaccination.

RESULTS

NLP methods proved to be able to identify and analyze experience-based knowledge and value considerations in large data sets. They provide insights into a variety of experiential knowledge that is difficult to obtain otherwise for rapid guideline development. Some topics addressed by citizens, patients, and professionals can serve as direct feedback to recommendations in the guideline. For example, a topic pointed out that although travel was not considered as a reason warranting prioritization for vaccination in the national vaccination campaign, there was a considerable need for vaccines for indispensable travel, such as cross-border informal caregiving, work or study, or accessing specialized care abroad. Another example is the ambiguity regarding the definition of medical risk groups prioritized for vaccination, with many citizens not meeting the formal priority criteria while being equally at risk. Such experiential knowledge may help the early identification of problems with the guideline's application and point to frequently occurring exceptions that might initiate a revision of the guideline text.

CONCLUSIONS

This proof-of-concept study presents NLP methods as viable tools to access and use experience-based knowledge and value considerations, possibly contributing to robust, equitable, and applicable guidelines. They offer a way for guideline developers to gain insights into health professionals, citizens, and patients' experience-based knowledge, especially when conventional methods are difficult to implement. AI-based methods can thus broaden the evidence and knowledge base available for rapid guideline development and may therefore be considered as an important addition to the toolbox of pandemic preparedness.

Culture intelligent workflow, structure, and steps

Introduction

Technologies abstract intelligence and provide predictor and precision insight in workflows that manage disorders, similar to cardiology and hematological disease. Positive perceptions of Artificial Intelligence (AI) that support Machine Learning (ML) and Deep Learning (DL) manage transformations with a safe system that improves wellbeing. In sections, workflow introduces an eXamination (X = AI) as an end-to-end structure to culture workstreams in a step-by-step design to manage populace health in a governed system.

Method

To better healthcare outcomes, communities and personnel benefit from an explanation and an interpretive that elucidates workflow for citizens or practitioners to comprehend personalized platforms. Therefore, the author undertook structure and practice reviews and appraised perspectives that impact the management of AI in public health and medicine.

Results

Figures for the management of AI workflow illustrate and inform on the model, structure, culture, assurance, process steps, values, and governance required for abstract insights in public health and medicine. The papers' end-to-end structure with explanans in a work culture interprets the step-by-step designs that manage the success of AI. Personalized care graphics offer an explanandum in the management of biological analytic value.

Discussion

Healthcare leadership collaboratives plan population health with an upstream, workplace and workstream format. Secure workflow and safety wellbeing system requirements prove that genomics and AI improve medicine. Therefore, the paper discusses group understanding of current practice, ethics, policy, and legality.

Conclusion

"Culture, intelligent workflow, structure, and steps" improve wellbeing with personalized care and align a percept for national opportunities, regional control, and local needs. Personalized practice cultures support analytic systems to describe, predict, precision, and prescript medicine in population health management eXaminations.

Research on emergency management of global public health emergencies driven by digital technology: A bibliometric analysis

Background

The frequent occurrence of major public health emergencies globally poses a threat to people's life, health, and safety, and the convergence development of digital technology is very effective and necessary to cope with the outbreak and transmission control of public epidemics such as COVID-19, which is essential to improve the emergency management capability of global public health emergencies.

Methods

The published literatures in the Web of Science Core Collection database from 2003 to 2022 were utilized to analyze the contribution and collaboration of the authors, institutions, and countries, keyword co-occurrence analysis, and research frontier identification using the CiteSpace, VOSviewer, and COOC software.

Results

The results are shown as follows: (1) Relevant research can be divided into growth and development period and rapid development period, and the total publications show exponential growth, among which the USA, China, and the United Kingdom are the most occupied countries, but the global authorship cooperation is not close; (2) clustering analysis of high-frequency keyword, all kinds of digital technologies are utilized, ranging from artificial intelligence (AI)-driven machine learning (ML) or deep learning (DL), and focused application big data analytics and blockchain technology enabled the internet of things (IoT) to identify, and diagnose major unexpected public diseases are hot spots for future research; (3) Research frontier identification indicates that data analysis in social media is a frontier issue that must continue to be focused on to advance digital and smart governance of public health events.

Conclusion

This bibliometric study provides unique insights into the role of digital technologies in the emergency management of public health. It provides research guidance for smart emergency management of global public health emergencies.

