Global disease monitoring and forecasting with Wikipedia

Infectious disease is a leading threat to public health, economic stability, and other key social structures. Efforts to mitigate these impacts depend on accurate and timely monitoring to measure the risk and progress of disease. Traditional, biologically-focused monitoring techniques are accurate but costly and slow; in response, new techniques based on social internet data such as social media and search queries are emerging. These efforts are promising, but important challenges in the areas of scientific peer review, breadth of diseases and countries, and forecasting hamper their operational usefulness. We examine a freely available, open data source for this use: access logs from the online encyclopedia Wikipedia. Using linear models, language as a proxy for location, and a systematic yet simple article selection procedure, we tested 14 location-disease combinations and demonstrate that these data feasibly support an approach that overcomes these challenges. Specifically, our proof-of-concept yields models with $r^2$ up to 0.92, forecasting value up to the 28 days tested, and several pairs of models similar enough to suggest that transferring models from one location to another without re-training is feasible. Based on these preliminary results, we close with a research agenda designed to overcome these challenges and produce a disease monitoring and forecasting system that is significantly more effective, robust, and globally comprehensive than the current state of the art.Comment: 27 pages; 4 figures; 4 tables. Version 2: Cite McIver & Brownstein and adjust novelty claims accordingly; revise title; various revisions for clarit

When Infodemic Meets Epidemic: a Systematic Literature Review

Epidemics and outbreaks present arduous challenges requiring both individual and communal efforts. Social media offer significant amounts of data that can be leveraged for bio-surveillance. They also provide a platform to quickly and efficiently reach a sizeable percentage of the population, hence their potential impact on various aspects of epidemic mitigation. The general objective of this systematic literature review is to provide a methodical overview of the integration of social media in different epidemic-related contexts. Three research questions were conceptualized for this review, resulting in over 10000 publications collected in the first PRISMA stage, 129 of which were selected for inclusion. A thematic method-oriented synthesis was undertaken and identified 5 main themes related to social media enabled epidemic surveillance, misinformation management, and mental health. Findings uncover a need for more robust applications of the lessons learned from epidemic post-mortem documentation. A vast gap exists between retrospective analysis of epidemic management and result integration in prospective studies. Harnessing the full potential of social media in epidemic related tasks requires streamlining the results of epidemic forecasting, public opinion understanding and misinformation propagation, all while keeping abreast of potential mental health implications. Pro-active prevention has thus become vital for epidemic curtailment and containment

Mining social media data for biomedical signals and health-related behavior

Social media data has been increasingly used to study biomedical and health-related phenomena. From cohort level discussions of a condition to planetary level analyses of sentiment, social media has provided scientists with unprecedented amounts of data to study human behavior and response associated with a variety of health conditions and medical treatments. Here we review recent work in mining social media for biomedical, epidemiological, and social phenomena information relevant to the multilevel complexity of human health. We pay particular attention to topics where social media data analysis has shown the most progress, including pharmacovigilance, sentiment analysis especially for mental health, and other areas. We also discuss a variety of innovative uses of social media data for health-related applications and important limitations in social media data access and use.Comment: To appear in the Annual Review of Biomedical Data Scienc

Reframing viral infections as acute metabolic disorders: dengue viruses and their dependency on host metabolic pathways

