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- Creator:
- Grosh, Karl and Li, Yizeng
- Description:
- In a sensitive cochlea, the basilar membrane response to transient excitation of any kind--normal acoustic or artificial intracochlear excitation--consists of not only a primary impulse but also a coda of delayed secondary responses with varying amplitudes but similar spectral content around the characteristic frequency of the measurement location. The coda, sometimes referred to as echoes or ringing, has been described as a form of local, short term memory which may influence the ability of the auditory system to detect gaps in an acoustic stimulus such as speech. Depending on the individual cochlea, the temporal gap between the primary impulse and the following coda ranges from once to thrice the group delay of the primary impulse (the group delay of the primary impulse is on the order of a few hundred microseconds). The coda is physiologically vulnerable, disappearing when the cochlea is compromised even slightly. The multicomponent sensitive response is not yet completely understood. We use a physiologically-based, mathematical model to investigate (i) the generation of the primary impulse response and the dependence of the group delay on the various stimulation methods, (ii) the effect of spatial perturbations in the properties of mechanically sensitive ion channels on the generation and separation of delayed secondary responses. The model suggests that the presence of the secondary responses depends on the wavenumber content of a perturbation and the activity level of the cochlea. In addition, the model shows that the varying temporal gaps between adjacent coda seen in experiments depend on the individual profiles of perturbations. Implications for non-invasive cochlear diagnosis are also discussed.
- Discipline:
- Engineering and Health Sciences
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- Creator:
- Gliske, Stephen V and Stacey, William C
- Description:
- This data is part of a large program to translate detection and interpretation of HFOs into clinical use. A zip file is included which contains hfo detections, metadata, and Matlab scripts. The matlab scripts analyze this input data and produce figures as in the referenced paper (note: the blind source separation method is stochastic, and so the figures may not be exactly the same). A file "README.txt" provides more detail about each individual file within the zip file.
- Keyword:
- hfo, high frequency oscillation, ripple, fast ripple, blind source separation, non-negative matrix factorization, and temporal variability
- Discipline:
- Science, Engineering, and Health Sciences
-
- Creator:
- Mirshams Shahshahani, Payam
- Description:
- Investigating minimum human reaction times is often confounded by the motivation, training, and state of arousal of the subjects. We used the reaction times of athletes competing in the shorter sprint events in the Athletics competitions in recent Olympics (2004-2016) to determine minimum human reaction times because there's little question as to their motivation, training, or state of arousal. The reaction times of sprinters however are only available on the IAAF web page for each individual heat, in each event, at each Olympic. Therefore we compiled all these data into two separate excel sheets which can be used for further analyses.
- Keyword:
- minimum reaction time, sprinter, Olympics, Athletics, sex difference, starting block, and false start
- Citation to related publication:
- Mirshams Shahshahani P, Lipps DB, Galecki AT, Ashton-Miller JA (2018) On the apparent decrease in Olympic sprinter reaction times. PLoS ONE 13(6): e0198633. https://doi.org/10.1371/journal.pone.0198633
- Discipline:
- Engineering, Health Sciences, Science, Other, and General Information Sources
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- Creator:
- Figueroa, C. Alberto
- Description:
- This information provides the data and commands to manually setup the computational simulations used in the PLOS ONE paper 'Patient-specific modeling of right coronary circulation vulnerability post-liver transplant in Alagille’s syndrome' using CRIMSON (CARDIOVASCULAR INTEGRATED MODELLING & SIMULATION) a prototype simulation environment developed under the support of the European Research Council (( http://www.crimson.software/)., Note that a Windows version of the CRIMSON flowsolver is provided as part of the CRIMSON Windows installer, but you will need a very powerful Windows computer to run these simulations, as the models used in the present work are extremely computationally-demanding. It is recommended that you use a Linux version of the CRIMSON flowsolver on a high-performance computer., Option 1 (ready-to-use files to immediately start the simulation): 1. Please unzip the Ready-to-use files. 2. Copy the folders of each of the three conditions to the high performance computer. 3. In addition to different codes used, each folder provides the boundary conditions applied in the simulations described in the manuscript (e.g. LPN parameters). To run the 3D simulations for each condition simply launch the it using the CRIMSON flowsolver. In addition, the solver.inp file can be modified to run a 0D "real-time simulation" (please open solver.inp with a text editor and modify line 4 "Simulate in Purely Zero Dimensions:" to "True")., Option 2 (using the MITK files): 1. Please download and install Crimson software ( http://www.crimson.software/). 2. Please unzip the MITK files and the Ready-to-use files. 3. From amongst the provided MITK files, load the MITK file of interest to CRIMSON (using the MITK files, additional changes can be made to the computational model in case the user wants to explore different settings/boundary conditions e.g. change the vascular wall properties, introducing a change in the geometry to create a virtual stenosis). 3. Navigate to the tree in the "Data Manager" panel and select the "Pulmonaries", "CRIMSON SOLVER" and then "Solver study 3D" items, in the described order. 4. In the right hand panel select the "CRIMSON Solver setup" tab and scroll down the right hand bar until to find the "Setup Solver" box; click to output the simulation files (faceInfo.dat, geombc.dat.1, multidomain.dat, netlist_surface.dat,numstart.dat, presolver folder, solver.inp, restart.0.1). 5. Copy and replace the geombc.dat.1 and restart.0.1 generated by CRIMSON for each individual condition to the respective unziped folder in the Ready-to-use file (discard the remaining files that were output by CRIMSON). Note that if you have not changed anything about the model (e.g. vascular wall properties), then doing this will produce restart.0.1 and geombc.dat.1 files which are identical to the ready-to-use versions. 6. Finally copy each Condition folder to the high performance computer and simply launch the simulation using the CRIMSON flowsolver., and For technical queries please contact crimson-users@googlegroups.com. --October 2018.
- Citation to related publication:
- Silva Vieira M, Arthurs CJ, Hussain T, Razavi R, Figueroa CA (2018) Patient-specific modeling of right coronary circulation vulnerability post-liver transplant in Alagille’s syndrome. PLOS ONE 13(11): e0205829. https://doi.org/10.1371/journal.pone.0205829
- Discipline:
- Engineering and Health Sciences
-
- Creator:
- Crisp, Dakota N., Saggio, Maria L., Scott, Jared, Stacey, William C., Nakatani, Mitsuyoshi, Gliske, Stephen V., and Lin, Jack
- Description:
- This data and scripts are meant to test and show seizure differentiation based on bifurcation theory. A zip file is included which contains real and simulated seizure waveforms, Matlab scripts, and metadata. The matlab scripts allow for visual review validation and objective feature analysis. The file “README.txt” provides more detail about each individual file within the zip file. and Data citation: Crisp, D.N., Saggio, M.L., Scott, J., Stacey, W.C., Nakatani, M., Gliske, S.F., Lin, J. (2019). Epidynamics: Navigating the map of seizure dynamics - Code & Data [Data set]. University of Michigan Deep Blue Data Repository. https://doi.org/10.7302/ejhy-5h41
- Keyword:
- Bifurcation, Epilepsy, Seizure, and Divergence
- Citation to related publication:
- Saggio, M.L., Crisp, D., Scott, J., Karoly, P.J., Kuhlmann, L., Nakatani, M., Murai, T., Dümpelmann, M., Schulze-Bonhage, A., Ikeda, A., Cook, M., Gliske, S.V., Lin, J., Bernard, C., Jirsa, V., Stacey, W., 2020. In pre-print. Epidynamics characterize and navigate the map of seizure dynamics. bioRxiv 2020.02.08.940072. https://doi.org/10.1101/2020.02.08.940072
- Discipline:
- Engineering, Science, and Health Sciences
-
- Creator:
- Crisp, Dakota N., Cheung, Warwick, Gliske, Stephen V., Lai, Alan, Freestone, Dean R., Grayden, David B., Cook, Mark J., and Stacey, William C.