Machine Learning Successfully Detects Patients with COVID-19 Prior to PCR Results and Predicts Their Survival Based on Standard Laboratory Parameters in an Observational Study

INTRODUCTION

In the current COVID-19 pandemic, clinicians require a manageable set of decisive parameters that can be used to (i) rapidly identify SARS-CoV-2 positive patients, (ii) identify patients with a high risk of a fatal outcome on hospital admission, and (iii) recognize longitudinal warning signs of a possible fatal outcome.

METHODS

This comparative study was performed in 515 patients in the Maria Skłodowska-Curie Specialty Voivodeship Hospital in Zgierz, Poland. The study groups comprised 314 patients with COVID-like symptoms who tested negative and 201 patients who tested positive for SARS-CoV-2 infection; of the latter, 72 patients with COVID-19 died and 129 were released from hospital. Data on which we trained several machine learning (ML) models included clinical findings on admission and during hospitalization, symptoms, epidemiological risk, and reported comorbidities and medications.

RESULTS

We identified a set of eight on-admission parameters: white blood cells, antibody-synthesizing lymphocytes, ratios of basophils/lymphocytes, platelets/neutrophils, and monocytes/lymphocytes, procalcitonin, creatinine, and C-reactive protein. The medical decision tree built using these parameters differentiated between SARS-CoV-2 positive and negative patients with up to 90-100% accuracy. Patients with COVID-19 who on hospital admission were older, had higher procalcitonin, C-reactive protein, and troponin I levels together with lower hemoglobin and platelets/neutrophils ratio were found to be at highest risk of death from COVID-19. Furthermore, we identified longitudinal patterns in C-reactive protein, white blood cells, and D dimer that predicted the disease outcome.

CONCLUSIONS

Our study provides sets of easily obtainable parameters that allow one to assess the status of a patient with SARS-CoV-2 infection, and the risk of a fatal disease outcome on hospital admission and during the course of the disease.

Evidence synthesis, digital scribes, and translational challenges for artificial intelligence in healthcare

Healthcare has well-known challenges with safety, quality, and effectiveness, and many see artificial intelligence (AI) as essential to any solution. Emerging applications include the automated synthesis of best-practice research evidence including systematic reviews, which would ultimately see all clinical trial data published in a computational form for immediate synthesis. Digital scribes embed themselves in the process of care to detect, record, and summarize events and conversations for the electronic record. However, three persistent translational challenges must be addressed before AI is widely deployed. First, little effort is spent replicating AI trials, exposing patients to risks of methodological error and biases. Next, there is little reporting of patient harms from trials. Finally, AI built using machine learning may perform less effectively in different clinical settings.

Applications of Artificial Intelligence to Obesity Research: Scoping Review of Methodologies

BACKGROUND

Obesity is a leading cause of preventable death worldwide. Artificial intelligence (AI), characterized by machine learning (ML) and deep learning (DL), has become an indispensable tool in obesity research.

OBJECTIVE

This scoping review aimed to provide researchers and practitioners with an overview of the AI applications to obesity research, familiarize them with popular ML and DL models, and facilitate the adoption of AI applications.

METHODS

We conducted a scoping review in PubMed and Web of Science on the applications of AI to measure, predict, and treat obesity. We summarized and categorized the AI methodologies used in the hope of identifying synergies, patterns, and trends to inform future investigations. We also provided a high-level, beginner-friendly introduction to the core methodologies to facilitate the dissemination and adoption of various AI techniques.

RESULTS

We identified 46 studies that used diverse ML and DL models to assess obesity-related outcomes. The studies found AI models helpful in detecting clinically meaningful patterns of obesity or relationships between specific covariates and weight outcomes. The majority (18/22, 82%) of the studies comparing AI models with conventional statistical approaches found that the AI models achieved higher prediction accuracy on test data. Some (5/46, 11%) of the studies comparing the performances of different AI models revealed mixed results, indicating the high contingency of model performance on the data set and task it was applied to. An accelerating trend of adopting state-of-the-art DL models over standard ML models was observed to address challenging computer vision and natural language processing tasks. We concisely introduced the popular ML and DL models and summarized their specific applications in the studies included in the review.

CONCLUSIONS

This study reviewed AI-related methodologies adopted in the obesity literature, particularly ML and DL models applied to tabular, image, and text data. The review also discussed emerging trends such as multimodal or multitask AI models, synthetic data generation, and human-in-the-loop that may witness increasing applications in obesity research.

GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics

We seek to transform how new and emergent variants of pandemic-causing viruses, specifically SARS-CoV-2, are identified and classified. By adapting large language models (LLMs) for genomic data, we build genome-scale language models (GenSLMs) which can learn the evolutionary landscape of SARS-CoV-2 genomes. By pre-training on over 110 million prokaryotic gene sequences and fine-tuning a SARS-CoV-2-specific model on 1.5 million genomes, we show that GenSLMs can accurately and rapidly identify variants of concern. Thus, to our knowledge, GenSLMs represents one of the first whole genome scale foundation models which can generalize to other prediction tasks. We demonstrate scaling of GenSLMs on GPU-based supercomputers and AI-hardware accelerators utilizing 1.63 Zettaflops in training runs with a sustained performance of 121 PFLOPS in mixed precision and peak of 850 PFLOPS. We present initial scientific insights from examining GenSLMs in tracking evolutionary dynamics of SARS-CoV-2, paving the path to realizing this on large biological data.

Artificial intelligence applications used in the clinical response to COVID-19: A scoping review

Research into using artificial intelligence (AI) in health care is growing and several observers predicted that AI would play a key role in the clinical response to the COVID-19. Many AI models have been proposed though previous reviews have identified only a few applications used in clinical practice. In this study, we aim to (1) identify and characterize AI applications used in the clinical response to COVID-19; (2) examine the timing, location, and extent of their use; (3) examine how they relate to pre-pandemic applications and the U.S. regulatory approval process; and (4) characterize the evidence that is available to support their use. We searched academic and grey literature sources to identify 66 AI applications that performed a wide range of diagnostic, prognostic, and triage functions in the clinical response to COVID-19. Many were deployed early in the pandemic and most were used in the U.S., other high-income countries, or China. While some applications were used to care for hundreds of thousands of patients, others were used to an unknown or limited extent. We found studies supporting the use of 39 applications, though few of these were independent evaluations and we found no clinical trials evaluating any application's impact on patient health. Due to limited evidence, it is impossible to determine the extent to which the clinical use of AI in the pandemic response has benefited patients overall. Further research is needed, particularly independent evaluations on AI application performance and health impacts in real-world care settings.

Den Patienten wirklich verstehen lernen: Real-world-Evidenz aus der „patient journey“

Hintergrund

Die COVID-19-Pandemie („coronavirus disease 2019“) hat die Bedeutung von Real World Data (RWD) im klinischen Alltag unterstrichen und die fatalen Folgen von längst existierenden Problemen wie Lücken in der Primärdatenerfassung, Hürden bei der Auswertung von Patientendaten sowie erschwertem Patientendatenaustausch zwischen verschiedenen Einrichtungen nochmal deutlich gemacht. Darüber hinaus haben Entwicklungen weg von einem paternalistischen hin zu einem partnerschaftlichen Modell der Arzt-Patienten-Beziehung sowie die zunehmende Digitalisierung unser Verständnis von Gesundheitsversorgung geprägt, das Thema der Patientenautonomie und Selbstwirksamkeit in den Vordergrund gebracht und den Bedarf an innovativen, patientenzentrierten Lösungsansätzen verdeutlicht.

Methoden

Wir nutzen die „patient journey“ als theoretisches Konstrukt, entlang dessen wir die Sammlung von verschiedenen Typen von RWD, ihre Bedeutung und Umgang damit beschreiben.

Schlussfolgerung

Die Abbildung der „patient journey“ in Verbindung mit der Nutzung eines einheitlichen Datenstandards kann zur Erfassung von Primärdaten im Gesundheitswesen führen, die von allen medizinischen Behandlungseinrichtungen genutzt werden können. Dies wird den Austausch von Daten zwischen Einrichtungen erleichtern. Darüber hinaus könnte die fortlaufende Auswertung von patientenberichteten Ereignissen als Standard in der klinischen Routine die Patientenautonomie stärken und die Behandlung optimieren. Zusammenfassend lässt sich sagen, dass der Behandlungserfolg, das Gesamtüberleben und das Wohlbefinden der Patienten durch die Schaffung einer gemeinsamen Datensprache und eines ganzheitlichen, menschenzentrierten Ansatzes verbessert werden können.

