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An open source tool to infer epidemiological and immunological dynamics from serological data: serosolver.

ABSTRACT: We present a flexible, open source R package designed to obtain biological and epidemiological insights from serological datasets. Characterising past exposures for multi-strain pathogens poses a specific statistical challenge: observed antibody responses measured in serological assays depend on multiple unobserved prior infections that produce cross-reactive antibody responses. We provide a general modelling framework to jointly infer infection histories and describe immune responses generated by these infections using antibody titres against current and historical strains. We do this by linking latent infection dynamics with a mechanistic model of antibody kinetics that generates expected antibody titres over time. Our aim is to provide a flexible package to identify infection histories that can be applied to a range of pathogens. We present two case studies to illustrate how our model can infer key immunological parameters, such as antibody titre boosting, waning and cross-reaction, as well as latent epidemiological processes such as attack rates and age-stratified infection risk.

SUBMITTER: Hay JA

PROVIDER: S-EPMC7241836 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

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An open source tool to infer epidemiological and immunological dynamics from serological data: serosolver.

Hay James A JA Minter Amanda A Ainslie Kylie E C KEC Lessler Justin J Yang Bingyi B Cummings Derek A T DAT Kucharski Adam J AJ Riley Steven S

PLoS computational biology 20200504 5

We present a flexible, open source R package designed to obtain biological and epidemiological insights from serological datasets. Characterising past exposures for multi-strain pathogens poses a specific statistical challenge: observed antibody responses measured in serological assays depend on multiple unobserved prior infections that produce cross-reactive antibody responses. We provide a general modelling framework to jointly infer infection histories and describe immune responses generated ...[more]

PMID: 32365062

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Project description:PurposeThere is an increasing availability of large imaging cohorts [such as through The Cancer Imaging Archive (TCIA)] for computational model development and imaging research. To ensure development of generalizable computerized models, there is a need to quickly determine relative quality differences in these cohorts, especially when considering MRI datasets which can exhibit wide variations in image appearance. The purpose of this study is to present a quantitative quality control tool, MRQy, to help interrogate MR imaging datasets for: (a) site- or scanner-specific variations in image resolution or image contrast, and (b) imaging artifacts such as noise or inhomogeneity; which need correction prior to model development.MethodsUnlike existing imaging quality control tools, MRQy has been generalized to work with images from any body region to efficiently extract a series of quality measures (e.g., noise ratios, variation metrics) and MR image metadata (e.g., voxel resolution and image dimensions). MRQy also offers a specialized HTML5-based front-end designed for real-time filtering and trend visualization of quality measures.ResultsMRQy was used to evaluate (a) n = 133 brain MRIs from TCIA (7 sites) and (b) n = 104 rectal MRIs (3 local sites). MRQy measures revealed significant site-specific variations in both cohorts, indicating potential batch effects. Before processing, MRQy measures could be used to identify each of the seven sites within the TCIA cohort with 87.5%, 86.4%, 90%, 93%, 90%, 60%, and 92.9% accuracy and the three sites within the rectal cohort with 91%, 82.8%, and 88.9% accuracy using unsupervised clustering. After processing, none of the sites could be distinctively clustered via MRQy measures in either cohort; suggesting that batch effects had been largely accounted for. Marked differences in specific MRQy measures were also able to identify outlier MRI datasets that needed to be corrected for common acquisition artifacts.ConclusionsMRQy is designed to be a standalone, unsupervised tool that can be efficiently run on a standard desktop computer. It has been made freely accessible and open-source at http://github.com/ccipd/MRQy for community use and feedback.

Project description:IntroductionIn smoking cessation clinical trials, timeline followback (TLFB) interviews are widely used to track daily cigarette consumption. However, there are no standard tools for calculating abstinence based on TLFB data. Individual research groups have to develop their own calculation tools, which is not only time- and resource-consuming but might also lead to variability in the data processing and calculation procedures.Aims and methodsTo address these issues, we developed a novel open-source Python package named abstcal to calculate abstinence using TLFB data. This package provides data verification, duplicate and outlier detection, missing-data imputation, integration of biochemical verification data, and calculation of a variety of definitions of abstinence, including continuous, point-prevalence, and prolonged abstinence.ResultsWe verified the accuracy of the calculator using data derived from a clinical smoking cessation study. To improve the package's accessibility, we have made it available as a free web app.ConclusionsThe abstcal package is a reliable abstinence calculator with open-source access, providing a shared validated online tool to the addiction research field. We expect that this open-source abstinence calculation tool will improve the rigor and reproducibility of smoking and addiction research by standardizing TLFB-based abstinence calculation.ImplicationsAbstinence calculation is an essential task in any smoking intervention study. However, there have not been standard open-source tools available to the researchers. This commentary describes a Python-based package called abstcal that can calculate abstinence from TLFB data, a common methodology to collect smoking consumption data in research settings. The package supports the calculation of point-prevalence, prolonged, and continuous abstinence. Importantly, the package has a web app interface that allows researchers to use the tool without any coding experience. This tool will facilitate smoking research by providing a standardized and easy-to-use abstinence calculation tool.

Dataset Information

An open source tool to infer epidemiological and immunological dynamics from serological data: serosolver.

Publications

An open source tool to infer epidemiological and immunological dynamics from serological data: serosolver.

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