Trajectories of the heart rate characteristics index, a physiomarker of sepsis in premature infants, predict Neonatal ICU mortality

Version 1.0

Zimmet, Amanda M; Sullivan, Brynne A; Moorman, J Randall; Lake, Douglas E; Ratcliffe, Sarah J, 2020, "Trajectories of the heart rate characteristics index, a physiomarker of sepsis in premature infants, predict Neonatal ICU mortality", https://doi.org/10.18130/V3/2XENWC, University of Virginia Dataverse, V1, UNF:6:S3FYMHGFUcyal63xyeldrA== [fileUNF]

Learn about Data Citation Standards.

Contact Owner

Dataset Metrics

6,941 Downloads

Dataset Description	This repository contains the dataset and code for the manuscript: 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. ABSTRACT OBJECTIVE: 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. METHODS: We examined the trajectories of a validated continuous physiomarker, abnormal heart rate characteristics, using functional data analysis and clustering techniques. PARTICIPANTS: We analyzed continuous heart rate characteristics data from 2989 very low birth weight infants (<1500 grams) from nine NICUs from 2004-2010. RESULT: 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. CONCLUSION: Time courses of a heart rate characteristics physiomarker reveal snapshots of illness patterns, some of which were more deadly than others. SOURCE OF ORIGINAL DATASET 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): 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. Culture result information was curated originally for the following manuscript: 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
Subject	Medicine, Health and Life Sciences
Related Publication	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. doi: 10.1177/2048004020945142
Notes	ACKNOWLEDGMENTS: 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. 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. QUICK START GUIDE: - Be sure to start by reading our ReadMe file, titled: ReadMe_TrajectoriesoftheHRCIndex_20200721 - To generate any of the figures or tables from our manuscript, open the file runthis.m. Inside are instructions (in the comments) to create all of the figures/tables from our manuscript. - There is a zip folder within the Ramsay folder called RamsaySubfolders.zip 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 Ramsay directory. An example of the correct file path should be: Ramsay/@basis NOT Ramsay/RamsaySubfolders/@basis. - The main script that does the bulk of the computation is runFPCA_clean.m. To get a good understanding of our mathematical pipeline, start here.
License/Data Use Agreement	CC0 1.0

Change View

Table

Tree

Filter by

	1 to 10 of 263 Files	Original Format Archival Format (.tab)
	Fig1Data.mat MATLAB Data - 3.1 MB Published Jul 30, 2020 26 Downloads MD5: 20fa8d33ad8b21f33d14145da0bb6fa5 contains a derived dataset that makes plotting Fig 1 A,B,D more streamlined	Access File File Access Public Download Options MATLAB Data Download Metadata Data File Citation EndNote XML RIS BibTeX
	findBW_DOA_priorprob.m Plain Text - 1.7 KB Published Jul 30, 2020 26 Downloads MD5: 6233728c0922e87b8845b6454b22467e computes the prior probability of an event given the birthweight and days of age of the infant	Access File File Access Public Download Options Plain Text Download Metadata Data File Citation EndNote XML RIS BibTeX Explore Options Read Text
	findclustercentroids.m Plain Text - 328 B Published Jul 30, 2020 26 Downloads MD5: d540f3d6df93f617d4a99c358e81e673 finds the principal component coefficients for the centroid of each cluster	Access File File Access Public Download Options Plain Text Download Metadata Data File Citation EndNote XML RIS BibTeX Explore Options Read Text
	harmfdParHero.mat MATLAB Data - 1.8 KB Published Jul 30, 2020 34 Downloads MD5: b368dee342cb1dbbb57d8dc661ffc522 contains the harmfd and harmfdPar values from the display infants so they can be reused exactly for the non-display infants (these are objects created by Ramsay's code)	Access File File Access Public Download Options MATLAB Data Download Metadata Data File Citation EndNote XML RIS BibTeX
	HeRO_subset.mat MATLAB Data - 16.0 MB Published Jul 30, 2020 34 Downloads MD5: 56b4942436b72a812a5a0dab7ec113f3 contains the variables bwt, c, clinsep, cmenu, control, daysofage, diedin30days, diedin7days, hero, id, negsep, pg, pnum, pres, sep, tt. This data is from 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.	Access File File Access Public Download Options MATLAB Data Download Metadata Data File Citation EndNote XML RIS BibTeX
	load_data_for_loop_rng_value_30daymortality.mat MATLAB Data - 45.2 MB Published Jul 30, 2020 28 Downloads MD5: 9b6eedd0bd36fb6b0aed6fbfd1461865 used for running 100 different seed initializations for 30 day mortality	Access File File Access Public Download Options MATLAB Data Download Metadata Data File Citation EndNote XML RIS BibTeX
	load_data_for_loop_rng_value_7daymortality.mat MATLAB Data - 45.2 MB Published Jul 30, 2020 28 Downloads MD5: f874259ea0ff87845a61435197d4d902 used for running 100 different seed initializations for 7 day mortality	Access File File Access Public Download Options MATLAB Data Download Metadata Data File Citation EndNote XML RIS BibTeX
	loop_rng_value2.m Plain Text - 15.1 KB Published Jul 30, 2020 28 Downloads MD5: c5c4a2190aace48fd147d96d06e525cb this contains code for running through 100 different seed values in order to generate Supplemental Tables 2 and 3	Access File File Access Public Download Options Plain Text Download Metadata Data File Citation EndNote XML RIS BibTeX Explore Options Read Text
	makeFig1.m Plain Text - 1.8 KB Published Jul 30, 2020 28 Downloads MD5: baabb26c04496b3723f9ec148859201f this contains instructions for making Fig 1 A, B, and D	Access File File Access Public Download Options Plain Text Download Metadata Data File Citation EndNote XML RIS BibTeX Explore Options Read Text
	NearestNeighborPCs.m Plain Text - 9.2 KB Published Jul 30, 2020 28 Downloads MD5: 73485413d64d61d98d755ff71f58fc7f this makes the figures showing the characteristic curves for each neighborhood	Access File File Access Public Download Options Plain Text Download Metadata Data File Citation EndNote XML RIS BibTeX Explore Options Read Text