Google earth engine based computational system for the earth and environment monitoring applications during the COVID-19 pandemic using thresholding technique on SAR datasets

Observing the earth and environmental conditions during the COVID-19 pandemic lockdown along with travel restrictions headed to worse circumstance. These scenarios amplified the hurdles of flood management. In order to resolves these issues, an efficient and resilient geospatial framework with unconventional systems is also required for the generation of instantaneous results. Hence to avoid these deficiencies, the google earth engine based computational system integrated with analytical tools for large-scale data handling is introduced for the earth and environmental monitoring applications. The present study proposes a working model for geospatial data processing to understand socio-demographic implications with a web-based analytical interface. The research introduces a histogram-based thresholding approach for real-time surface water mapping along with precise data processing and analysis for automated monitoring. The study integrates geospatial datasets to a enhanced data processing methods in a web-based platform to deliver the required results for extensive planning and decision making. Furthermore, a similar type of work can be undertaken for other disaster management applications.

Development of gold nanoparticle-based biosensors for COVID-19 diagnosis

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative organism of coronavirus disease 2019 (COVID-19) which poses a significant threat to public health worldwide. Though there are certain recommended drugs that can cure COVID-19, their therapeutic efficacy is limited. Therefore, the early and rapid detection without compromising the test accuracy is necessary in order to provide an appropriate treatment for the disease suppression.

Main body

Nanoparticles (NPs) can closely mimic the virus and interact strongly with its proteins due to their morphological similarities. NPs have been widely applied in a variety of medical applications, including biosensing, drug delivery, antimicrobial treatment, and imaging. Recently, NPs-based biosensors have attracted great interest for their biological activities and specific sensing properties, which allows the detection of analytes such as nucleic acids (DNA or RNA), aptamers, and proteins in clinical samples. Further, the advances of nanotechnologies have enabled the development of miniaturized detection systems for point-of-care biosensors, a new strategy for detecting human viral diseases. Among the various NPs, the specific physicochemical properties of gold NPs (AuNPs) are being widely used in the field of clinical diagnostics. As a result, several AuNP-based colorimetric detection methods have been developed.

Short conclusion

The purpose of this review is to provide an overview of the development of AuNPs-based biosensors by virtue of its powerful characteristics as a signal amplifier or enhancer that target pathogenic RNA viruses that provide a reliable and effective strategy for detecting of the existing or newly emerging SARS-CoV-2.

Personalized survival probabilities for SARS-CoV-2 positive patients by explainable machine learning

Interpretable risk assessment of SARS-CoV-2 positive patients can aid clinicians to implement precision medicine. Here we trained a machine learning model to predict mortality within 12 weeks of a first positive SARS-CoV-2 test. By leveraging data on 33,938 confirmed SARS-CoV-2 cases in eastern Denmark, we considered 2723 variables extracted from electronic health records (EHR) including demographics, diagnoses, medications, laboratory test results and vital parameters. A discrete-time framework for survival modelling enabled us to predict personalized survival curves and explain individual risk factors. Performance on the test set was measured with a weighted concordance index of 0.95 and an area under the curve for precision-recall of 0.71. Age, sex, number of medications, previous hospitalizations and lymphocyte counts were identified as top mortality risk factors. Our explainable survival model developed on EHR data also revealed temporal dynamics of the 22 selected risk factors. Upon further validation, this model may allow direct reporting of personalized survival probabilities in routine care.

Big data-based risk assessment of poultry farms during the 2020/2021 highly pathogenic avian influenza epidemic in Korea

Outbreaks of H5-type highly pathogenic avian influenza (HPAI) in poultry have been reported in various parts of the world. To respond to these continuous threats, numerous surveillance programs have been applied to poultry raising facilities as well as wild birds. In Korea, a surveillance program was developed aimed at providing a preemptive response to possible outbreaks at poultry farms. The purpose of this study is to comprehensively present the risks of HPAI evaluated by this program in relation to actual outbreak farms during the epidemic of 2020/2021. A deep learning-based risk assessment program was trained based on the pattern of livestock vehicles visiting poultry farms and HPAI outbreaks to calculate the risk of HPAI for farms linked by the movement of livestock vehicles (such farms are termed “epidemiologically linked farms”). A total of 7,984 risk assessments were conducted, and the results were categorized into four groups. The proportion of the highest risk level was greater in duck farms (13.6%) than in chicken farms (8.8%). Among the duck farms, the proportion of the highest risk level was much greater in farms where breeder ducks were raised (accounting for 26.4% of the risk) than in farms where ducks were raised to obtain meat (12.8% of the risk). A higher risk level was also found in cases where the species of the outbreak farm and epidemiologically linked farms were the same (proportion of the highest risk level = 13.2%) compared to that when the species between the two farms were different (7.9%). The overall proportion of farms with HPAI outbreaks among epidemiologically linked farms (attack rate, AR) was 1.7% as HPAI was confirmed on 67 of the 3,883 epidemiologically linked farms. The AR was highest for breeder ducks (15.3%) among duck farms and laying hens (4.8%) among chicken farms. The AR of the pairs where livestock vehicles entered the inner farm area was 1.3 times (95% confidence interval: 1.4–2.9) higher than that of all pairs. With the risk information provided, customized preventive measures can be implemented for each epidemiologically linked farm. The use of this risk assessment program would be a good example of information-based surveillance and support decision-making for controlling animal diseases.

