These frequencies were used to simulate patients to find the likeliest paths of symptom onset for discernible symptoms of COVID-19. The dataset from China contains 55,924 patients, and the dataset from USA contains 373,883 patients. (XLSX)

We release these four diffusion MRI data sets as part of our recent journal publication; Fick, Rutger H.J., et al. "Non-Parametric GraphNet-Regularized Representation of dMRI in Space and Time." Medical Image Analysis (2017). More detailed information about the use of these data sets can also be found in the publication.

We acquired test-retest diffusion MRI spin echo sequences from two C57Bl6 wild-type mice on an 11.7 Tesla Bruker scanner. The test and retest acquisition were taken 48 hours from each other. The data consists of 80x160x5 voxels of size 110x110x500\(\mu\)m. Each data set consists of 515 Diffusion-Weighted Images (DWIs) spread over 35 acquisition shells. The shells are spread over 7 gradient strength shells with a maximum gradient strength of 491 mT/m, 5 pulse separation shells between [10.8 - 20.0]ms, and a pulse length of 5ms. We manually created a brain mask and corrected the data from eddy currents and motion artifacts using FSL's eddy. We then drew a region of interest in the middle slice in the corpus callosum, where the tissue is reasonably coherent.

- The diffusion MRI data are contained in the files with 'dwis' in the name.

- The corpus callosum masks are contained in the files with 'mask' in the name.

- The acquisition parameters are contained in the .txt files.

This dataset is obsolete, superseded by this one and will not be updated anymore..

Fitted on data points as on 3 April 2020

Context

This dataset is created as a part of covid-19 global forecasting challenge. It contains parameters for the SIR model for different locations worldwide.

The model is defined as ODE system as follows: https://wikimedia.org/api/rest_v1/media/math/render/svg/29728a7d4bebe8197dca7d873d81b9dce954522e" alt="SIR ODE equations">

The models are fitted on John Hopkins University data (time series) using several runs of Nelder-Mead simplex optimization method (best run is taken) starting at different initial locations and RMSE as a loss.

What parameters are fitted (estimated) per country/province: * the day when the infection emerged in the country * the initial infected count on the first day of the infection * beta - an average number of contacts (sufficient to spread the disease) per day each infected individual has * gamma - fixed fraction of the infected group that will recover during any given day * R0 - how many susceptible people are infected (on average) by single infected individual. Equals beta/gamma * initial susceptible population (e.g. init suscept pop in the figures) - how many people are susceptible with regards to the quarantine measures at the modelled location

How to read the figures. * points are real observed data provided by Johns Hopkins University * curves are model prediction

• blue is susceptible population - people that are not yet infected but can get the infection
• red is infected population
• green is removed population (recovered or dead). people that are not susceptible any more as they came through the infection.

Content

The dataset contains 3 data portions:

1. Fitted SIR model parameters for different locations worldwide.
2. Figures that visually show how the fitted parameters match the data points.
3. CSV files with prediction for one year in the future for each individual location.

Warning

Always do visual check of the model fit (per_location_figures directory) for quality control before start to use the corresponding parameter values in your analysis.

Acknowledgements

Thanks a lot Kaggle for organizing data sharing and challenges that make the world better.

Also many thanks to John Hopkins University for their hard work of gathering COVID-19 statistics worldwide.

Inspiration

You can try to find correlation between model parameters (e.g. gamma - patient recovery rate) and other properties of the modelled locations worldwide (e.g. weather, population density, level of medical care, etc.)