Citation Metadata

Persistent Identifier	doi:10.18130/V3/2XENWC
Publication Date	2020-07-30
Title	Trajectories of the heart rate characteristics index, a physiomarker of sepsis in premature infants, predict Neonatal ICU mortality
Alternative Title	Trajectories of the HRC Index
Author	Zimmet, Amanda M (Cardiovascular Medicine) - ORCID: 0000-0003-1457-3072 Sullivan, Brynne A (Pediatrics) - ORCID: 0000-0001-9580-4121 Moorman, J Randall (Cardiovascular Medicine) - ORCID: 0000-0002-5772-1648 Lake, Douglas E (Cardiovascular Medicine) - ORCID: 0000-0001-6259-4850 Ratcliffe, Sarah J (Public Health Sciences) - ORCID: 0000-0002-6644-8284
Point of Contact	Use email button above to contact. Sarah J Ratcliffe (Public Health Sciences)
Dataset Description	This repository contains the dataset and code for the manuscript: 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. ABSTRACT OBJECTIVE: 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. METHODS: We examined the trajectories of a validated continuous physiomarker, abnormal heart rate characteristics, using functional data analysis and clustering techniques. PARTICIPANTS: We analyzed continuous heart rate characteristics data from 2989 very low birth weight infants (<1500 grams) from nine NICUs from 2004-2010. RESULT: 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. CONCLUSION: Time courses of a heart rate characteristics physiomarker reveal snapshots of illness patterns, some of which were more deadly than others. SOURCE OF ORIGINAL DATASET 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): 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. Culture result information was curated originally for the following manuscript: 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
Subject	Medicine, Health and Life Sciences
Topic Classification	Predictive Modeling Continuous Monitoring Functional Data Analysis Clinical Phenotypes HeRO
Related Publication	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. doi: 10.1177/2048004020945142 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. doi: 10.1016/j.jpeds.2011.06.044 https://pubmed.ncbi.nlm.nih.gov/21864846/ 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). doi: 10.1038/s41390-019-0701-4 https://www.nature.com/articles/s41390-019-0701-4
Notes	ACKNOWLEDGMENTS: 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. 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. QUICK START GUIDE: - Be sure to start by reading our ReadMe file, titled: ReadMe_TrajectoriesoftheHRCIndex_20200721 - To generate any of the figures or tables from our manuscript, open the file runthis.m. Inside are instructions (in the comments) to create all of the figures/tables from our manuscript. - There is a zip folder within the Ramsay folder called RamsaySubfolders.zip 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 Ramsay directory. An example of the correct file path should be: Ramsay/@basis NOT Ramsay/RamsaySubfolders/@basis. - The main script that does the bulk of the computation is runFPCA_clean.m. To get a good understanding of our mathematical pipeline, start here.
Language	English
Data Creation Date	2010
Production Location	Dataset was collected at: University of Alabama at Birmingham, University of Miami, Winnie Palmer Hospital for Women and Babies, Wake Forest University Health Sciences, Milton S. Hershey Medical Center, Greenville Hospital System, Vanderbilt Children's Hospital, and University of Virginia. New analysis for the Trajectories of the HRC Index paper took place at University of Virginia.
Funding Information	National Institutes of Health: R01- HD48562 Translational Health Research Institute of Virginia Medical Predictive Science Corporation
Depositor	Zimmet, Amanda
Deposit Date	2020-07-21
Date of Collection	Start Date: 2004 ; End Date: 2010
Data Type	Heart Rate Characteristics Index data was collected from 2989 very low birthweight infants
Software	Matlab, Version: R2019a
Related Material	The EnsembleClustering folder contains slightly modified code from the following publication: Huang D, Wang C, Lai J. Locally Weighted Ensemble Clustering. IEEE Trans Cybern 2018; 48: 1460–1473. The original code can be found here: https://www.researchgate.net/publication/316681928. The code citation is: Huang, Dong & Wang, Chang-Dong & Lai, Jian-Huang. (2018). MATLAB source code for locally weighted ensemble clustering (IEEE TCYB 2018). The Ramsay folder contains modified code from the following book: Ramsay JO, Hooker G, Graves S. Functional Data Analysis with R and MATLAB. Springer, 2009. DOI: 10.1007/978-0-387-98185-7. The original code can be found here: http://www.psych.mcgill.ca/misc/fda/

Dataset Terms

License/Data Use Agreement

Our Community Norms as well as good scientific practices expect that proper credit is given via citation. Please use the data citation shown on the dataset page.