Artificial intelligence and clinical deterioration

PURPOSE OF REVIEW

To provide an overview of the systems being used to identify and predict clinical deterioration in hospitalised patients, with focus on the current and future role of artificial intelligence (AI).

RECENT FINDINGS

There are five leading AI driven systems in this field: the Advanced Alert Monitor (AAM), the electronic Cardiac Arrest Risk Triage (eCART) score, Hospital wide Alert Via Electronic Noticeboard, the Mayo Clinic Early Warning Score, and the Rothman Index (RI). Each uses Electronic Patient Record (EPR) data and machine learning to predict adverse events. Less mature but relevant evolutions are occurring in the fields of Natural Language Processing, Time and Motion Studies, AI Sepsis and COVID-19 algorithms.

SUMMARY

Research-based AI-driven systems to predict clinical deterioration are increasingly being developed, but few are being implemented into clinical workflows. Escobar et al. (AAM) provide the current gold standard for robust model development and implementation methodology. Multiple technologies show promise, however, the pathway to meaningfully affect patient outcomes remains challenging.

COVID-19 GPH: tracking the contribution of genomics and precision health to the COVID-19 pandemic response

The scientific response to the COVID-19 pandemic has produced an abundance of publications, including peer-reviewed articles and preprints, across a wide array of disciplines, from microbiology to medicine and social sciences. Genomics and precision health (GPH) technologies have had a particularly prominent role in medical and public health investigations and response; however, these domains are not simply defined and it is difficult to search for relevant information using traditional strategies. To quantify and track the ongoing contributions of GPH to the COVID-19 response, the Office of Genomics and Precision Public Health at the Centers for Disease Control and Prevention created the COVID-19 Genomics and Precision Health database (COVID-19 GPH), an open access knowledge management system and publications database that is continuously updated through machine learning and manual curation. As of February 11, 2022, COVID-GPH contained 31,597 articles, mostly on pathogen and human genomics (72%). The database also includes articles describing applications of machine learning and artificial intelligence to the investigation and control of COVID-19 (28%). COVID-GPH represents about 10% (22983/221241) of the literature on COVID-19 on PubMed. This unique knowledge management database makes it easier to explore, describe, and track how the pandemic response is accelerating the applications of genomics and precision health technologies. COVID-19 GPH can be freely accessed via https://phgkb.cdc.gov/PHGKB/coVInfoStartPage.action.

Machine Learning and Deep Learning based AI Tools for Development of Diagnostic Tools

Artificial intelligence (AI) systems exhibit human-like intelligence. Human intelligence is converted to machines or computer technologies using AI algorithms. Machine learning (ML) is a subset of AI that can learn from extracted data and models to perform a task whereas deep learning (DL) is a subset of ML that imitates the human brain functioning to solve real-world problems in almost all fields. AI caused a paradigm shift in healthcare that can be employed for decision support and forecasting. Medical diagnostic tools developed using AI, perform disease diagnosis based on the symbolic models of disease and provide therapy recommendations. The key AI applications employed with medical diagnosis are characterized as learning systems and expert systems. Diagnostic tools, developed using Expert systems utilize facts, implications, and knowledge processing techniques for disease diagnosis, whereas a learning system utilizes statistical pattern recognition, ML, and neural networks. In March 2020, an infectious disease caused by the severe acute respiratory syndrome-Coronavirus-2 (SARS-CoV-2) virus, Coronavirus disease-2019 (COVID-19) was declared a pandemic by the World Health Organization. Recent research studies have shown that AI, ML, and DL can be leveraged to combat COVID-19 having objectives of disease diagnosis, to forecast epidemic and sustainable development, and so on. DL algorithms are implemented on image data, more specifically on chest X-rays and computed tomography scans, for developing diagnostic tools. In this chapter, various ML and DL-based AI tools for the development of diagnostic tools have been discussed.