These frequencies were used to simulate patients to find the likeliest paths of symptom onset for discernible symptoms of COVID-19. The dataset from Hong Kong contains 59 patients, and the dataset from Brazil contains at least 50,000 patients. (XLSX)

spatial_mathematical_modelThe file contains 1) a system of ordinary differential equations used in the model and 2). a model runner that calls the function

These frequencies were used to simulate patients to find the likeliest paths of symptom onset for discernible symptoms of COVID-19. The dataset from Japan before the outbreak of the D614G variant contains 244 patients, and the dataset from Japan after the outbreak of the D614G variant reports symptoms of 2,636 patients, except for cough, where only 2,634 of the patients were recorded. (XLSX)

These are the results from 10000 simulations of the CMV stochastic ODE model. Replication code and analysis available on github at: https://github.com/bryanmayer/CMV-Transient-Infections

Context

This dataset is created as a part of covid-19 global forecasting challenge. It contains parameters for the SIR model for different locations worldwide. But the main value of the dataset is estimated transmission period (average period between single infected individual infects next susceptible in pure susceptible population) per week per location.

The model is defined as ODE system as follows: https://wikimedia.org/api/rest_v1/media/math/render/svg/29728a7d4bebe8197dca7d873d81b9dce954522e" alt="SIR ODE equations">

In order to reflect the transmission rate changes caused by spread constraining measures (social distancing, etc.) the Beta parameter is modelled separately as spline model (spline node estimate for every week). See paramsWeekly.csv which holds the Beta parameter values for every week as well as estimated R0 values (derived from Beta and Gamma paramters) for every week.

The models are fitted on John Hopkins University data (time series) using several runs of Nelder-Mead simplex optimization method (best run is taken) starting at different initial locations and RMSE as a loss.

What parameters are fitted (estimated) per country/province: * the day when the infection emerged in the country * the initial infected count on the first day of the infection * beta (separate value for every week) - an average number of contacts (sufficient to spread the disease) per day each infected individual has * gamma - fixed fraction of the infected group that will recover during any given day * R0 - Equals beta/gamma

How to read the figures. * points are real observed data provided by Johns Hopkins University * curves are model prediction

• blue is susceptible population - people that are not yet infected but can get the infection
• red is infected population
• green is removed population (recovered or dead). people that are not susceptible any more as they came through the infection.

Content

The dataset contains 3 data portions:

1. Fitted SIR model parameters for different locations worldwide. a. Params.csv - parameters (and derived values) constant over time b. ParamsWeekly.csv - parameters (and derived values) that are estimated for every week separatly
2. Figures directory that visually show how the fitted parameters match the data points.
3. Predictions directory with CSV files with prediction for one year in the future for each individual location.

Warning

Always do visual check of the model fit (Figures directory) for quality control before start to use the corresponding parameter values in your analysis, as the dataset is obtained by automatic fitting procedure without manual quality control.

Acknowledgements

Thanks a lot Kaggle for organizing data sharing and challenges that make the world better.

Also many thanks to John Hopkins University for their hard work of gathering COVID-19 statistics worldwide.

Inspiration

You can try to find correlation between model parameters (e.g. gamma - patient recovery rate) and other properties of the modelled locations worldwide (e.g. weather, population density, level of medical care, etc.)

The columns of the frequencies correspond to dataset. From left to right, they represent a dataset containing patients with COVID-19 and comorbidities in China [33], patients with COVID-19 and comorbidities in the USA [31], patients with COVID-19 and cancer in China [36], patients with COVID-19 and cancer in the USA [37], patients with COVID-19 and COPD in the USA [35], and patients with COVID-19 and HIV in the USA [34]. These frequencies were used to simulate patients to find the likeliest paths of symptom onset for discernible symptoms of COVID-19. The dataset representing patients with comorbidities from China and the USA contains 399 and 463, respectively. The dataset representing patients with cancer from China and the USA contains 205 and 423, respectively. The dataset representing patients with COPD and HIV contains 164 and 93, respectively. (XLSX)

Please refer to the published manuscript for methods associated with data collection and analysis.

This dataset contains code implementing the finite element method based on Kaskade 7 (C++) and code implementing the finite difference method (Python) for the development of hybrid PDE-ODE models aimed at efficiently simulating infection spread in epidemiology. It is part of the Math+ EF45-4 project, which aims to develop hybrid models for large-scale infection spread simulations.

