Biological Time Series Analysis Using a Context Free Language: Applicability to Pulsatile Hormone Data
Year: 2014
Type: article
Abstract: We present a novel approach for analyzing biological time-series data using a context-free language (CFL) representation that allows the extraction and quantification of important features from the time-series. This representation results in Hierarchically AdaPtive (HAP) analysis, a suite of multiple complementary techniques that enable rapid analysis of data and does not require the user to set parameters. HAP analysis generates hierarchically organized parameter distributions that allow multi-scale components of the time-series to be quantified and includes a data analysis pipeline that applies recursive analyses to generate hierarchically organized results that extend traditional outcome measures such as pharmacokinetics and inter-pulse interval. Pulsicons, a novel text-based time-series representation also derived from the CFL approach, are introduced as an objective qualitative comparison nomenclature. We apply HAP to the analysis of 24 hours of frequently sampled pulsatile cortisol hormone data, which has known analysis challenges, from 14 healthy women. HAP analysis generated results in seconds and produced dozens of figures for each participant. The results quantify the observed qualitative features of cortisol data as a series of pulse clusters, each consisting of one or more embedded pulses, and identify two ultradian phenotypes in this dataset. HAP analysis is designed to be robust to individual differences and to missing data and may be applied to other pulsatile hormones. Future work can extend HAP analysis to other time-series data types, including oscillatory and other periodic physiological signals.
Source: PLoS ONE
Language: English
Subfield: Signal Processing
Field: Computer Science
Domain: Physical Sciences
Open Access status: gold
Estimated APC paid: $2,382
Funders: National Aeronautics and Space Administration, Deutsches Krebsforschungszentrum, National Space Biomedical Research Institute, National Institutes of Health, U.S. Public Health Service, National Institute on Aging, National Heart, Lung, and Blood Institute, National Institute of Mental Health, National Institute of General Medical Sciences, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Center for Research Resources, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Air Force Office of Scientific Research
Awards: G1357089762, G1519142367, G1523888516, ASSOCIATION OF SLEEP DISORDERS WITH CARDIOVASCULAR HEALTH ACROSS ETHNIC GROUPS, G177218894, Sleep Duration Required to Restore Performance during Chronic Sleep Restriction, G3192201473, Harvard Clinical and Translational Science Center (UL1), REGULATION OF ADRENAL FUNCTION IN FIBROMYALGIA, G383842459, G4022436119, General Clinical Research Center, G4420413849, Human circadian sensitivity to very short light pulses, G4770261233, Sleep, Aging and Circadian Rhythm Disorders, Impact of Sleep Disruption on Menstrual Cycle Dynamics, Sleep duration required to restore performance during chronic sleep restriction, Circadian Constrained Schedule Optimization for Maximal Performance, G690245692, G7188459038, G7603022272, G7833065126, NATIONAL SPACE BIOMEDICAL RESEARCH INSTITUTE, G8011426225, G816501378, Dynamic Analyses of Learning in Behavioral Experiments, G8788630870, Aldosterone and Cardiovascular Disease: Research and Mentoring Program, G9000118385, G9000195782, Training in Sleep, Circadian, and Respiratory Neurobiology, G972361780
OpenAlex ID: W2071972262