- Description:
- The data and the scripts are to show that seizure onset dynamics and evoked responses change over the progression of epileptogenesis defined in this intrahippocampal tetanus toxin rat model. All tests explored in this study can be repeated with the data and scripts included in this repository. and Dataset citation: Crisp, D.N., Cheung, W., Gliske, S.V., Lai, A., Freestone, D.R., Grayden, D.B., Cook, MJ., Stacey, W.C. (2019). Epileptogenesis modulates spontaneous and responsive brain state dynamics [Data set]. University of Michigan Deep Blue Data Repository. https://doi.org/10.7302/r6vg-9658
- Keyword:
- evoked response, stimulation, bifurcation, epilepsy, seizure, divergence, and dynamics
- Citation to related publication:
- Crisp, D. N., Cheung, W., Gliske, S. V., Lai, A., Freestone, D. R., Grayden, D. B., Cook, M. J., & Stacey, W. C. (2020). Quantifying epileptogenesis in rats with spontaneous and responsive brain state dynamics. Brain Communications, 2(1). https://doi.org/10.1093/braincomms/fcaa048
- Discipline:
- Science, Engineering, and Health Sciences
-
- Creator:
- Whitaker, Steven T., Nataraj, Gopal, Nielsen, Jon-Fredrik, and Fessler, Jeffrey A.
- Description:
- File: P,jf06Sep2019,mese.7 The multi-echo spin echo (MESE) data was acquired using a 3D acquisition with an initial 90 degree excitation pulse followed by 32 refocusing (180 degree) pulses, resulting in 32 echoes with echo spacing of 10 ms. The repetition time of the sequence was 1200 ms. Each refocusing pulse was flanked by crusher gradients to impart 14 cycles of phase across the imaging volume. The initial excitation pulse had time-bandwidth product of 6, duration of 3 ms, and slab thickness of 0.9 cm, and each refocusing pulse had time-bandwidth product of 2, duration of 2 ms, and slab thickness of 2.1 cm. The scan took 36 min 11 s and covered a field of view (FOV) of 22 x 22 x 0.99 cm^3 with matrix size 200 x 200 x 9., File: P,jf06Sep2019,b1.7 The Bloch-Siegert (BS) scans were acquired using a 3D acquisition. The excitation pulse of these scans had time-bandwidth product of 8 and duration of 1 ms. The pair of scans used +/-4 kHz off-resonant Fermi pulses between excitation and readout. The BS scans took 2 min 40 s in total and covered a FOV of 22 x 22 x 0.99 cm^3 with matrix size 200 x 50 x 9., File: P,jf06Sep2019,mwf.7 The small-tip fast recovery (STFR) scans were acquired using a 3D acquisition. The first two and last two scans were pairs of spoiled gradient-recalled echo (SPGR) scans with echo time difference of 2.3 ms. (In the related paper, only the first set was used, i.e., only 11 of the 13 scans were used.) The remaining scans used scan parameters that were optimized to minimize the Cramer-Rao Lower Bound (CRLB) of estimates of myelin water fraction (MWF). The RF pulses had time-bandwidth product of 8 and duration of 1 ms. Each pair of SPGR scans took 58 s and the nine STFR scans took 3 min 36 s for a total scan time of 5 min 32 s (4 min 34 s if one pair of SPGR scans is ignored). The scans covered a field of view (FOV) of 22 x 22 x 0.99 cm^3 with matrix size 200 x 200 x 9., File: meseslice5.mat Contains the 32 echoes of the MESE image data for the middle slice of the imaging volume. Saved using Mathworks MATLAB R2019a., File: b1slice5.mat Contains the transmit field inhomogeneity map for the middle slice of the imaging volume., File: recon.jld Key "img" contains the 11 STFR images for the middle slice of the imaging volume. Key "b0map" contains a field map estimated from the two SPGR scans. Key "mask" contains a mask of the voxels for which to estimate MWF. Key "T1img" contains a T1-weighted image for anatomical reference., File: headmask.mat Contains a mask for visualizing just the brain (ignores the skull) for the middle slice of the imaging