Rigorous Policy-Making Amid COVID-19 and Beyond: Literature Review and Critical Insights

Policies shape society. Public health policies are of particular importance, as they often dictate matters in life and death. Accumulating evidence indicates that good-intentioned COVID-19 policies, such as shelter-in-place measures, can often result in unintended consequences among vulnerable populations such as nursing home residents and domestic violence victims. Thus, to shed light on the issue, this study aimed to identify policy-making processes that have the potential of developing policies that could induce optimal desirable outcomes with limited to no unintended consequences amid the pandemic and beyond. Methods: A literature review was conducted in PubMed, PsycINFO, and Scopus to answer the research question. To better structure the review and the subsequent analysis, theoretical frameworks such as the social ecological model were adopted to guide the process. Results: The findings suggested that: (1) people-centered; (2) artificial intelligence (AI)-powered; (3) data-driven, and (4) supervision-enhanced policy-making processes could help society develop policies that have the potential to yield desirable outcomes with limited unintended consequences. To leverage these strategies' interconnectedness, the people-centered, AI-powered, data-driven, and supervision-enhanced (PADS) model of policy making was subsequently developed. Conclusions: The PADS model can develop policies that have the potential to induce optimal outcomes and limit or eliminate unintended consequences amid COVID-19 and beyond. Rather than serving as a definitive answer to problematic COVID-19 policy-making practices, the PADS model could be best understood as one of many promising frameworks that could bring the pandemic policy-making process more in line with the interests of societies at large; in other words, more cost-effectively, and consistently anti-COVID and pro-human.

Application of Artificial Intelligence in COVID-19 Diagnosis and Therapeutics

The coronavirus disease 2019 (COVID-19) pandemic began at the end of December 2019, giving rise to a high rate of infections and causing COVID-19-associated deaths worldwide. It was first reported in Wuhan, China, and since then, not only global leaders, organizations, and pharmaceutical/biotech companies, but also researchers, have directed their efforts toward overcoming this threat. The use of artificial intelligence (AI) has recently surged internationally and has been applied to diverse aspects of many problems. The benefits of using AI are now widely accepted, and many studies have shown great success in medical research on tasks, such as the classification, detection, and prediction of disease, or even patient outcome. In fact, AI technology has been actively employed in various ways in COVID-19 research, and several clinical applications of AI-equipped medical devices for the diagnosis of COVID-19 have already been reported. Hence, in this review, we summarize the latest studies that focus on medical imaging analysis, drug discovery, and therapeutics such as vaccine development and public health decision-making using AI. This survey clarifies the advantages of using AI in the fight against COVID-19 and provides future directions for tackling the COVID-19 pandemic using AI techniques.

Fundamentals of genomic epidemiology, lessons learned from the coronavirus disease 2019 (COVID-19) pandemic, and new directions

The coronavirus disease 2019 (COVID-19) pandemic was one of the significant causes of death worldwide in 2020. The disease is caused by severe acute coronavirus syndrome (SARS) coronavirus 2 (SARS-CoV-2), an RNA virus of the subfamily Orthocoronavirinae related to 2 other clinically relevant coronaviruses, SARS-CoV and MERS-CoV. Like other coronaviruses and several other viruses, SARS-CoV-2 originated in bats. However, unlike other coronaviruses, SARS-CoV-2 resulted in a devastating pandemic. The SARS-CoV-2 pandemic rages on due to viral evolution that leads to more transmissible and immune evasive variants. Technology such as genomic sequencing has driven the shift from syndromic to molecular epidemiology and promises better understanding of variants. The COVID-19 pandemic has exposed critical impediments that must be addressed to develop the science of pandemics. Much of the progress is being applied in the developed world. However, barriers to the use of molecular epidemiology in low- and middle-income countries (LMICs) remain, including lack of logistics for equipment and reagents and lack of training in analysis. We review the molecular epidemiology literature to understand its origins from the SARS epidemic (2002-2003) through influenza events and the current COVID-19 pandemic. We advocate for improved genomic surveillance of SARS-CoV and understanding the pathogen diversity in potential zoonotic hosts. This work will require training in phylogenetic and high-performance computing to improve analyses of the origin and spread of pathogens. The overarching goals are to understand and abate zoonosis risk through interdisciplinary collaboration and lowering logistical barriers.