High-resolution epidemiological landscape from ~290,000 SARS-CoV-2 genomes from Denmark.

Vast amounts of pathogen genomic, demographic and spatial data are transforming our understanding of SARS-CoV-2 emergence and spread. We examined the drivers of molecular evolution and spread of 291,791 SARS-CoV-2 genomes from Denmark in 2021. With a sequencing rate consistently exceeding 60%, and up to 80% of PCR-positive samples between March and November, the viral genome set is broadly whole-epidemic representative. We identify a consistent rise in viral diversity over time, with notable spikes upon the importation of novel variants (e.g., Delta and Omicron). By linking genomic data with rich individual-level demographic data from national registers, we find that individuals aged  < 15 and  > 75 years had a lower contribution to molecular change (i.e., branch lengths) compared to other age groups, but similar molecular evolutionary rates, suggesting a lower likelihood of introducing novel variants. Similarly, we find greater molecular change among vaccinated individuals, suggestive of immune evasion. We also observe evidence of transmission in rural areas to follow predictable diffusion processes. Conversely, urban areas are expectedly more complex due to their high mobility, emphasising the role of population structure in driving virus spread. Our analyses highlight the added value of integrating genomic data with detailed demographic and spatial information, particularly in the absence of structured infection surveys.

Using smartphones to study vaccination decisions in the wild.

One of the most important tools available to limit the spread and impact of infectious diseases is vaccination. It is therefore important to understand what factors determine people's vaccination decisions. To this end, previous behavioural research made use of, (i) controlled but often abstract or hypothetical studies (e.g., vignettes) or, (ii) realistic but typically less flexible studies that make it difficult to understand individual decision processes (e.g., clinical trials). Combining the best of these approaches, we propose integrating real-world Bluetooth contacts via smartphones in several rounds of a game scenario, as a novel methodology to study vaccination decisions and disease spread. In our 12-week proof-of-concept study conducted with N = 494 students, we found that participants strongly responded to some of the information provided to them during or after each decision round, particularly those related to their individual health outcomes. In contrast, information related to others' decisions and outcomes (e.g., the number of vaccinated or infected individuals) appeared to be less important. We discuss the potential of this novel method and point to fruitful areas for future research.

Nonrepresentativeness of Human Mobility Data and its Impact on Modeling Dynamics of the COVID-19 Pandemic: Systematic Evaluation.

BACKGROUND: In recent years, a range of novel smartphone-derived data streams about human mobility have become available on a near-real-time basis. These data have been used, for example, to perform traffic forecasting and epidemic modeling. During the COVID-19 pandemic in particular, human travel behavior has been considered a key component of epidemiological modeling to provide more reliable estimates about the volumes of the pandemic's importation and transmission routes, or to identify hot spots. However, nearly universally in the literature, the representativeness of these data, how they relate to the underlying real-world human mobility, has been overlooked. This disconnect between data and reality is especially relevant in the case of socially disadvantaged minorities. OBJECTIVE: The objective of this study is to illustrate the nonrepresentativeness of data on human mobility and the impact of this nonrepresentativeness on modeling dynamics of the epidemic. This study systematically evaluates how real-world travel flows differ from census-based estimations, especially in the case of socially disadvantaged minorities, such as older adults and women, and further measures biases introduced by this difference in epidemiological studies. METHODS: To understand the demographic composition of population movements, a nationwide mobility data set from 318 million mobile phone users in China from January 1 to February 29, 2020, was curated. Specifically, we quantified the disparity in the population composition between actual migrations and resident composition according to census data, and shows how this nonrepresentativeness impacts epidemiological modeling by constructing an age-structured SEIR (Susceptible-Exposed-Infected- Recovered) model of COVID-19 transmission. RESULTS: We found a significant difference in the demographic composition between those who travel and the overall population. In the population flows, 59% (n=20,067,526) of travelers are young and 36% (n=12,210,565) of them are middle-aged (P<.001), which is completely different from the overall adult population composition of China (where 36% of individuals are young and 40% of them are middle-aged). This difference would introduce a striking bias in epidemiological studies: the estimation of maximum daily infections differs nearly 3 times, and the peak time has a large gap of 46 days. CONCLUSIONS: The difference between actual migrations and resident composition strongly impacts outcomes of epidemiological forecasts, which typically assume that flows represent underlying demographics. Our findings imply that it is necessary to measure and quantify the inherent biases related to nonrepresentativeness for accurate epidemiological surveillance and forecasting.

