PhysioBank, PhysioToolkit, and PhysioNet: components of a new research resource for complex physiologic signals.
TL;DR: The newly inaugurated Research Resource for Complex Physiologic Signals (RRSPS) as mentioned in this paper was created under the auspices of the National Center for Research Resources (NCR Resources).
Abstract: —The newly inaugurated Research Resource for Complex Physiologic Signals, which was created under the auspices of the National Center for Research Resources of the National Institutes of He...
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Emory University1, University of Oxford2, Massachusetts Institute of Technology3, Georgia Institute of Technology4, Polytechnic University of Valencia5, University of Valencia6, University of Michigan7, Aalborg University8, Aristotle University of Thessaloniki9, K.N.Toosi University of Technology10, University of Upper Alsace11, University of Strasbourg12, Dalian University of Technology13, Shiraz University14, Isfahan University of Medical Sciences15
TL;DR: A public heart sound database, assembled for an international competition, the PhysioNet/Computing in Cardiology (CinC) Challenge 2016, which comprises nine different heart sound databases sourced from multiple research groups around the world is described.
Abstract: In the past few decades, analysis of heart sound signals (i.e. the phonocardiogram or PCG), especially for automated heart sound segmentation and classification, has been widely studied and has been reported to have the potential value to detect pathology accurately in clinical applications. However, comparative analyses of algorithms in the literature have been hindered by the lack of high-quality, rigorously validated, and standardized open databases of heart sound recordings. This paper describes a public heart sound database, assembled for an international competition, the PhysioNet/Computing in Cardiology (CinC) Challenge 2016. The archive comprises nine different heart sound databases sourced from multiple research groups around the world. It includes 2435 heart sound recordings in total collected from 1297 healthy subjects and patients with a variety of conditions, including heart valve disease and coronary artery disease. The recordings were collected from a variety of clinical or nonclinical (such as in-home visits) environments and equipment. The length of recording varied from several seconds to several minutes. This article reports detailed information about the subjects/patients including demographics (number, age, gender), recordings (number, location, state and time length), associated synchronously recorded signals, sampling frequency and sensor type used. We also provide a brief summary of the commonly used heart sound segmentation and classification methods, including open source code provided concurrently for the Challenge. A description of the PhysioNet/CinC Challenge 2016, including the main aims, the training and test sets, the hand corrected annotations for different heart sound states, the scoring mechanism, and associated open source code are provided. In addition, several potential benefits from the public heart sound database are discussed.
477 citations
TL;DR: Continuous sampling of data from the electronic health records and calculation of TREWScore may allow clinicians to identify patients at risk for septic shock and provide earlier interventions that would prevent or mitigate the associated morbidity and mortality.
Abstract: Sepsis is a leading cause of death in the United States, with mortality highest among patients who develop septic shock. Early aggressive treatment decreases morbidity and mortality. Although automated screening tools can detect patients currently experiencing severe sepsis and septic shock, none predict those at greatest risk of developing shock. We analyzed routinely available physiological and laboratory data from intensive care unit patients and developed “TREWScore,” a targeted real-time early warning score that predicts which patients will develop septic shock. TREWScore identified patients before the onset of septic shock with an area under the ROC (receiver operating characteristic) curve (AUC) of 0.83 [95% confidence interval (CI), 0.81 to 0.85]. At a specificity of 0.67, TREWScore achieved a sensitivity of 0.85 and identified patients a median of 28.2 [interquartile range (IQR), 10.6 to 94.2] hours before onset. Of those identified, two-thirds were identified before any sepsis-related organ dysfunction. In comparison, the Modified Early Warning Score, which has been used clinically for septic shock prediction, achieved a lower AUC of 0.73 (95% CI, 0.71 to 0.76). A routine screening protocol based on the presence of two of the systemic inflammatory response syndrome criteria, suspicion of infection, and either hypotension or hyperlactatemia achieved a lower sensitivity of 0.74 at a comparable specificity of 0.64. Continuous sampling of data from the electronic health records and calculation of TREWScore may allow clinicians to identify patients at risk for septic shock and provide earlier interventions that would prevent or mitigate the associated morbidity and mortality.
