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Register a new userUsing smartphones and wearable devices to monitor behavioural changes during COVID-19
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We aimed to explore the utility of the recently developed open-source mobile health platform RADAR-base as a toolbox to rapidly test the effect and response to NPIs aimed at limiting the spread of COVID-19. We analysed data extracted from smartphone and wearable devices and managed by the RADAR-base from 1062 participants recruited in Italy, Spain, Denmark, the UK, and the Netherlands. We derived nine features on a daily basis including time spent at home, maximum distance travelled from home, maximum number of Bluetooth-enabled nearby devices (as a proxy for physical distancing), step count, average heart rate, sleep duration, bedtime, phone unlock duration, and social app use duration. We performed Kruskal-Wallis tests followed by post-hoc Dunns tests to assess differences in these features among baseline, pre-, and during-lockdown periods. We also studied behavioural differences by age, gender, body mass index (BMI), and educational background. We were able to quantify expected changes in time spent at home, distance travelled, and the number of nearby Bluetooth-enabled devices between pre- and during-lockdown periods. We saw reduced sociality as measured through mobility features, and increased virtual sociality through phone usage. People were more active on their phones, spending more time using social media apps, particularly around major news events. Furthermore, participants had lower heart rate, went to bed later, and slept more. We also found that young people had longer homestay than older people during lockdown and fewer daily steps. Although there was no significant difference between the high and low BMI groups in time spent at home, the low BMI group walked more. RADAR-base can be used to rapidly quantify and provide a holistic view of behavioural changes in response to public health interventions as a result of infectious outbreaks such as COVID-19.
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Nosocomial infections place a substantial burden on health care systems and represent a major issue in current public health, requiring notable efforts for its prevention. Understanding the dynamics of infection transmission in a hospital setting is essential for tailoring interventions and predicting the spread among individuals. Mathematical models need to be informed with accurate data on contacts among individuals. We used wearable active Radio-Frequency Identification Devices to detect face-to-face contacts among individuals with a spatial resolution of about 1.5 meters, and a time resolution of 20 seconds. The study was conducted in a general pediatrics hospital ward, during a one-week period, and included 119 participants. Nearly 16,000 contacts were recorded during the study, with a median of approximately 20 contacts per participants per day. Overall, 25% of the contacts involved a ward assistant, 23% a nurse, 22% a patient, 22% a caregiver, and 8% a physician. The majority of contacts were of brief duration, but long and frequent contacts especially between patients and caregivers were also found. In the setting under study, caregivers do not represent a significant potential for infection spread to a large number of individuals, as their interactions mainly involve the corresponding patient. Nurses would deserve priority in prevention strategies due to their central role in the potential propagation paths of infections. Our study shows the feasibility of accurate and reproducible measures of the pattern of contacts in a hospital setting. The results are particularly useful for the study of the spread of respiratory infections, for monitoring critical patterns, and for setting up tailored prevention strategies. Proximity-sensing technology should be considered as a valuable tool for measuring such patterns and evaluating nosocomial prevention strategies in specific settings.
There have been more than 850,000 confirmed cases and over 48,000 deaths from the human coronavirus disease 2019 (COVID-19) pandemic, caused by novel severe acute respiratory syndrome coronavirus (SARS-CoV-2), in the United States alone. However, there are currently no proven effective medications against COVID-19. Drug repurposing offers a promising way for the development of prevention and treatment strategies for COVID-19. This study reports an integrative, network-based deep learning methodology to identify repurposable drugs for COVID-19 (termed CoV-KGE). Specifically, we built a comprehensive knowledge graph that includes 15 million edges across 39 types of relationships connecting drugs, diseases, genes, pathways, and expressions, from a large scientific corpus of 24 million PubMed publications. Using Amazon AWS computing resources, we identified 41 repurposable drugs (including indomethacin, toremifene and niclosamide) whose therapeutic association with COVID-19 were validated by transcriptomic and proteomic data in SARS-CoV-2 infected human cells and data from ongoing clinical trials. While this study, by no means recommends specific drugs, it demonstrates a powerful deep learning methodology to prioritize existing drugs for further investigation, which holds the potential of accelerating therapeutic development for COVID-19.
