The NHANES study contains objectively measured physical activity data collected using hip-worn accelerometers from multiple cohorts. However, using the accelerometry data has proven daunting because: 1) currently, there are no agreed upon standard protocols for data storage and analysis; 2) data exhibit heterogeneous patterns of missingness due to varying degrees of adherence to weartime protocols; 3) sampling weights need to be carefully adjusted and accounted for in individual analyses; 4) there is a lack of reproducible software that transforms the data from its published format into analytic form; and 5) the high dimensional nature of accelerometry data complicates analyses. Here, we provide a framework for processing, storing, and analyzing the NHANES accelerometry data for the 2003-2004 and 2005-2006 surveys. We also provide an NHANES data package in R, to help disseminate high quality, processed activity data combined with mortality and demographic information. Thus, we provide the tools to transition from "available data online" to "easily accessible and usable data", which substantially reduces the large upfront costs of initiating studies of association between physical activity and human health outcomes using NHANES. We apply these tools in an analysis showing that accelerometry features have the potential to predict 5-year all cause mortality better than known risk factors such as age, cigarette smoking, and various comorbidities.

Background Declining physical activity (PA) is a hallmark of aging. Wearable technology provides reliable measures of the frequency, duration, intensity, and timing of PA. Accelerometry-derived measures of PA are compared with established predictors of 5-year all-cause mortality in older adults in terms of individual, relative, and combined predictive performance. Methods Participants aged between 50 and 85 years from the 2003–2006 National Health and Nutritional Examination Survey (NHANES, n = 2,978) wore a hip-worn accelerometer in the free-living environment for up to 7 days. A total of 33 predictors of 5-year all-cause mortality (number of events = 297), including 20 measures of objective PA, were compared using univariate and multivariate logistic regression. Results In univariate logistic regression, the total activity count was the best predictor of 5-year mortality (Area under the Curve (AUC) = 0.771) followed by age (AUC = 0.758). Overall, 9 of the top 10 predictors were objective PA measures (AUC from 0.771 to 0.692). In multivariate regression, the 10-fold cross-validated AUC was 0.798 for the model without objective PA variables (9 predictors) and 0.838 for the forward selection model with objective PA variables (13 predictors). The Net Reclassification Index was substantially improved by adding objective PA variables (p < .001). Conclusions Objective accelerometry-derived PA measures outperform traditional predictors of 5-year mortality, including age. This highlights the importance of wearable technology for providing reproducible, unbiased, and prognostic biomarkers of health.

Abstract Background: Accuracy of microbial community detection in 16S rRNA marker-gene and metagenomic studies suffers from contamination and sequencing errors that lead to either falsely identifying microbial taxa that were not in the sample or misclassifying the taxa of DNA fragment reads. Filtering is defined as removing taxa that are present in a small number of samples and have small counts in the samples where they are observed. This approach reduces extreme sparsity of microbiome data and has been shown to correctly remove contaminant taxa in cultured "mock" datasets, where the true taxa compositions are known. Although filtering is frequently used, careful evaluation of its effect on the data analysis and scientific conclusions remains unreported. Here, we assess the effect of filtering on the alpha and beta diversity estimation, as well as its impact on identifying taxa that discriminate between disease states. Results: The effect of filtering on microbiome data analysis is illustrated on four datasets: two mock quality control datasets where same cultured samples with known microbial composition are processed at different labs and two disease study datasets. Results show that in microbiome quality control datasets, filtering reduces the magnitude of differences in alpha diversity and alleviates technical variability between labs, while preserving between samples similarity (beta diversity). In the disease study datasets, DESeq2 and linear discriminant analysis Effect Size (LEfSe) methods were used to identify taxa that are differentially expressed across groups of samples, and random forest models to rank features with largest contribution towards disease classiffcation. Results reveal that filtering retains significant taxa and preserves the model classification ability measured by the area under the receiver operating characteristic curve (AUC). The comparison between filtering and contaminant removal method shows that they have complementary effects and are advised to be used in conjunction. Conclusions: Filtering reduces the complexity of microbiome data, while preserving their integrity in downstream analysis. This leads to mitigation of the classification methods' sensitivity and reduction of technical variability, allowing researchers to generate more reproducible and comparable results in microbiome data analysis.