2022 Summer.Includes bibliographical references.Dengue viruses (DENVs) are the etiological agent of the world's most aggressive arthropod-borne disease. At present, there are no available antivirals against DENVs. This fact underscores a dire need to examine host-virus interactions to identify and develop novel therapeutic approaches. As obligate intracellular parasites, DENVs are reliant upon and hijack several host metabolic pathways both to fulfill their replicative needs, and to evade the host immune response. We and others have previously established that infection with DENVs causes significant perturbation to host lipid metabolism, including elevations in sphingolipids in both the human and mosquito host. In addition, we and others previously discovered that the DENV NS1 protein increases sialidase activity in both in vitro and in vivo models leading to increased endothelial hyperpermeability and vascular leakage which are hallmarks of severe dengue. To further clarify and characterize these previous works, we have performed siRNA-mediated loss of function studies using human hepatoma cells (Huh7 cells) on several metabolic pathways altered during DENV2 infection. First, we examined the role of acyl-CoA thioesterases, enzymes responsible for controlling the intracellular balance of activated fatty acids and free fatty acids, on the DENV2 lifecycle. In these analyses, we determined that the cytosolic ACOT1 enzyme had an inhibitory effect on DENV2 replication and release, while mitochondrial ACOT (ACOTs 2 and 7) functionality was critical for viral replication and release. Moreover, we identified several enzymes within the ACOT family whose expression was dependent on ACOT2 and ACOT7 expression. These results highlighted complex relationships between ACOTs and DENVs, as well as identified yet unknown functional interdependence between ACOT enzymes. Next, we expanded our previous understanding of the relationship between DENVs and the human sialidase enzymes (NEU1-4). While previously studies linked upregulation of these enzymes with DENV2 pathology, we provide the first evidence showing that NEU1-4 functionality is vital for DENV2 genome replication and viral egress. Moreover, our analyses also revealed previously unknown functionality of NEU4 or its downstream products as transcriptional regulators for NEU1-3. Finally, we provide the first profile of the effect of loss of function of enzymes within the entire sphingolipid metabolic pathway (as identified through KEGG pathway database) on the DENV2 life cycle. In this study, we identified that enzymes involved the sphingomyelinase and salvage pathways of ceramide synthesis as opposed to de novo ceramide synthesis were critical to DENV2 release from Huh7 cells. In addition, we determined that enzymes involved in the synthesis and degradation of glycosphingolipids were vital for DENV2 release. An especially intriguing result within this arm of sphingolipid metabolism was that the two enzymes which hydrolyze GluCer had differential effects on DENV2 replication and release. GBA1 (lysosomal) had an antiviral effect on DENV2, while GBA2 (non-lysosomal) was required for DENV2 replication and release. This prompted us to profile the changes that occur to glycosphingolipids (GSLs) during infection, and we uncovered several species of GSLs that are elevated during infection. Moreover, we identified that Ambroxol HCl, a pharmaceutical GBA1 chaperone/GBA2 inhibitor, was able to abrogate these elevations in GSLs. Combined, our results allowed us to propose a novel function for GBA2 as a GluCer recycling enzyme during DENV2 infection. In conclusion, together, the work in this dissertation highlights critical metabolic nodes that impact virus replication and provides new directions for investigating viral infections as acute metabolic diseases

A Historical and Political Review of the Response to the 2015-2016 Zika Outbreak in Puerto Rico

The Zika virus was first identified in 1948 but was relatively unknown until 2015, when Brazil began to report a significant increase in the numbers of babies with congenital defects. It is a virus that is primarily transmitted by mosquitos and primarily effects the nervous system. With its tropical climate and constant mosquito presence, Puerto Rico was the location of a massive outbreak during 2015-2016. However, the response to the outbreak faced several hurdles despite Brazil already reporting an increase in microcephaly. The purpose of this review is to examine the political and historical factors that hampered the initial response to the 2015 Zika outbreak in Puerto Rico and how they affected the perceived risk of the Zika virus. It is crucial that intensive health education campaigns and vaccine development continue in order to ensure that a second outbreak does not occur and result in a greater number of babies diagnosed with Congenital Zika Syndrome

A Historical and Political Review of the Response to the 2015-2016 Zika Outbreak in Puerto Rico

The Zika virus was first identified in 1948 but was relatively unknown until 2015, when Brazil began to report a significant increase in the numbers of babies with congenital defects. It is a virus that is primarily transmitted by mosquitos and primarily effects the nervous system. With its tropical climate and constant mosquito presence, Puerto Rico was the location of a massive outbreak during 2015-2016. However, the response to the outbreak faced several hurdles despite Brazil already reporting an increase in microcephaly. The purpose of this review is to examine the political and historical factors that hampered the initial response to the 2015 Zika outbreak in Puerto Rico and how they affected the perceived risk of the Zika virus. It is crucial that intensive health education campaigns and vaccine development continue in order to ensure that a second outbreak does not occur and result in a greater number of babies diagnosed with Congenital Zika Syndrome

Socio-Life Science and the COVID-19 Outbreak

This open access book presents the first step towards building socio-life science, a field of science investigating humans in such a way that both social and life-scientific factors are integrated. Because humans are both living and social creatures, a human action can never be understood fully without knowing both the biological traits of a person and the social scientific environments in which he exists. With this consideration, the editors of this book have initiated a research project promoting a deeper and more integrated understanding of human behavior and human health. This book aims to show what can, and could be, achieved through our interdisciplinary project. One important product is the newly formed three-party collaboration between Pasteur Institut, Kyoto University, and the Research Institute of Economy, Trade and Industry. Covering many different fields, including medicine, epidemiology, anthropology, economics, sociology, demography, geography, and policy, researchers in these institutes, and many others, present their studies on the COVID-19 pandemic. Although based on different methodologies, the studies show the importance of behavioral change and governmental policy in the fight against a huge pandemic. The book explains the unique genome cohort–panel data that the project builds to study social and life scientific aspects of humans

International Society for Disease Surveillance Conference 2011: Building the Future of Public Health Surveillance: Building the Future of Public Health Surveillance

Daniel Reidpath - ORCID: 0000-0002-8796-0420 https://orcid.org/0000-0002-8796-04204pubpub1117