Investigating the effect of cochlear synaptopathy on envelope following responses using a model of the auditory nerve

Dataset containing the recorded and simulated data reported in the manuscript "Investigating the effect of cochlear synaptopathy on envelope following responses using a model of the auditory nerve" published in the Journal of the Association for Research in Otolaryngology, JARO (https://doi.org/10.1007/s10162-019-00721-7):

1. RECORDED Envelope Following Responses (EFR) in normal-hearing (NH) threshold and hearing-impaired (HI) human listeners using deeply (m = 85%) and shallowly (m = 25%) modulated sinusoidally amplitude modulated (SAM) tones.
2. SIMULATED EFRs using the auditory nerve (AN) model by Zilany et al. (2009, 2014).

Files content and structure:

Recorded EFRs:

• 01_data__efr.csv:                      
  EFR recordings as a function of stimulus level (EFR magnitude-level functions) for the NH and HI listeners using two modulation depths.

The file containing the recorded EFR data have the following columns:

• lvl:                             Stimulation level
• m85_ok:                    EFR magnitude (dB re to 1 µV) using m = 85%. Significant responses (F-test = 1)
• m85_ko:                    EFR magnitude (dB re to 1 µV) using m = 85%. Non-significant responses (F-test = 0)
• m85_bkg:                  Estimated background noise magnitude (dB re to 1 µV) for the recordings when m = 85%
• m25_ok:                    EFR magnitude (dB re to 1 µV) using m = 25%. Significant responses (F-test = 1)
• m25_ko:                    EFR magnitude (dB re to 1 µV) using m = 25%. Non-significant responses (F-test = 0)
• m25_bkg:                  Estimated background noise magnitude (dB re to 1 µV) for the recordings when m = 25% 
• subj:                          Listener id
• hearing:                     Hearing group (nh | hi) of the listener

Simulated EFRs:

Files with the simulation results summing across frequency and SR fiber type

Fig. 4:

• fig4a__simul_efr__nh_23ohc_13ihc__no_cs.csv:                       
  Simulated EFR magnitude-level function for the NH threshold listeners (average) assuming 2/3 of OHC loss and 1/3 of IHC loss (Fig. 4a).
• fig4b__simul_efr__nh_slp_thres_all_ohc__no_cs.csv:              
  Simulated EFR magnitude-level function for the NH threshold listeners (average) assuming sloping threshold at extended high frequencies (EHF) and all of OHC loss (Fig. 4b).
• fig4c__simul_efr__nh_slp_thres_all_ihc__no_cs.csv:               
  Simulated EFR magnitude-level function for the NH threshold listeners (average) assuming sloping threshold at extended high frequencies (EHF) and all of IHC loss (Fig. 4c).
• fig4d__simul_efr__hi_23ohc_13ihc__no_cs.csv:                       
  Simulated EFR magnitude-level function for the HI listeners (average) assuming 2/3 of OHC loss and 1/3 of IHC loss (Fig. 4d).
• fig4e__simul_efr__hi_all_ohc__no_cs.csv:                               
  Simulated EFR magnitude-level function for the HI threshold listeners (average) assuming all of OHC loss (Fig. 4e).
• fig4f__simul_efr__hi_all_ihc__no_cs.csv:               
  Simulated EFR magnitude-level function for the HI threshold listeners (average) assuming all of IHC loss (Fig. 4f).
• fig4g__simul_efr__hi_slp_thres_23ohc_13ihc__no_cs.csv:                       
  Simulated EFR magnitude-level function for the HI listeners (average) assuming sloping threshold at EHF and 2/3 of OHC loss and 1/3 of IHC loss (Fig. 4d).
• fig4h__simul_efr__hi_slp_thres_all_ohc__no_cs.csv:                               
  Simulated EFR magnitude-level function for the HI threshold listeners (average) assuming sloping threshold at EHF and all of OHC loss (Fig. 4e).
• fig4i__simul_efr__hi_slp_thres_all_ihc__no_cs.csv:               
  Simulated EFR magnitude-level function for the HI threshold listeners (average) assuming sloping threshold at EHF and and all of IHC loss (Fig. 4f).