volume., File: rois.mat Contains masks for various regions of interest (ROIs), used for computing statistics. Keys "mtopleft", "mtopright", "mbottomleft", and "mbottomright" refer to the corresponding locations on the anatomical reference image (see related paper). Key "mic" refers to the internal capsules, and key "mgm" refers to a gray matter ROI., The raw data files (P-files) can be read into the Julia programming language using the Julia version of the Michigan Image Reconstruction Toolbox ( https://github.com/JeffFessler/MIRT.jl) or into MATLAB using TOPPE ( https://github.com/toppeMRI/toppe). The reconstructed slices used in the related paper are provided for convenience, and are stored in .mat files that can be loaded into Julia (using the package MAT.jl) or MATLAB, and a .jld file that can be loaded into Julia (using the package JLD.jl). The Julia code for processing the data to create MWF maps is hosted publicly on GitHub at https://github.com/StevenWhitaker/STFR-MWF., and Files: toppe-master.zip and MIRT.jl-master.zip are archived versions of the TOPPE and Michigan Image Reconstruction Toolbox code sets from GitHub as of 2/28/2020.
- Keyword:
- myelin, machine learning, kernel learning, magnetic resonance imaging, and scan design
- Citation to related publication:
- Whitaker, S. T., Nataraj, G., Nielsen, J.-F., & Fessler, J. A. (2020). Myelin water fraction estimation using small-tip fast recovery MRI. Magnetic Resonance in Medicine, 84(4), 1977–1990. https://doi.org/10.1002/mrm.28259
- Discipline:
- Health Sciences and Engineering
-
- Creator:
- Batterman, Stuart; University of Michigan
- Description:
- We evaluated PM levels at the Agbogbloshie e-waste and scrap yard site in Accra, Ghana, and at upwind and downwind locations. This monitoring forms part of the West Africa-Michigan Charter II for GEOHealth cohort study, which is analyzing occupational exposures and health risks at this site.
- Keyword:
- Air pollution, particulate matter, e-waste, Fires, and monitoring
- Citation to related publication:
- Kwarteng, L., Baiden, E. A., Fobil, J., Arko-Mensah, J., Robins, T., & Batterman, S. (2020). Air Quality Impacts at an E-Waste Site in Ghana Using Flexible, Moderate-Cost and Quality-Assured Measurements. GeoHealth, 4(8), e2020GH000247. https://doi.org/10.1029/2020GH000247
- Discipline:
- Health Sciences and Engineering
-
- Creator:
- Crisp, Dakota N., Parent, Rachel, Nakatani, Mitsuyoshi, Murphy, Geoffrey G. , and Stacey, William C.
- Description:
- This data and scripts are meant to test and show that seizure onset dynamics can be modulated using anti-epileptic drugs. A zip file is included that contains all waveform data, MATLAB processing scripts, and metadata. The MATLAB scripts allow for visual review validation and objective feature analysis. The file includes various README files explaining the scripts and their relationships in greater detail.
- Keyword:
- Bifurcation, Epilepsy, Seizure, and Electrophysiology
- Discipline:
- Health Sciences, Engineering, and Science
-
- Creator:
- Payam Mirshams Shahshahani
- Description:
- The two R codes are related to the feasible balance region calculations for Figures 2, 3, and 4 in the paper. The MATLAB codes are related to the simulations of the recoverable initial quasi-static states, the results of which are shown in Figure 5 of the paper.
- Keyword:
- One-legged balance, Biomechanics, Hip Abductor, and Unipedal Stance
- Citation to related publication:
- Shahshahani, P. M., & Ashton-Miller, J. A. (2020). On the importance of the hip abductors during a clinical one legged balance test: A theoretical study. PLOS ONE, 15(11), e0242454. https://doi.org/10.1371/journal.pone.0242454
- Discipline:
- Health Sciences and Engineering
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