470 citations
TL;DR: A selection procedure of mother wavelet basis functions applied for denoising of the ECG signal in wavelet domain while retaining the signal peaks close to their full amplitude is presented.
457 citations
11 Jun 2014
TL;DR: This work is the first research to compare multiple disaggregation approaches across multiple publicly available data sets, and demonstrates the range of reproducible analyses made possible by the toolkit.
Abstract: Non-intrusive load monitoring, or energy disaggregation, aims to separate household energy consumption data collected from a single point of measurement into appliance-level consumption data. In recent years, the field has rapidly expanded due to increased interest as national deployments of smart meters have begun in many countries. However, empirically comparing disaggregation algorithms is currently virtually impossible. This is due to the different data sets used, the lack of reference implementations of these algorithms and the variety of accuracy metrics employed. To address this challenge, we present the Non-intrusive Load Monitoring Toolkit (NILMTK); an open source toolkit designed specifically to enable the comparison of energy disaggregation algorithms in a reproducible manner. This work is the first research to compare multiple disaggregation approaches across multiple publicly available data sets. Our toolkit includes parsers for a range of existing data sets, a collection of preprocessing algorithms, a set of statistics for describing data sets, two reference benchmark disaggregation algorithms and a suite of accuracy metrics. We demonstrate the range of reproducible analyses which are made possible by our toolkit, including the analysis of six publicly available data sets and the evaluation of both benchmark disaggregation algorithms across such data sets.
453 citations
TL;DR: Assessment of the ability of an overnight ECG recording to distinguish between patients with and without apnoea and the best algorithms made use of frequency-domain features to estimate changes in heart rate and the effect of respiration on the ECG waveform.
Abstract: Sleep apnoea is a common disorder that is usually diagnosed through expensive studies conducted in sleep laboratories. Sleep apnoea is accompanied by a characteristic cyclic variation in heart rate or other changes in the waveform of the electrocardiogram (ECG). If sleep apnoea could be diagnosed using only the ECG, it could be possible to diagnose sleep apnoea automatically and inexpensively from ECG recordings acquired in the patient's home. This study had two parts. The first was to assess the ability of an overnight ECG recording to distinguish between patients with and without apnoea. The second was to assess whether the ECG could detect apnoea during each minute of the recording. An expert, who used additional physiological signals, assessed each of the recordings for apnoea. Research groups were invited to access data via the world-wide web and submit algorithm results to an international challenge linked to a conference. A training set of 35 recordings was made available for algorithm development, and results from a test set of 35 different recordings were made available for independent scoring. Thirteen algorithms were compared. The best algorithms made use of frequency-domain features to estimate changes in heart rate and the effect of respiration on the ECG waveform. Four of these algorithms achieved perfect scores of 100% in the first part of the study, and two achieved an accuracy of over 90% in the second part of the study.
428 citations
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TL;DR: In this paper, the authors investigate the possibility that time series generated by certain physiological control systems may be members of a special class of complex processes, termed multifractal, which require a large number of exponents to characterize their scaling properties.
Abstract: There is evidence that physiological signals under healthy conditions may have a fractal temporal structure. Here we investigate the possibility that time series generated by certain physiological control systems may be members of a special class of complex processes, termed multifractal, which require a large number of exponents to characterize their scaling properties. We report on evidence for multifractality in a biological dynamical system, the healthy human heartbeat, and show that the multifractal character and nonlinear properties of the healthy heart rate are encoded in the Fourier phases. We uncover a loss of multifractality for a life-threatening condition, congestive heart failure.
1,448 citations
TL;DR: One of the most interesting features of the book is that it makes a start at explaining "dynamical diseases" that are not the result of infection by pathogens but that stem from abnormalities in the timing of essential functions.