Modeling biological rhythms helps understand the complex principles behind the physical and psychological abnormalities of human bodies, to plan life schedules, and avoid persisting fatigue and mood and sleep alterations due to the desynchronization of those rhythms. The first step in modeling biological rhythms is to identify their characteristics, such as cyclic periods, phase, and amplitude. However, human rhythms are susceptible to external events, which cause irregular fluctuations in waveforms and affect the characterization of each rhythm. In this paper, we present our exploratory work towards developing a computational framework for automated discovery and modeling of human rhythms. We first identify cyclic periods in time series data using three different methods and test their performance on both synthetic data and real fine-grained biological data. We observe consistent periods are detected by all three methods. We then model inner cycles within each period through identifying change points to observe fluctuations in biological data that may inform the impact of external events on human rhythms. The results provide initial insights into the design of a computational framework for discovering and modeling human rhythms.
We analyze risk factors correlated with the initial transmission growth rate of the recent COVID-19 pandemic in different countries. The number of cases follows in its early stages an almost exponential expansion; we chose as a starting point in each country the first day $d_i$ with 30 cases and we fitted for 12 days, capturing thus the early exponential growth. We looked then for linear correlations of the exponents $alpha$ with other variables, for a sample of 126 countries. We find a positive correlation, {it i.e. faster spread of COVID-19}, with high confidence level with the following variables, with respective $p$-value: low Temperature ($4cdot10^{-7}$), high ratio of old vs.~working-age people ($3cdot10^{-6}$), life expectancy ($8cdot10^{-6}$), number of international tourists ($1cdot10^{-5}$), earlier epidemic starting date $d_i$ ($2cdot10^{-5}$), high level of physical contact in greeting habits ($6 cdot 10^{-5}$), lung cancer prevalence ($6 cdot 10^{-5}$), obesity in males ($1 cdot 10^{-4}$), share of population in urban areas ($2cdot10^{-4}$), cancer prevalence ($3 cdot 10^{-4}$), alcohol consumption ($0.0019$), daily smoking prevalence ($0.0036$), UV index ($0.004$, 73 countries). We also find a correlation with low Vitamin D levels ($0.002-0.006$, smaller sample, $sim 50$ countries, to be confirmed on a larger sample). There is highly significant correlation also with blood types: positive correlation with types RH- ($3cdot10^{-5}$) and A+ ($3cdot10^{-3}$), negative correlation with B+ ($2cdot10^{-4}$). Several of the above variables are intercorrelated and likely to have common interpretations. We performed a Principal Component Analysis, in order to find their significant independent linear combinations. We also analyzed a possible bias: countries with low GDP-per capita might have less testing and we discuss correlation with the above variables.
In this paper we propose a novel SEIR stochastic epidemic model. A distinguishing feature of this new model is that it allows us to consider a set up under general latency and infectious period distributions. To some extent, queuing systems with infinitely many servers and a Markov chain with time-varying transition rate are the very technical underpinning of the paper. Although more general, the Markov chain is as tractable as previous models for exponentially distributed latency and infection periods. It is also significantly simpler and more tractable than semi-Markov models with a similar level of generality. Based on the notion of stochastic stability, we derive a sufficient condition for a shrinking epidemic in terms of the queuing systems occupation rate that drives the dynamics. Relying on this condition, we propose a class of ad-hoc stabilising mitigation strategies that seek to keep a balanced occupation rate after a prescribed mitigation-free period. We validate the approach in the light of recent data on the COVID-19 epidemic and assess the effect of different stabilising strategies. The results suggest that it is possible to curb the epidemic with various occupation rate levels, as long as the mitigation is not excessively procrastinated.
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