Dataset Information

Extracting Instantaneous Respiratory Rate From Multiple Photoplethysmogram Respiratory-Induced Variations.

ABSTRACT: In this study, we proposed a novel method for extracting the instantaneous respiratory rate (IRR) from the pulse oximeter photoplethysmogram (PPG). The method was performed in three main steps: (1) a time-frequency transform called synchrosqueezing transform (SST) was used to extract the respiratory-induced intensity, amplitude and frequency variation signals from PPG, (2) the second SST was applied to each extracted respiratory-induced variation signal to estimate the corresponding IRR, and (3) the proposed peak-conditioned fusion method then combined the IRR estimates to calculate the final IRR. We validated the implemented method with capnography and nasal/oral airflow as the reference RR using the limits of agreement (LOA) approach. Compared to simple fusion and single respiratory-induced variation estimations, peak-conditioned fusion shows better performance. It provided a bias of 0.28 bpm with the 95% LOAs ranging from -3.62 to 4.17, validated against capnography and a bias of 0.04 bpm with the 95% LOAs ranging from -5.74 to 5.82, validated against nasal/oral airflow. This algorithm would expand the functionality of a conventional pulse oximetry beyond the measurement of heart rate and oxygen saturation to measure the respiratory rate continuously and instantly.

SUBMITTER: Dehkordi P

PROVIDER: S-EPMC6058306 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Extracting Instantaneous Respiratory Rate From Multiple Photoplethysmogram Respiratory-Induced Variations.

Dehkordi Parastoo P Garde Ainara A Molavi Behnam B Ansermino J Mark JM Dumont Guy A GA

Frontiers in physiology 20180718

In this study, we proposed a novel method for extracting the instantaneous respiratory rate (IRR) from the pulse oximeter photoplethysmogram (PPG). The method was performed in three main steps: (1) a time-frequency transform called synchrosqueezing transform (SST) was used to extract the respiratory-induced intensity, amplitude and frequency variation signals from PPG, (2) the second SST was applied to each extracted respiratory-induced variation signal to estimate the corresponding IRR, and (3) ...[more]

PMID: 30072918

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Project description:BACKGROUND: Time delays are important factors that are often neglected in gene regulatory network (GRN) inference models. Validating time delays from knowledge bases is a challenge since the vast majority of biological databases do not record temporal information of gene regulations. Biological knowledge and facts on gene regulations are typically extracted from bio-literature with specialized methods that depend on the regulation task. In this paper, we mine evidences for time delays related to the transcriptional regulation of yeast from the PubMed abstracts. RESULTS: Since the vast majority of abstracts lack quantitative time information, we can only collect qualitative evidences of time delays. Specifically, the speed-up or delay in transcriptional regulation rate can provide evidences for time delays (shorter or longer) in GRN. Thus, we focus on deriving events related to rate changes in transcriptional regulation. A corpus of yeast regulation related abstracts was manually labeled with such events. In order to capture these events automatically, we create an ontology of sub-processes that are likely to result in transcription rate changes by combining textual patterns and biological knowledge. We also propose effective feature extraction methods based on the created ontology to identify the direct evidences with specific details of these events. Our ontologies outperform existing state-of-the-art gene regulation ontologies in the automatic rule learning method applied to our corpus. The proposed deterministic ontology rule-based method can achieve comparable performance to the automatic rule learning method based on decision trees. This demonstrates the effectiveness of our ontology in identifying rate-changing events. We also tested the effectiveness of the proposed feature mining methods on detecting direct evidence of events. Experimental results show that the machine learning method on these features achieves an F1-score of 71.43%. CONCLUSIONS: The manually labeled corpus of events relating to rate changes in transcriptional regulation for yeast is available in https://sites.google.com/site/wentingntu/data. The created ontologies summarized both biological causes of rate changes in transcriptional regulation and corresponding positive and negative textual patterns from the corpus. They are demonstrated to be effective in identifying rate-changing events, which shows the benefits of combining textual patterns and biological knowledge on extracting complex biological events.

Dataset Information

Extracting Instantaneous Respiratory Rate From Multiple Photoplethysmogram Respiratory-Induced Variations.

Publications

Extracting Instantaneous Respiratory Rate From Multiple Photoplethysmogram Respiratory-Induced Variations.

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