Automated Processing of Pipelines Managing Now- and Forecasting of Infectious Diseases

When faced with the challenge of now- and forecasting infectious diseases, multiple data sources and state-of-the-art models have to be considered. Automatic aggregation, processing, and publishing to relevant data sinks is paramount to achieving consistent, reproducible, and timely results given daily-reported data. To facilitate scientific collaboration and reproducibility of workflows, open and extensible architectures for compute pipelines are required. In this research, we devise an architecture realizing the seamless management and processing of reproducible pipelines. Our case-study is a daily pipeline for nowcasting the state of SARS-CoV-2 in Germany based on public data and state-of-the-art models implemented in the simulation software MEmilio. The results of our pipeline are pushed to ESID (Epidemiological Scenarios for Infectious Diseases), a user interface to epidemiological simulations. To realize the given pipeline, a workflow management system is required to ensure pipeline processing and secure access to multiple heterogeneous data storages. For this purpose, we based our work on an open-source workflow management system - Apache Airflow, which provides the orchestration, coordination and management of complex connected tasks. S3 is utilized as an intermediate data storage service for sharing data between workflow steps and persisting experiment output. We provide a comprehensive view on our work on automated, end-to-end and reproducible pipelines, with detailed commentary on use case, and its realization

Use of the Nominal Group Technique (NGT) to understand the perceptions of the healthiness of foods associated with African Americans

Purpose To determine the degree of overlap between foods considered part of African American (AA) culture and those considered to be healthy.Methods A total of 44 AA men and women were recruited from the Birmingham, AL area, 25 years of age and older to participate in four Nominal Group Technique (NGT) meetings. Participants from the first two groups generated 90 unique food items in response to the question "What are the foods you associate with being African American?" Participants individually ranked their top three most unhealthy foods. The next two groups generated 116 unique food items in response to the question "What foods do you consider to be healthy?" Participants individually ranked their top three foods that were considered most associated with AA.Results The top five foods associated with AA were chitterlings, fried chicken, pig parts, greens prepared with ham hock, and pork ribs. Of the foods associated with AA, chitterlings, pig parts, fatback, fried chicken, and greens prepared with ham hocks were ranked as the unhealthiest. The top five healthy foods were broccoli, boiled greens, baked fish, grapefruit, and broiled fish. From these top five healthy foods, only boiled greens were considered to be associated with AA.Conclusions Many of the foods AA consider as traditional foods are also perceived as unhealthy. On the contrary, foods perceived to have the most health value may not be a routine part of AA food patterns. Understanding AA perceptions of the healthfulness of foods can be informative for culturally appropriate nutrition intervention development.African American Food perceptions Traditional foods Cultural food patterns Poor diet Nutrition Soul Food Preparation techniques