Background: The time variation between consecutive heartbeats is commonly referred to as heart rate variability (HRV). Loss of complexity in HRV has been documented in several cardiovascular diseases and has been associated with an increase in morbidity and mortality. However, the mechanisms that control HRV are not well understood. Animal experiments are the key to investigating this question. However, to date, there are no standard open source tools for HRV analysis of mammalian electrocardiogram (ECG) data and no centralized public databases for researchers to access.Methods: We created an open source software solution specifically designed for HRV analysis from ECG data of multiple mammals, including humans. We also created a set of public databases of mammalian ECG signals (dog, rabbit and mouse) with manually corrected R-peaks (>170,000 annotations) and signal quality annotations. The platform (software and databases) is called PhysioZoo.Results: PhysioZoo makes it possible to load ECG data and perform very accurate R-peak detection (F1 > 98%). It also allows the user to manually correct the R-peak locations and annotate low signal quality of the underlying ECG. PhysioZoo implements state of the art HRV measures adapted for different mammals (dogs, rabbits, and mice) and allows easy export of all computed measures together with standard data representation figures. PhysioZoo provides databases and standard ranges for all HRV measures computed on healthy, conscious humans, dogs, rabbits, and mice at rest. Study of these measures across different mammals can provide new insights into the complexity of heart rate dynamics across species.Conclusion: PhysioZoo enables the standardization and reproducibility of HRV analysis in mammalian models through its open source code, freely available software, and open access databases. PhysioZoo will support and enable new investigations in mammalian HRV research. The source code and software are available on www.physiozoo.com.

Synonymous codons translate into chemically identical amino acids. Once considered inconsequential to the formation of the protein product, there is evidence to suggest that codon usage affects co-translational protein folding and the final structure of the expressed protein. Here we develop a method for computing and comparing codon-specific Ramachandran plots and demonstrate that the backbone dihedral angle distributions of some synonymous codons are distinguishable with statistical significance for some secondary structures. This shows that there exists a dependence between codon identity and backbone torsion of the translated amino acid. Although these findings cannot pinpoint the causal direction of this dependence, we discuss the vast biological implications should coding be shown to directly shape protein conformation and demonstrate the usefulness of this method as a tool for probing associations between codon usage and protein structure. Finally, we urge for the inclusion of exact genetic information into structural databases.

Pulse oximetry is routinely used to non-invasively monitor oxygen saturation levels. A low oxygen level in the blood means low oxygen in the tissues, which can ultimately lead to organ failure. Yet, contrary to heart rate variability measures, a field which has seen the development of stable standards and advanced toolboxes and software, no such standards and open tools exist for continuous oxygen saturation time series variability analysis. The primary objective of this research was to identify, implement and validate key digital oximetry biomarkers (OBMs) for the purpose of creating a standard and associated reference toolbox for continuous oximetry time series analysis. We review the sleep medicine literature to identify clinically relevant OBMs. We implement these biomarkers and demonstrate their clinical value within the context of obstructive sleep apnea (OSA) diagnosis on a total of n = 3806 individual polysomnography recordings totaling 26,686 h of continuous data. A total of 44 digital oximetry biomarkers were implemented. Reference ranges for each biomarker are provided for individuals with mild, moderate, and severe OSA and for non-OSA recordings. Linear regression analysis between biomarkers and the apnea hypopnea index (AHI) showed a high correlation, which reached $$\overline R ^2 = 0.82$$ R ¯ 2 = 0.82 . The resulting python OBM toolbox, denoted “pobm”, was contributed to the open software PhysioZoo (physiozoo.org). Studying the variability of the continuous oxygen saturation time series using pbom may provide information on the underlying physiological control systems and enhance our understanding of the manifestations and etiology of diseases, with emphasis on respiratory diseases.

Heart rate and heart rate variability (HRV) are mainly determined by the autonomic nervous system (AnS), which interacts with receptors on the sinoatrial node (SAn; the heart's primary pacemaker), and by the "coupled-clock" system within the SAn cells. HRV changes are associated with cardiac diseases. However, the relative contributions of the ANS and SAN to HRV are not clear, impeding effective treatment. to discern the SAn's contribution, we performed HRV analysis on canine electrocardiograms containing basal and AnS-blockade segments. We also analyzed human electrocardiograms of atrial fibrillation and heart failure patients, as well as healthy aged subjects. Finally, we used a mathematical model to simulate HRV under decreased "coupled-clock" regulation. We found that (a) in canines, the SAn and AnS contribute mainly to long-and short-term HRV, respectively; (b) there is evidence suggesting a similar relative SAn contribution in humans; (c) SAn features can be calculated from beat-intervals obtained in-vivo, without intervention; (d) AnS contribution can be modeled by sines embedded in white noise; (e) HRV changes associated with cardiac diseases and aging can be interpreted as deterioration of both SAn and AnS; and (f) SAn clock-coupling can be estimated from changes in HRV. this may enable future non-invasive diagnostic applications.

