title: Diagnostic tools for evaluating the impact of Focal Axonal Swellings arising in neurodegenerative diseases and/or traumatic brain injury.
abstract: BACKGROUND
  Focal Axonal Swellings arise in several leading neurodegenerative diseases of the central nervous system and are hallmark features of concussions and traumatic brain injuries. Recent theories mapped how the shape of each swelling affects the propagation of spike trains and consequently the information encoded in them. Spikes can be selectively deleted, have their speed affected, or blocked depending upon the severity of the swelling.
  
  
  METHODS
  Our computational toolbox extracts meaningful geometrical parameters from sequential images of injured axon segments. The algorithm provides a principled approach for dealing with imaging distortions caused by experimental artifacts in order to extract the cross-section of an axon by detecting local symmetries, turning points and turning regions.
  
  
  RESULTS
  Our characterization of the Focal Axonal Swelling allows for an assessment of its impact on spike propagation, leading to a color coding of the axon that highlights problematic regions for information propagation.
  
  
  METHODS
  Many theoretical works reported distortions in spike propagation related to axonal enlargements. Such estimates, however, were not incorporated to a toolbox that could classify axonal swellings directly from experimental images.
  
  
  CONCLUSIONS
  Our MATLAB toolbox thus highlights potential trouble spots of axonal morphology, and similar to car traffic maps, identify blocked or impaired routes for information flow. This computational framework is a promising starting point for diagnosing and assessing the impact of axonal swellings implicated in concussions, Alzheimer's and Parkinson's disease, Multiple Sclerosis and other neurological pathologies.
authors.affiliation: Department of Applied Mathematics, University of Washington, Seattle, WA 98195-3925, United States. Electronic address: pedro.doria.maia@gmail.com.
authors.forename: Pedro D
authors.initials: PD
authors.lastname: Maia
authors.affiliation: Disease Biophysics Group, Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, United States. Electronic address: matt.hemphill@gmail.com.
authors.forename: Matthew A
authors.initials: MA
authors.lastname: Hemphill
authors.affiliation: Department of Applied Mathematics, University of Washington, Seattle, WA 98195-3925, United States. Electronic address: brendan.zehnder@gmail.com.
authors.forename: Brendan
authors.initials: B
authors.lastname: Zehnder
authors.affiliation: Department of Applied Mathematics, University of Washington, Seattle, WA 98195-3925, United States.
authors.forename: Chenfei
authors.initials: C
authors.lastname: Zhang
authors.affiliation: Disease Biophysics Group, Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, United States. Electronic address: kkparker@seas.harvard.edu.
authors.forename: Kevin K
authors.initials: KK
authors.lastname: Parker
authors.affiliation: Department of Applied Mathematics, University of Washington, Seattle, WA 98195-3925, United States. Electronic address: kutz@uw.edu.
authors.forename: J Nathan
authors.initials: JN
authors.lastname: Kutz
mesh_terms: D000200:Action Potentials / Q000502:physiology; D000465:Algorithms; D001369:Axons / Q000473:pathology*; D001929:Brain Edema / Q000175:diagnosis* / Q000209:etiology*; D001930:Brain Injuries / Q000150:complications*; D003936:Diagnosis, Computer-Assisted; D006801:Humans; D008959:Models, Neurological; D019636:Neurodegenerative Diseases / Q000150:complications*
keywords: Alzheimer; Concussions; Focal Axonal Swelling; Multiple Sclerosis; Parkinson; Spike train propagation; Traumatic brain injury