Understanding scholar-trajectories across scientific periodicals.

Despite the rapid growth in the number of scientific publications, our understanding of author publication trajectories remains limited. Here we propose an embedding-based framework for tracking author trajectories in a geometric space that leverages the information encoded in the publication sequences, namely the list of the consecutive publication venues for each scholar. Using the publication histories of approximately 30,000 social media researchers, we obtain a knowledge space that broadly captures essential information about periodicals as well as complex (inter-)disciplinary structures of science. Based on this space, we study academic success through the prism of movement across scientific periodicals. We use a measure from human mobility, the radius of gyration, to characterize individual scholars' trajectories. Results show that author mobility across periodicals negatively correlates with citations, suggesting that successful scholars tend to publish in a relatively proximal range of periodicals. Overall, our framework discovers intricate structures in large-scale sequential data and provides new ways to explore mobility and trajectory patterns.

Using sequences of life-events to predict human lives.

Here we represent human lives in a way that shares structural similarity to language, and we exploit this similarity to adapt natural language processing techniques to examine the evolution and predictability of human lives based on detailed event sequences. We do this by drawing on a comprehensive registry dataset, which is available for Denmark across several years, and that includes information about life-events related to health, education, occupation, income, address and working hours, recorded with day-to-day resolution. We create embeddings of life-events in a single vector space, showing that this embedding space is robust and highly structured. Our models allow us to predict diverse outcomes ranging from early mortality to personality nuances, outperforming state-of-the-art models by a wide margin. Using methods for interpreting deep learning models, we probe the algorithm to understand the factors that enable our predictions. Our framework allows researchers to discover potential mechanisms that impact life outcomes as well as the associated possibilities for personalized interventions.

Science Communication as a Collective Intelligence Endeavor: A Manifesto and Examples for Implementation.

Effective science communication is challenging when scientific messages are informed by a continually updating evidence base and must often compete against misinformation. We argue that we need a new program of science communication as collective intelligence-a collaborative approach, supported by technology. This would have four key advantages over the typical model where scientists communicate as individuals: scientific messages would be informed by (a) a wider base of aggregated knowledge, (b) contributions from a diverse scientific community, (c) participatory input from stakeholders, and (d) better responsiveness to ongoing changes in the state of knowledge.

Exposure to urban and rural contexts shapes smartphone usage behavior.

Smartphones have profoundly changed human life. Nevertheless, the factors that shape how we use our smartphones remain unclear, in part due to limited availability of usage-data. Here, we investigate the impact of a key environmental factor: users' exposure to urban and rural contexts. Our analysis is based on a global dataset describing mobile app usage and location for ∼500,000 individuals. We uncover strong and nontrivial patterns. First, we confirm that rural users tend to spend less time on their phone than their urban counterparts. We find, however, that individuals in rural areas tend to use their smartphones for activities such as gaming and social media. In cities, individuals preferentially use their phone for activities such as navigation and business. Are these effects (1) driven by differences between individuals who choose to live in urban vs. rural environments or do they (2) emerge because the environment itself affects online behavior? Using a quasi-experimental design based on individuals that move from the city to the countryside-or vice versa-we confirm hypothesis (2) and find that smartphone use changes according to users's environment. This work presents a quantitative step forward towards understanding how the interplay between environment and smartphones impacts human lives. As such, our findings could provide information to better regulate persuasive technologies embedded in smartphone apps. Further, our work opens the door to understanding new mechanisms leading to urban/rural divides in political and socioeconomic attitudes.

Epidemic modelling of monitoring public behavior using surveys during pandemic-induced lockdowns.

BACKGROUND: Implementing a lockdown for disease mitigation is a balancing act: Non-pharmaceutical interventions can reduce disease transmission significantly, but interventions also have considerable societal costs. Therefore, decision-makers need near real-time information to calibrate the level of restrictions. METHODS: We fielded daily surveys in Denmark during the second wave of the COVID-19 pandemic to monitor public response to the announced lockdown. A key question asked respondents to state their number of close contacts within the past 24 hours. Here, we establish a link between survey data, mobility data, and hospitalizations via epidemic modelling of a short time-interval around Denmark's December 2020 lockdown. Using Bayesian analysis, we then evaluate the usefulness of survey responses as a tool to monitor the effects of lockdown and then compare the predictive performance to that of mobility data. RESULTS: We find that, unlike mobility, self-reported contacts decreased significantly in all regions before the nation-wide implementation of non-pharmaceutical interventions and improved predicting future hospitalizations compared to mobility data. A detailed analysis of contact types indicates that contact with friends and strangers outperforms contact with colleagues and family members (outside the household) on the same prediction task. CONCLUSIONS: Representative surveys thus qualify as a reliable, non-privacy invasive monitoring tool to track the implementation of non-pharmaceutical interventions and study potential transmission paths.

