DOI: 10.18130/v3/2xenwc
title: Trajectories of the heart rate characteristics index, a physiomarker of sepsis in premature infants, predict Neonatal ICU mortality
title: Trajectories of the HRC Index

description: This repository contains the dataset and code for the manuscript: 
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&lt;i&gt; Zimmet AM, Sullivan BA, Moorman JR, Lake DE, & Ratcliffe SJ. Trajectories of the heart rate characteristics index, a physiomarker of sepsis in premature infants, predict Neonatal ICU mortality. JRSM Cardiovascular Disease 2020. https://doi.org/10.1177/2048004020945142. &lt;/i&gt;
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&lt;b&gt; ABSTRACT &lt;/b&gt;
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&lt;b&gt;OBJECTIVE:&lt;/b&gt; Trajectories of physiomarkers over time can be useful to define phenotypes of disease progression and as predictors of clinical outcomes. The aim of this study was to identify phenotypes of the time course of late-onset sepsis in premature infants in Neonatal Intensive Care Units.
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&lt;b&gt; METHODS: &lt;/b&gt; We examined the trajectories of a validated continuous physiomarker, abnormal heart rate characteristics, using functional data analysis and clustering techniques.
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&lt;b&gt; PARTICIPANTS: &lt;/b&gt; We analyzed continuous heart rate characteristics data from 2989 very low birth weight infants (&lt;1500 grams) from nine NICUs from 2004-2010. 
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&lt;b&gt; RESULT: &lt;/b&gt; Despite the relative homogeneity of the patients, we found extreme variability in the physiomarker trajectories. We identified phenotypes that were indicative of seven and 30 day mortality beyond that predicted by individual heart rate characteristics values or baseline demographic information. 
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&lt;b&gt; CONCLUSION: &lt;/b&gt; Time courses of a heart rate characteristics physiomarker reveal snapshots of illness patterns, some of which were more deadly than others.
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&lt;b&gt; SOURCE OF ORIGINAL DATASET &lt;/b&gt;
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The dataset was originally collected for the following trial of a display of the Heart Rate Characteristics Index (using the HeRO Monitor made by Medical Predictive Science Corporation):
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&lt;i&gt; Moorman JR, Carlo WA, Kattwinkel J, et al. Mortality Reduction by Heart Rate Characteristic Monitoring in Very Low Birth Weight Neonates: A Randomized Trial. J Pediatr 2011; 159: 900-906.e1. &lt;/i&gt;
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Culture result information was curated originally for the following manuscript:
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&lt;i&gt; Weitkamp, J., Aschner, J.L., Carlo, W.A. et al. Meningitis, urinary tract, and bloodstream infections in very low birth weight infants enrolled in a heart rate characteristics monitoring trial. Pediatr Res 87, 1226–1230 (2020). https://doi.org/10.1038/s41390-019-0701-4 &lt;/i&gt;
description: Matlab, R2019a
description: <b>ACKNOWLEDGMENTS:</b>
<br>We would like to thank the original HeRO trial clinical investigators: Waldemar A. Carlo, MD, John Kattwinkel, MD, Robert L. Schelonka, MD, Peter J. Porcelli, MD, Christina T. Navarrete, MD, Eduardo Bancalari, MD, Judy L. Aschner, MD, Marshall Whit Walker, MD, Jose A. Perez, MD, Charles Palmer, MD, George J. Stukenborg, PhD, and Thomas Michael O’Shea, MD. 
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We are grateful to the original HeRO trial study coordinators as well: Stella Parolisi, Cathy Horton, Terri Smoot, Patty Brown, Monica Collins, Shirley Cosby, Daniela Castano, Steven Steele, Amy (Law) Beller, Nikki Barrett, Charlene Wells, Catherine Wilson, Paige Wilson, Judy Vallati, and Amy Blackman.
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<b>QUICK START GUIDE:</b>
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- Be sure to start by reading our ReadMe file, titled: <i> ReadMe_TrajectoriesoftheHRCIndex_20200721 </i>
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- To generate any of the figures or tables from our manuscript, open the file <i>runthis.m</i>. Inside are instructions (in the comments) to create all of the figures/tables from our manuscript.
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- There is a zip folder within the <i>Ramsay</i> folder called <i>RamsaySubfolders.zip</i> that MUST BE UNZIPPED before running any of the scripts. The user of this dataset MUST unzip this folder and place the subfolders within the <i>Ramsay</i> directory. An example of the correct file path should be: <i>Ramsay/@basis</i> NOT <i>Ramsay/RamsaySubfolders/@basis</i>.
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- The main script that does the bulk of the computation is <i>runFPCA_clean.m</i>. To get a good understanding of our mathematical pipeline, start here.