Background: Coronavirus disease 2019 (COVID-19) was first identified in Wuhan, China, in December 2019 and quickly spread throughout China and the rest of the world. Many mathematical models have been developed to understand and predict the infectiousness of COVID-19. We aim to summarize these models to inform efforts to manage the current outbreak.Methods: We searched PubMed, Web of science, EMBASE, bioRxiv, medRxiv, arXiv, Preprints, and National Knowledge Infrastructure (Chinese database) for relevant studies published between 1 December 2019 and 21 February 2020. References were screened for additional publications. Crucial indicators were extracted and analysed. We also built a mathematical model for the evolution of the epidemic in Wuhan that synthesised extracted indicators.Results: Fifty-two articles involving 75 mathematical or statistical models were included in our systematic review. The overall median basic reproduction number (R0) was 3.77 [interquartile range (IQR) 2.78–5.13], which dropped to a controlled reproduction number (Rc) of 1.88 (IQR 1.41–2.24) after city lockdown. The median incubation and infectious periods were 5.90 (IQR 4.78–6.25) and 9.94 (IQR 3.93–13.50) days, respectively. The median case-fatality rate (CFR) was 2.9% (IQR 2.3–5.4%). Our mathematical model showed that, in Wuhan, the peak time of infection is likely to be March 2020 with a median size of 98,333 infected cases (range 55,225–188,284). The earliest elimination of ongoing transmission is likely to be achieved around 7 May 2020.Conclusions: Our analysis found a sustained Rc and prolonged incubation/ infectious periods, suggesting COVID-19 is highly infectious. Although interventions in China have been effective in controlling secondary transmission, sustained global efforts are needed to contain an emerging pandemic. Alternative interventions can be explored using modelling studies to better inform policymaking as the outbreak continues.

Appendix A Derivation of contact tracing terms with early and late infectious individuals, Appendix B Modeling social and hygiene measures and changes in the tracing coverage, Appendix C Parameterization, Appendix D Stability analysis. (ZIP)

Sexual contact patterns determine the spread of sexually transmitted infections and are a central input parameter for mathematical models in this field. We evaluated the importance of country-specific sexual contact pattern parametrization for high-income countries with similar cultural backgrounds by comparing data from two independent studies (HaBIDS and SBG) in Germany, a country without systematic sexual contact pattern data, with data from the National Survey of Sexual Attitudes and Lifestyles (Natsal) in the UK, and the National Survey of Family Growth (NSFG) in the US, the two longest running sexual contact studies in high-income countries. We investigated differences in the distribution of the reported number of opposite-sex partners, same-sex partners and both-sex partners using weighted negative binomial regression adjusted for age and sex (as well as stratified by age). In our analyses, UK and US participants reported a substantially higher number of lifetime opposite-sex sexual partners compared to both German studies. The difference in lifetime partners was caused by a higher proportion of individuals with many partners in the young age group (

Despite continued efforts to improve biosecurity protocols, Campylobacter continues to be detected in the majority of commercial chicken flocks across Europe. Using an extensive data set of Campylobacter prevalence within a chicken breeder flock for over a year, multiple Bayesian models are presented to explore the dynamics of the spread of Campylobacter in response to seasonal variation, species-specificity, bird health, and total colonization prevalence. These models indicated that birds within the flock varied greatly in their response to bacterial challenge, and that this phenomenon had a large impact on the overall prevalence of different species of Campylobacter. Campylobacter jejuni appeared more frequently in the summer, while Campylobacter coli persisted for a longer duration, amplified by the most susceptible birds in the flock. Our study suggests that strains of Campylobacter that appear most frequently likely possess no demographic advantage, but are instead amplified due to the health of the birds that ingest it.

List of mitigation measures utilized by some or all plants.

Transition probabilities for the CTMC-SEIRS model.