Mobile phone data obtained from companies such as Google and Apple have often been used to monitor public compliance with pandemic lockdowns and make predictions of future disease spread. Survey data obtained by asking people a series of questions can provide an alternative source of information. We undertook daily surveys of a representative subset of the Danish population immediately before, and during, a lockdown during the COVID19 pandemic. We compared the modeling results obtained from the surveys with data derived from the movement of mobile phones. The self-reported survey data was more predictive of future hospitalizations due to COVID than mobility data. Our data suggest that surveys can be used to monitor compliance during lockdowns.

Quantifying daily rhythms with non-negative matrix factorization applied to mobile phone data.

Human activities follow daily, weekly, and seasonal rhythms. The emergence of these rhythms is related to physiology and natural cycles as well as social constructs. The human body and its biological functions undergo near 24-h rhythms (circadian rhythms). While their frequencies are similar across people, their phases differ. In the chronobiology literature, people are categorized into morning-type, evening-type, and intermediate-type groups called chronotypes based on their tendency to sleep at different times of day. Typically, this typology builds on carefully designed questionnaires or manually crafted features of time series data on people's activity. Here, we introduce a method where time-stamped data from smartphones are decomposed into components using non-negative matrix factorization. The method does not require any predetermined assumptions about the typical times of sleep or activity: the results are fully context-dependent and determined by the most prominent features of the activity data. We demonstrate our method by applying it to a dataset of mobile phone screen usage logs of 400 university students, collected over a year. We find four emergent temporal components: morning activity, night activity, evening activity and activity at noon. Individual behavior can be reduced to weights on these four components. We do not observe any clear categories of people based on the weights, but individuals are rather placed on a continuous spectrum according to the timings of their phone activities. High weights for the morning and night components strongly correlate with sleep and wake-up times. Our work points towards a data-driven way of characterizing people based on their full daily and weekly rhythms of activity and behavior, instead of only focusing on the timing of their sleeping periods.

Using machine learning to identify quality-of-care predictors for emergency caesarean sections: a retrospective cohort study.

OBJECTIVES: Emergency caesarean sections (ECS) are time-sensitive procedures. Multiple factors may affect team efficiency but their relative importance remains unknown. This study aimed to identify the most important predictors contributing to quality of care during ECS in terms of the arrival-to-delivery interval. DESIGN: A retrospective cohort study. ECS were classified by urgency using emergency categories one/two and three (delivery within 30 and 60 min). In total, 92 predictor variables were included in the analysis and grouped as follows: 'Maternal objective', 'Maternal psychological', 'Fetal factors', 'ECS Indication', 'Emergency category', 'Type of anaesthesia', 'Team member qualifications and experience' and 'Procedural'. Data was analysed with a linear regression model using elastic net regularisation and jackknife technique to improve generalisability. The relative influence of the predictors, percentage significant predictor weight (PSPW) was calculated for each predictor to visualise the main determinants of arrival-to-delivery interval. SETTING AND PARTICIPANTS: Patient records for mothers undergoing ECS between 2010 and 2017, Nordsjællands Hospital, Capital Region of Denmark. PRIMARY OUTCOME MEASURES: Arrival-to-delivery interval during ECS. RESULTS: Data was obtained from 2409 patient records for women undergoing ECS. The group of predictors representing 'Team member qualifications and experience' was the most important predictor of arrival-to-delivery interval in all ECS emergency categories (PSPW 25.9% for ECS category one/two; PSPW 35.5% for ECS category three). In ECS category one/two the 'Indication for ECS' was the second most important predictor group (PSPW 24.9%). In ECS category three, the second most important predictor group was 'Maternal objective predictors' (PSPW 24.2%). CONCLUSION: This study provides empirical evidence for the importance of team member qualifications and experience relative to other predictors of arrival-to-delivery during ECS. Machine learning provides a promising method for expanding our current knowledge about the relative importance of different factors in predicting outcomes of complex obstetric events.

Sleep during travel balances individual sleep needs.