Creative Commons CC0 1.0 Universal Public Domain Dedication. CC0 1.0

Dataset Version	Summary	Contributors	Published on
No records found.

Edit File

This file has already been deleted (or replaced) in the current version. It may not be edited.

Restrict Access

Restricting limits access to published files. People who want to use the restricted files can request access by default. If you disable request access, you must add information about access to the Terms of Access field.

Learn about restricting files and dataset access in the User Guide.

Request Access

Enable access request

You must enable request access or add terms of access to restrict file access.

Terms of Access for Restricted Files

Save Changes

Edit Embargo

The selected file or files have already been published. Contact an administrator to change the embargo date or reason of the file or files.

Delete Files

The file will be deleted after you click on the Delete button.

Files will not be removed from previously published versions of the dataset.

Select File(s)

Please select one or more files.

Share Dataset

Share this dataset on your favorite social media networks.

Continue

Dataset Citations

Citations for this dataset are retrieved from Crossref via DataCite using Make Data Count standards. For more information about dataset metrics, please refer to the User Guide.

Sorry, no citations were found.

Restricted Files Selected

The selected file(s) may not be downloaded because you have not been granted access.

Download Options

The files selected are too large to download as a ZIP.

You can select individual files that are below the 953.7 MB download limit from the files table, or use the Data Access API for programmatic access to the files.

Select File(s)

Please select a file or files to be downloaded.

Restricted Files Selected

The restricted file(s) selected may not be downloaded because you have not been granted access.

Click Continue to download the files you have access to download.

Ineligible Files Selected

Some file(s) cannot be transferred. (They are restricted, embargoed, or not Globus accessible.)

Click Continue to transfer the elligible files.

Delete Dataset

Are you sure you want to delete this dataset and all of its files? You cannot undelete this dataset.

Delete Draft Version

Are you sure you want to delete this draft version? Files will be reverted to the most recently published version. You cannot undelete this draft.

Unpublished Dataset Private URL

Private URL can only be used with unpublished versions of datasets.

Unpublished Dataset Private URL

Are you sure you want to disable the Private URL? If you have shared the Private URL with others they will no longer be able to use it to access your unpublished dataset.

Delete Files

The file(s) will be deleted after you click on the Delete button.

Files will not be removed from previously published versions of the dataset.

Compute

This dataset contains restricted files you may not compute on because you have not been granted access.

Deaccession Dataset

Are you sure you want to deaccession? This is permanent and the selected version(s) will no longer be viewable by the public.

Deaccession Dataset

Are you sure you want to deaccession this dataset? This is permanent an it will no longer be viewable by the public.

Version Differences Details

Please select two versions to view the differences.

Version Differences Details

Version:
Last Updated:

Select File(s)

Please select a file or files for access request.

Select File(s)

Embargoed files cannot be accessed. Please select an unembargoed file or files for your access request.

Edit Tags

Select existing file tags or create new tags to describe your files. Each file can have more than one tag.

Request Access

You need to Log In to request access.

Dataset Terms

Please confirm and/or complete the information needed below in order to request access to files in this dataset.

This dataset is made available under the following terms. Please confirm and/or complete the information needed below in order to continue.

License/Data Use Agreement

Our Community Norms as well as good scientific practices expect that proper credit is given via citation. Please use the data citation shown on the dataset page.

Creative Commons CC0 1.0 Universal Public Domain Dedication. CC0 1.0

Preview Guestbook

Upon downloading files the guestbook asks for the following information.

Guestbook Name

Collected Data

Account Information

Package File Download

Use the Download URL in a Wget command or a download manager to download this package file. Download via web browser is not recommended. User Guide - Downloading a Dataverse Package via URL

Download URL

https://dataverse.lib.virginia.edu/api/access/datafile/

Compute Batch

Clear Batch

Dataset	Persistent Identifier	Change Compute Batch

Compute Batch

Submit for Review

You will not be able to make changes to this dataset while it is in review.

Publish Dataset

Are you sure you want to republish this dataset?

Select if this is a minor or major version update.

Minor Release (1.1)

Major Release (2.0)

Publish Dataset

This dataset cannot be published until Center for Advanced Medical Analytics (CAMA) is published by its administrator.

Publish Dataset

This dataset cannot be published until Center for Advanced Medical Analytics (CAMA) and School of Medicine are published.

Return to Author

Return this dataset to contributor for modification. The reason for return entered below will be sent by email to the author.