Countries around the world are in a state of lockdown to help limit the spread of SARS-CoV-2. However, as the number of new daily confirmed cases begins to decrease, governments must decide how to release their populations from quarantine as efficiently as possible without overwhelming their health services. We applied an optimal control framework to an adapted Susceptible-Exposure-Infection-Recovery (SEIR) model framework to investigate the efficacy of two potential lockdown release strategies, focusing on the UK population as a test case. To limit recurrent spread, we find that ending quarantine for the entire population simultaneously is a high-risk strategy, and that a gradual re-integration approach would be more reliable. Furthermore, to increase the number of people that can be first released, lockdown should not be ended until the number of new daily confirmed cases reaches a sufficiently low threshold. We model a gradual release strategy by allowing different fractions of those in lockdown to re-enter the working non-quarantined population. Mathematical optimization methods, combined with our adapted SEIR model, determine how to maximize those working while preventing the health service from being overwhelmed. The optimal strategy is broadly found to be to release approximately half the population 2–4 weeks from the end of an initial infection peak, then wait another 3–4 months to allow for a second peak before releasing everyone else. We also modeled an “on-off” strategy, of releasing everyone, but re-establishing lockdown if infections become too high. We conclude that the worst-case scenario of a gradual release is more manageable than the worst-case scenario of an on-off strategy, and caution against lockdown-release strategies based on a threshold-dependent on-off mechanism. The two quantities most critical in determining the optimal solution are transmission rate and the recovery rate, where the latter is defined as the fraction of infected people in any given day that then become classed as recovered. We suggest that the accurate identification of these values is of particular importance to the ongoing monitoring of the pandemic.

BackgroundTo date, there is a lack of sufficient evidence on the type of clusters in which severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is most likely to spread. Notably, the differences between cluster-level and population-level outbreaks in epidemiological characteristics and transmissibility remain unclear. Identifying the characteristics of these two levels, including epidemiology and transmission dynamics, allows us to develop better surveillance and control strategies following the current removal of suppression measures in China.MethodsWe described the epidemiological characteristics of SARS-CoV-2 and calculated its transmissibility by taking a Chinese city as an example. We used descriptive analysis to characterize epidemiological features for coronavirus disease 2019 (COVID-19) incidence database from 1 Jan 2020 to 2 March 2020 in Chaoyang District, Beijing City, China. The susceptible-exposed-infected-asymptomatic-recovered (SEIAR) model was fitted with the dataset, and the effective reproduction number (Reff) was calculated as the transmissibility of a single population. Also, the basic reproduction number (R0) was calculated by definition for three clusters, such as household, factory and community, as the transmissibility of subgroups.ResultsThe epidemic curve in Chaoyang District was divided into three stages. We included nine clusters (subgroups), which comprised of seven household-level and one factory-level and one community-level cluster, with sizes ranging from 2 to 17 cases. For the nine clusters, the median incubation period was 17.0 days [Interquartile range (IQR): 8.4–24.0 days (d)], and the average interval between date of onset (report date) and diagnosis date was 1.9 d (IQR: 1.7 to 6.4 d). At the population level, the transmissibility of the virus was high in the early stage of the epidemic (Reff = 4.81). The transmissibility was higher in factory-level clusters (R0 = 16) than in community-level clusters (R0 = 3), and household-level clusters (R0 = 1).ConclusionsIn Chaoyang District, the epidemiological features of SARS-CoV-2 showed multi-stage pattern. Many clusters were reported to occur indoors, mostly from households and factories, and few from the community. The risk of transmission varies by setting, with indoor settings being more severe than outdoor settings. Reported household clusters were the predominant type, but the population size of the different types of clusters limited transmission. The transmissibility of SARS-CoV-2 was different between a single population and its subgroups, with cluster-level transmissibility higher than population-level transmissibility.

TTIQ parameter ranges considered in the sensitivity analysis.