Travel is expected to have a deleterious effect on sleep, but an epidemiological-scale understanding of sleep changes associated with travel has been limited by a lack of large-scale data. Our global dataset of ~20,000 individuals and 3.17 million nights (~218,000 travel nights), while focused mainly on short, non-time-zone-crossing trips, reveals that travel has a balancing effect on sleep. Underslept individuals typically sleep more during travel than when at home, while individuals who average more than 7.5 hours of sleep at home typically sleep less when travelling. The difference in travel sleep quantity depends linearly on home sleep quantity and decreases as median sleep duration increases. On average, travel wake time advances to later hours on weekdays but earlier hours on weekends. Our study emphasizes the potential for consumer-grade wearable device data to explore how environment and behaviour affect sleep.

Communicate hope to motivate the public during the COVID-19 pandemic.

How should health authorities communicate to motivate the public to comply with health advice during a prolonged health crisis such as a pandemic? During the SARS-CoV-2 pandemic, for example, people have had to comply with successive restrictions as the world faced multiple races between controlling new waves of the virus and the development and implementation of vaccines. Here, we examine how health authorities and governments most effectively motivate the public by focusing on a specific race: between the Alpha variant and the implementation of the first generation of COVID-19 vaccinations in the winter of 2021. Following prior research on crisis communication, we focus on appeals to fear and hope using communicative aids in the form of visualizations based on epidemiological modelling. Using a population-based experiment conducted in United States ([Formula: see text]), we demonstrate that a hope-oriented visual communication aid, depicting the competing effects on the epidemic curve of (1) a more infectious variant and (2) vaccinations, motivates public action more effectively than a fear-oriented visual communication, focusing exclusively on the threat of the new variant. The importance of the implementation of such hope-oriented messages is further highlighted by cross-national representative surveys from eight countries ([Formula: see text]), which demonstrate that feelings of fear towards the Alpha variant alone were insufficient to activate strong compliance. Overall, these findings provide general insights into the importance of hope as a health communication strategy during the COVID-19 pandemic and beyond.

Characterizing polarization in online vaccine discourse-A large-scale study.

Vaccine hesitancy is currently recognized by the WHO as a major threat to global health. Recently, especially during the COVID-19 pandemic, there has been a growing interest in the role of social media in the propagation of false information and fringe narratives regarding vaccination. Using a sample of approximately 60 billion tweets, we conduct a large-scale analysis of the vaccine discourse on Twitter. We use methods from deep learning and transfer learning to estimate the vaccine sentiments expressed in tweets, then categorize individual-level user attitude towards vaccines. Drawing on an interaction graph representing mutual interactions between users, we analyze the interplay between vaccine stances, interaction network, and the information sources shared by users in vaccine-related contexts. We find that strongly anti-vaccine users frequently share content from sources of a commercial nature; typically sources which sell alternative health products for profit. An interesting aspect of this finding is that concerns regarding commercial conflicts of interests are often cited as one of the major factors in vaccine hesitancy. Further, we show that the debate is highly polarized, in the sense that users with similar stances on vaccination interact preferentially with one another. Extending this insight, we provide evidence of an epistemic echo chamber effect, where users are exposed to highly dissimilar sources of vaccine information, depending the vaccination stance of their contacts. Our findings highlight the importance of understanding and addressing vaccine mis- and dis-information in the context in which they are disseminated in social networks.

Understanding components of mobility during the COVID-19 pandemic.

Travel restrictions have proven to be an effective strategy to control the spread of the COVID-19 epidemics, in part because they help delay disease propagation across territories. The question, however, as to how different types of travel behaviour, from commuting to holiday-related travel, contribute to the spread of infectious diseases remains open. Here, we address this issue by using factorization techniques to decompose the temporal network describing mobility flows throughout 2020 into interpretable components. Our results are based on two mobility datasets: the first is gathered from Danish mobile network operators; the second originates from the Facebook Data-For-Good project. We find that mobility patterns can be described as the aggregation of three mobility network components roughly corresponding to travel during workdays, weekends and holidays, respectively. We show that, across datasets, in periods of strict travel restrictions the component corresponding to workday travel decreases dramatically. Instead, the weekend component, increases. Finally, we study how each type of mobility (workday, weekend and holiday) contributes to epidemics spreading, by measuring how the effective distance, which quantifies how quickly a disease can travel between any two municipalities, changes across network components. This article is part of the theme issue 'Data science approaches to infectious disease surveillance'.

The effect of co-location on human communication networks.