Abstract: In an important new contribution to the literature of chaos, two distinguished researchers in the field of physiology probe central theoretical questions about physiological rhythms. Topics discussed include: How are rhythms generated? How do they start and stop? What are the effects of perturbation of the rhythms? How are oscillations organized in space? Leon Glass and Michael Mackey address an audience of biological scientists, physicians, physical scientists, and mathematicians, but the work assumes no knowledge of advanced mathematics. Variation of rhythms outside normal limits, or appearance of new rhythms where none existed previously, are associated with disease. One of the most interesting features of the book is that it makes a start at explaining "dynamical diseases" that are not the result of infection by pathogens but that stem from abnormalities in the timing of essential functions. From Clocks to Chaos provides a firm foundation for understanding dynamic processes in physiology.
1,244 citations
TL;DR: An introduction to some key aspects of non-linear dynamics and selected applications to physiology and medicine is provided.
789 citations
TL;DR: It is demonstrated that HRV analysis of ambulatory ECG recordings based on fully automated methods can have prognostic value in a population-based study and that nonlinear HRV indices may contribute prognosticvalue to complement traditional HRV measures.
Abstract: BACKGROUND: Despite much recent interest in quantification of heart rate variability (HRV), the prognostic value of conventional measures of HRV and of newer indices based on nonlinear dynamics is not universally accepted. METHODS AND RESULTS: We have designed algorithms for analyzing ambulatory ECG recordings and measuring HRV without human intervention, using robust methods for obtaining time-domain measures (mean and SD of heart rate), frequency-domain measures (power in the bands of 0.001 to 0.01 Hz [VLF], 0.01 to 0.15 Hz [LF], and 0.15 to 0.5 Hz [HF] and total spectral power [TP] over all three of these bands), and measures based on nonlinear dynamics (approximate entropy [ApEn], a measure of complexity, and detrended fluctuation analysis [DFA], a measure of long-term correlations). The study population consisted of chronic congestive heart failure (CHF) case patients and sex- and age-matched control subjects in the Framingham Heart Study. After exclusion of technically inadequate studies and those with atrial fibrillation, we used these algorithms to study HRV in 2-hour ambulatory ECG recordings of 69 participants (mean age, 71.7+/-8.1 years). By use of separate Cox proportional-hazards models, the conventional measures SD (P .3), were not. In multivariable models, DFA was of borderline predictive significance (P=.06) after adjustment for the diagnosis of CHF and SD. CONCLUSIONS: These results demonstrate that HRV analysis of ambulatory ECG recordings based on fully automated methods can have prognostic value in a population-based study and that nonlinear HRV indices may contribute prognostic value to complement traditional HRV measures.
516 citations
TL;DR: High spatial and temporal resolution mapping of optical transmembrane potentials can easily detect transiently erupting rotors during the early phase of ventricular fibrillation, characterized by a relatively high spatiotemporal cross-correlation.
Abstract: Sudden cardiac death is the leading cause of death in the industrialized world, with the majority of such tragedies being due to ventricular fibrillation1. Ventricular fibrillation is a frenzied and irregular disturbance of the heart rhythm that quickly renders the heart incapable of sustaining life. Rotors, electrophysiological structures that emit rotating spiral waves, occur in several systems that all share with the heart the functional properties of excitability and refractoriness. These re-entrant waves, seen in numerical solutions of simplified models of cardiac tissue2, may occur during ventricular tachycardias3,4. It has been difficult to detect such forms of re-entry in fibrillating mammalian ventricles5,6,7,8. Here we show that, in isolated perfused dog hearts, high spatial and temporal resolution mapping of optical transmembrane potentials can easily detect transiently erupting rotors during the early phase of ventricular fibrillation. This activity is characterized by a relatively high spatiotemporal cross-correlation. During this early fibrillatory interval, frequent wavefront collisions and wavebreak generation9 are also dominant features. Interestingly, this spatiotemporal pattern undergoes an evolution to a less highly spatially correlated mechanism that lacks the epicardial manifestations of rotors despite continued myocardial perfusion.
448 citations