Synonymous codons translate into chemically identical amino acids. Once considered inconsequential to the formation of the protein product, there is now significant evidence to suggest that codon usage affects co-translational protein folding and the final structure of the expressed protein. Here we develop a method for computing and comparing codon-specific Ramachandran plots and demonstrate that the backbone dihedral angle distributions of some synonymous codons are distinguishable with statistical significance for some secondary structures. This shows that there exists a dependence between codon identity and backbone torsion of the translated amino acid. Although these findings cannot pinpoint the causal direction of this dependence, we discuss the vast biological implications should coding be shown to directly shape protein conformation and demonstrate the usefulness of this method as a tool for probing associations between codon usage and protein structure. Finally, we urge for the inclusion of exact genetic information into structural databases.

Background: Power spectral density (PSD) analysis of the heartbeat intervals in the three main frequency bands [very low frequency (VLF), low frequency (LF), and high frequency (HF)] provides a quantitative non-invasive tool for assessing the function of the cardiovascular control system. In humans, these frequency bands were standardized following years of empirical evidence. However, no quantitative approach has justified the frequency cutoffs of these bands and how they might be adapted to other mammals. Defining mammal-specific frequency bands is necessary if the PSD analysis of the HR is to be used as a proxy for measuring the autonomic nervous system activity in animal models.Methods: We first describe the distribution of prominent frequency peaks found in the normalized PSD of mammalian data using a Gaussian mixture model while assuming three components corresponding to the traditional VLF, LF and HF bands. We trained the algorithm on a database of human electrocardiogram recordings (n = 18) and validated it on databases of dogs (n = 17) and mice (n = 8). Finally, we tested it to predict the bands for rabbits (n = 4) for the first time.Results: Double-logarithmic analysis demonstrates a scaling law between the GMM-identified cutoff frequencies and the typical heart rate (HRm): fVLF-LF = 0.0037⋅HRm0.58, fLF-HF = 0.0017⋅HRm1.01 and fHFup = 0.0128⋅HRm0.86. We found that the band cutoff frequencies and Gaussian mean scale with a power law of 1/4 or 1/8 of the typical body mass (BMm), thus revealing allometric power laws.Conclusion: Our automated data-driven approach allowed us to define the frequency bands in PSD analysis of beat-to-beat time series from different mammals. The scaling law between the band frequency cutoffs and the HRm can be used to approximate the PSD bands in other mammals.

Introduction: Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia. Its prevalence is 1-2% of the general population and it is associated with increased risk of mortality and morbidity. Methods: The AliveCor mobile electrocardiogram (ECG) device was used to collect data. The Physionet Challenge aimed to create an intelligent algorithm for automated rhythm and quality classification. A database of 8528 single lead ECG was used for training and a closed database of 3658 ECG recordings was used for testing the participants algorithms on the Challenge server. The RR interval time-series was first estimated using a R-peak detector. Signal quality was estimated on a second-by-second basis and the continuous sub-segment with the highest quality was selected for further analysis. A number of features were estimated: heart rate variability (time domain based, fragmentation, coefficient of sample entropy etc.), ECG morphology (QRS length, QT interval etc.) and the presence of ectopic beats. The features were used to train support vector machine classifiers in a one-vs.-rest approach. Results: For the final score of the challenge we obtained an overall F 1 measure on the test set of 0.80. Conclusion: The feature based machine learning approach showed high performance in distinguishing between the different rhythms represented in the Challenge. This opens the horizon for computer automated interpretation of single lead mobile ECG.

Despite their great promise, artificial intelligence (AI) systems have yet to become ubiquitous in the daily practice of medicine largely due to several crucial unmet needs of healthcare practitioners. These include lack of explanations in clinically meaningful terms, handling the presence of unknown medical conditions, and transparency regarding the system’s limitations, both in terms of statistical performance as well as recognizing situations for which the system’s predictions are irrelevant. We articulate these unmet clinical needs as machine-learning (ML) problems and systematically address them with cutting-edge ML techniques. We focus on electrocardiogram (ECG) analysis as an example domain in which AI has great potential and tackle two challenging tasks: the detection of a heterogeneous mix of known and unknown arrhythmias from ECG and the identification of underlying cardio-pathology from segments annotated as normal sinus rhythm recorded in patients with an intermittent arrhythmia. We validate our methods by simulating a screening for arrhythmias in a large-scale population while adhering to statistical significance requirements. Specifically, our system 1) visualizes the relative importance of each part of an ECG segment for the final model decision; 2) upholds specified statistical constraints on its out-of-sample performance and provides uncertainty estimation for its predictions; 3) handles inputs containing unknown rhythm types; and 4) handles data from unseen patients while also flagging cases in which the model’s outputs are not usable for a specific patient. This work represents a significant step toward overcoming the limitations currently impeding the integration of AI into clinical practice in cardiology and medicine in general.