title: Topological data analysis for discovery in preclinical spinal cord injury and traumatic brain injury.
abstract: Data-driven discovery in complex neurological disorders has potential to extract meaningful syndromic knowledge from large, heterogeneous data sets to enhance potential for precision medicine. Here we describe the application of topological data analysis (TDA) for data-driven discovery in preclinical traumatic brain injury (TBI) and spinal cord injury (SCI) data sets mined from the Visualized Syndromic Information and Outcomes for Neurotrauma-SCI (VISION-SCI) repository. Through direct visualization of inter-related histopathological, functional and health outcomes, TDA detected novel patterns across the syndromic network, uncovering interactions between SCI and co-occurring TBI, as well as detrimental drug effects in unpublished multicentre preclinical drug trial data in SCI. TDA also revealed that perioperative hypertension predicted long-term recovery better than any tested drug after thoracic SCI in rats. TDA-based data-driven discovery has great potential application for decision-support for basic research and clinical problems such as outcome assessment, neurocritical care, treatment planning and rapid, precision-diagnosis.
authors.affiliation: Department of Neurosurgery, Brain and Spinal Injury Center, University of California, San Francisco, 1001 Potrero Avenue, Building 1, Room 101, San Francisco, California 94143, USA.
authors.forename: Jessica L
authors.initials: JL
authors.lastname: Nielson
authors.affiliation: Tagb.io, 1 Quartz Way, San Francisco, California 94131, USA.
authors.forename: Jesse
authors.initials: J
authors.lastname: Paquette
authors.affiliation: Department of Neurosurgery, Brain and Spinal Injury Center, University of California, San Francisco, 1001 Potrero Avenue, Building 1, Room 101, San Francisco, California 94143, USA.
authors.forename: Aiwen W
authors.initials: AW
authors.lastname: Liu
authors.affiliation: Department of Neurosurgery, Brain and Spinal Injury Center, University of California, San Francisco, 1001 Potrero Avenue, Building 1, Room 101, San Francisco, California 94143, USA.
authors.forename: Cristian F
authors.initials: CF
authors.lastname: Guandique
authors.affiliation: Department of Neuroscience, Ohio State University, 460 West 12th Avenue, 670 Biomedical Research Tower, Columbus, Ohio 43210, USA.
authors.forename: C Amy
authors.initials: CA
authors.lastname: Tovar
authors.affiliation: Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai city, Miyagi prefecture 980-0856, Japan.
authors.forename: Tomoo
authors.initials: T
authors.lastname: Inoue
authors.affiliation: Department of Neurology, San Francisco VA Medical Center, University of California San Francisco, San Francisco, California 94110, USA.
authors.forename: Karen-Amanda
authors.initials: KA
authors.lastname: Irvine
authors.affiliation: Department of Physiology, Spinal Cord and Brain Injury Research Center, Chandler Medical Center, University of Kentucky Lexington, B463 Biomedical &Biological Sciences Research Building, 741 South Limestone Street, Kentucky 40536, USA.
authors.forename: John C
authors.initials: JC
authors.lastname: Gensel
authors.affiliation: Ayasdi Inc., 4400 Bohannon Drive Suite #200, Menlo Park, California 94025, USA.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Kloke
authors.affiliation: GenePeeks, Inc., 777 Avenue of the Americas, New York, New York 10001, USA.
authors.forename: Tanya C
authors.initials: TC
authors.lastname: Petrossian
authors.affiliation: Capella Biosciences, 550 Hamilton Avenue, Palo Alto, California 94301, USA.
authors.forename: Pek Y
authors.initials: PY
authors.lastname: Lum
authors.affiliation: Ayasdi Inc., 4400 Bohannon Drive Suite #200, Menlo Park, California 94025, USA.|Department of Mathematics, Stanford University, Building 380, Stanford, California, 94305, USA.
authors.forename: Gunnar E
authors.initials: GE
authors.lastname: Carlsson
authors.affiliation: Department of Neurosurgery, Brain and Spinal Injury Center, University of California, San Francisco, 1001 Potrero Avenue, Building 1, Room 101, San Francisco, California 94143, USA.
authors.forename: Geoffrey T
authors.initials: GT
authors.lastname: Manley
authors.affiliation: Department of Cell Biology and Neuroscience, W.M. Keck Center for Collaborative Neuroscience, Rutgers University, Piscataway, New Jersey 08854, USA.
authors.forename: Wise
authors.initials: W
authors.lastname: Young
authors.affiliation: Department of Neurosurgery, Brain and Spinal Injury Center, University of California, San Francisco, 1001 Potrero Avenue, Building 1, Room 101, San Francisco, California 94143, USA.
authors.forename: Michael S
authors.initials: MS
authors.lastname: Beattie
authors.affiliation: Department of Neurosurgery, Brain and Spinal Injury Center, University of California, San Francisco, 1001 Potrero Avenue, Building 1, Room 101, San Francisco, California 94143, USA.
authors.forename: Jacqueline C
authors.initials: JC
authors.lastname: Bresnahan
authors.affiliation: Department of Neurosurgery, Brain and Spinal Injury Center, University of California, San Francisco, 1001 Potrero Avenue, Building 1, Room 101, San Francisco, California 94143, USA.|Department of Neurosurgery, San Francisco VA Medical Center, University of California San Francisco, San Francisco, California 94110, USA.
authors.forename: Adam R
authors.initials: AR
authors.lastname: Ferguson
mesh_terms: D000818:Animals; D001930:Brain Injuries; D019295:Computational Biology / Q000379:methods*; D003627:Data Interpretation, Statistical; D004195:Disease Models, Animal; D051381:Rats; D013119:Spinal Cord Injuries