Matlab release2012a

Manufactured by MathWorks

Sourced in United States

MATLAB Release2012a is a software package designed for numerical computing and visualization. It provides a programming environment for analyzing data, developing algorithms, and creating custom applications. MATLAB Release2012a includes a range of tools and functions for mathematical, engineering, and scientific computing.

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306 channel whole head meg system, by Elekta (1 mentions)

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5 protocols using matlab release2012a

Modeling Neuronal Energy Metabolism

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We simulated FAD transients and ATP consumption rates associated with ILEs and SLEs with a metabolic model of neuronal energy metabolism [19 (link)]. Using the OCRs obtained from pO₂ measurements during bicuculline and bicuculline plus XE-991 under interface conditions and assuming feasible cytosolic calcium transients we determined ATP consumption rates for the different conditions by using the maximal ATP consumption rate as adjustable parameter. We validated the model prediction by comparing the predicted FAD transients with experimental data obtained during the events under submerged conditions. For all simulations we used MATLAB Release2012a (The MathWorks, Inc., Natick, MA, USA) with the optimization tool box.

Schoknecht K., Berndt N., Rösner J., Heinemann U., Dreier J.P., Kovács R., Friedman A, & Liotta A. (2017). Event-Associated Oxygen Consumption Rate Increases ca. Five-Fold When Interictal Activity Transforms into Seizure-Like Events In Vitro. International Journal of Molecular Sciences, 18(9), 1925.

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Automated Waveform Analysis Pipeline

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The peak velocity over the cross section as a function of time, V_p(t), was obtained from the waveform ultrasound images using custom scripts written in the MATLAB Release 2012a environment (The MathWorks, Inc., Natick, Massachusetts, United States.). The scripts were designed to automate the process of the detection of the waveform envelope so as to minimize user interaction and lessen human bias. The characteristic metrics for each period were visually checked in an automatically generated figure, e.g. Figure 1. Some of the images were either of too poor resolution to be analyzed or not possible to be analyzed using the automated software and were thus excluded from the study. The metrics of the individual periods comprising the ensemble waveforms (consisting of three to eight periods per waveform) were simply averaged to produce period-averaged waveform metrics. Period-averaged waveforms which were produced for latter use in the study were produced by aligning the normalized waveforms by their maximum velocity to avoid artificial rounding or flattening of the systolic peaks which was otherwise unavoidable in many cases.

Durka M.J., Wong I.H., Kallmes D.F., Pasalic D., Mut F., Jagani M., Blanco P.J., Cebral J.R, & Robertson A.M. (2018). A data driven approach for addressing the lack of flow waveform data in studies of cerebral arterial flow in older adults. Physiological measurement, 39(1), 015006.

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Multilayer Metabolic Model of Brain Tissue

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We modeled the tissue as 10 concentric layers of neuronal cells surrounding a central supporting blood vessel. The tissue thickness was assumed to be 35 µm corresponding to the average inter-capillary distance of rodent brain [45 (link)]. Again, each layer was equipped with the metabolic model described above and it was assumed that the specific activity of all metabolic enzymes was equal in each layer. We modeled oxygen and glucose supply by diffusive transport between vessel and the first layer and by diffusion between the layers. It was assumed that the outflow of blood from the vessel was equal to the inflow of blood into the vessel in all conditions so that no accumulation of blood in the considered region occurs. Partial oxygen pressure in the blood was set at 50 mmHg and glucose concentration was set as 2.4 mM under standard conditions.
For technical details and all rate equations see [39 (link)]. All simulations were made using MATLAB Release2012a (The MathWorks, Inc., Natick, MA, USA).

Berndt N., Kovács R., Rösner J., Wallach I., Dreier J.P, & Liotta A. (2020). Flavin Adenine Dinucleotide Fluorescence as an Early Marker of Mitochondrial Impairment During Brain Hypoxia. International Journal of Molecular Sciences, 21(11), 3977.

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Magnetoencephalography Protocol for Brain Connectivity

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Magnetoencephalography (MEG) measurements were recorded using a 306-channel, whole-head MEG system (ElektaNeuromag Oy, Helsinki, Finland) in a magnetically shielded room (Vacuumschmelze GmbH, Hanau, Germany). Participants were instructed to lie on a bed with their eyes closed but to stay awake and reduce eye movements in order to minimize artifacts. Participants were scanned for 5 min with eyes closed, 2 min with eyes open, and another 5 min with eyes closed. On MEG we used source-reconstructed time series (10.1016/j.neuroimage.2011.11.005) to extract both frequency spectrum properties (relative band power and peak frequency) and functional connectivity between regions, as well as network topology using modern network theory (synchronization likelihood, modularity, path length, phase lag index) [79 (link), 80 (link)]. These analysis techniques were applied using BrainWave software (http://home.kpn.nl/stam7883/brainwave.html) [81 (link)] and inhouse MATLAB scripts (MATLAB Release 2012a; The MathWorks, Inc., Natick, MA, USA).

Konijnenberg E., Carter S.F., ten Kate M., den Braber A., Tomassen J., Amadi C., Wesselman L., Nguyen H.T., van de Kreeke J.A., Yaqub M., Demuru M., Mulder S.D., Hillebrand A., Bouwman F.H., Teunissen C.E., Serné E.H., Moll A.C., Verbraak F.D., Hinz R., Pendleton N., Lammertsma A.A., van Berckel B.N., Barkhof F., Boomsma D.I., Scheltens P., Herholz K, & Visser P.J. (2018). The EMIF-AD PreclinAD study: study design and baseline cohort overview. Alzheimer's Research & Therapy, 10, 75.

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Simulating Neuronal Energy Metabolism

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We used a metabolic model of neuronal energy metabolism (Berndt et al. 2015 (link)) to simulate stimulus-induced FAD transients and ATP consumption rates. Using the CMRO₂s obtained from pO₂ measurements under interface conditions and assuming feasible cytosolic calcium transients, we determined ATP consumption rates for the different conditions using the maximal ATP consumption rate as adjustable parameter. For all simulations we used MATLAB Release2012a (The MathWorks, Inc., Natick, MA, USA) with the optimization tool box.

Berndt N., Rösner J., Haq R.U., Kann O., Kovács R., Holzhütter H.G., Spies C, & Liotta A. (2018). Possible neurotoxicity of the anesthetic propofol: evidence for the inhibition of complex II of the respiratory chain in area CA3 of rat hippocampal slices. Archives of Toxicology, 92(10), 3191-3205.

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