Fig. 5:

• fig5a__simul_efr__nh__cs_ms_ls_100p.csv:                              
  Simulated EFR magnitude-level function for the NH threshold listeners (average) assuming cochlear synaptopathy (CS) of a 100% of loss of only medium- and low-spontaneous rate (SR) AN fibers (Fig. 5a).
• fig5b__simul_efr__nh09_cs__approx.csv:            
  Simulated EFR magnitude-level function to approximate the data for the NH threshold listener NH09 including CS (Fig. 5b).
• fig5c__simul_efr__hi04_cs__approx.csv:  
  Simulated EFR magnitude-level function to approximate the data for the HI listener HI04 including CS (Fig. 5c).

Fig. 6:

Files with the simulation results for the NH threshold listener in different frequency bands and SR fiber types

• 08_simul__efr_healthy__mod-12.mat:          Simulated EFR level-growth function for the healthy system using a SAM tone with m = 12%.
• 09_simul__efr_healthy__mod-25.mat:          Simulated EFR level-growth function for the healthy system using a SAM tone with m = 25%.
• 10_simul__efr_healthy__mod-50.mat:          Simulated EFR level-growth function for the healthy system using a SAM tone with m = 50%.
• 11_simul__efr_healthy__mod-85.mat:          Simulated EFR level-growth function for the healthy system using a SAM tone with m = 85%.
• 12_simul__efr_healthy__mod-100.mat:        Simulated EFR level-growth function for the healthy system using a SAM tone with m = 100%.

Fig. 7:

• fig7a__simul_efr__bw_analys__32oct_[20, 40, 60, 80, 100]p.csv:                              
  Simulated EFR magnitude-level function for the NH threshold listeners assuming CS of a bandwidth (BW) of 3/2-octave for a loss of AN fibers ranging from 20% to 100% (Fig. 7a).
• fig7b__simul_efr__bw_analys__1oct_[20, 40, 60, 80, 100]p.csv:            
  Simulated EFR magnitude-level function for the NH threshold listeners assuming CS of a bandwidth (BW) of 1-octave for a loss of AN fibers ranging from 20% to 100% (Fig. 7b).
• fig7c__simul_efr__bw_analys__13oct_[20, 40, 60, 80, 100]p.csv:
  Simulated EFR magnitude-level function for the NH threshold listeners assuming CS of a bandwidth (BW) of 1/3-octave for a loss of AN fibers ranging from 20% to 100% (Fig. 7c).

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The structure of the .csv files that contain the EFR simulations is:

• lvl:                          Stimulation level
• mgn_mxxx:            Simulated EFR magnitude (a.u. in dB) for each modulation depth (100%, 85%, 50%, 25% and 12%)
• bkg_mxxx:             Estimate of the background noise floor (a.u. in dB) for each modulation depth. 
• ftest_mxxx:            Result of the F-test statistical test (0 or 1) for each modulation depth.

The structure of the .mat files that contain the EFR simulations is:

• exper_type:           Name of the simulated experiment
• species:                 Species used in the AN model (in this study is always 2: human)
• species_age:         (Not used in this work). Age of the animal when species is 4: mouse
• modulation:            Modulation depth of the SAM tone used in the simulation (100%, 85%, 50%, 25% or 12%)
• f_on:                      Center frequency of the on-frequency band (2000 Hz)
• f_off_hf:                 Center frequency of the first off-frequency band (3000 Hz)
• f_off_vhf:               Center frequency of the second off-frequency band (7000 Hz) 
• f_off_uvhf:             Center frequency of the third off-frequency band (12000 Hz)
• lvl_vect:                 Stimulus level vector (from 5 to 100 dB SPL, in steps of 5 dB)
• simul_efr               Structure with the simulated data
  • The data structure contains many fields which are matricies of size 3x20. The columns are the 20 stimulus levels defined in lvl_vect, and the first row is the simulated EFR, the second row is the estimates background noise floor in the simulation, and the third row is the output of the F-test statistics.
  • The structure fields can be divided in 4 groups:
    • ihc_           Responses from the IHC (not shown in the paper)
    • an_hs_      Responses from the High-SR fibers in the AN
    • an_ms_     Responses from the Medium-SR fibers in the AN
    • an_ls_       Responses from the Low-SR fibers in the AN
  • Each group has 5 responses corresponding to the on-frequency band (_on) and the three off-frequency bands (_off_hf, _off_vhf, _off_uvhf); and the sum across frequencies (_across_f)