The ability to rewire ties in communication networks is vital for large-scale human cooperation and the spread of new ideas. We show that lack of researcher co-location during the COVID-19 lockdown caused the loss of more than 4,800 weak ties-ties between distant parts of the social system that enable the flow of novel information-over 18 months in the email network of a large North American university. Furthermore, we find that the reintroduction of partial co-location through a hybrid work mode led to a partial regeneration of weak ties. We quantify the effect of co-location in forming ties through a model based on physical proximity, which is able to reproduce all empirical observations. Results indicate that employees who are not co-located are less likely to form ties, weakening the spread of information in the workplace. Such findings could contribute to a better understanding of the spatiotemporal dynamics of human communication networks and help organizations that are moving towards the implementation of hybrid work policies to evaluate the minimum amount of in-person interaction necessary for a productive work environment.

Dose-response functions and surrogate models for exploring social contagion in the Copenhagen Networks Study.

Spreading dynamics and complex contagion processes on networks are important mechanisms underlying the emergence of critical transitions, tipping points and other non-linear phenomena in complex human and natural systems. Increasing amounts of temporal network data are now becoming available to study such spreading processes of behaviours, opinions, ideas, diseases and innovations to test hypotheses regarding their specific properties. To this end, we here present a methodology based on dose-response functions and hypothesis testing using surrogate data models that randomise most aspects of the empirical data while conserving certain structures relevant to contagion, group or homophily dynamics. We demonstrate this methodology for synthetic temporal network data of spreading processes generated by the adaptive voter model. Furthermore, we apply it to empirical temporal network data from the Copenhagen Networks Study. This data set provides a physically-close-contact network between several hundreds of university students participating in the study over the course of 3 months. We study the potential spreading dynamics of the health-related behaviour "regularly going to the fitness studio" on this network. Based on a hierarchy of surrogate data models, we find that our method neither provides significant evidence for an influence of a dose-response-type network spreading process in this data set, nor significant evidence for homophily. The empirical dynamics in exercise behaviour are likely better described by individual features such as the disposition towards the behaviour, and the persistence to maintain it, as well as external influences affecting the whole group, and the non-trivial network structure. The proposed methodology is generic and promising also for applications to other temporal network data sets and traits of interest.

Privacy and uniqueness of neighborhoods in social networks.

The ability to share social network data at the level of individual connections is beneficial to science: not only for reproducing results, but also for researchers who may wish to use it for purposes not foreseen by the data releaser. Sharing such data, however, can lead to serious privacy issues, because individuals could be re-identified, not only based on possible nodes' attributes, but also from the structure of the network around them. The risk associated with re-identification can be measured and it is more serious in some networks than in others. While various optimization algorithms have been proposed to anonymize networks, there is still only a limited theoretical understanding of which network features are important for the privacy problem. Using network models and real data, we show that the average degree of networks is a crucial parameter for the severity of re-identification risk from nodes' neighborhoods. Dense networks are more at risk, and, apart from a small band of average degree values, either almost all nodes are uniquely re-identifiable or they are all safe. Our results allow researchers to assess the privacy risk based on a small number of network statistics which are available even before the data is collected. As a rule-of-thumb, the privacy risks are high if the average degree is above 10. Guided by these results, we explore sampling of edges as a strategy to mitigate the re-identification risk of nodes. This approach can be implemented during the data collection phase, and its effect on various network measures can be estimated and corrected using sampling theory. The new understanding of the uniqueness of neighborhoods in networks presented in this work can support the development of privacy-aware ways of designing network data collection procedures, anonymization methods, and sharing network data.

The effectiveness of backward contact tracing in networks.

Effective control of an epidemic relies on the rapid discovery and isolation of infected individuals. Because many infectious diseases spread through interaction, contact tracing is widely used to facilitate case discovery and control. However, what determines the efficacy of contact tracing has not been fully understood. Here we reveal that, compared with 'forward' tracing (tracing to whom disease spreads), 'backward' tracing (tracing from whom disease spreads) is profoundly more effective. The effectiveness of backward tracing is due to simple but overlooked biases arising from the heterogeneity in contacts. We argue that, even if the directionality of infection is unknown, it is possible to perform backward-aiming contact tracing. Using simulations on both synthetic and high-resolution empirical contact datasets, we show that strategically executed contact tracing can prevent a substantial fraction of transmissions with a higher efficiency-in terms of prevented cases per isolation-than case isolation alone. Our results call for a revision of current contact-tracing strategies so that they leverage all forms of bias. It is particularly crucial that we incorporate backward and deep tracing in a digital context while adhering to the privacy-preserving requirements of these new platforms.