The minimal fluorescence intensity threshold value was set to only include prominent punctate or vesicle-like structures, and integrated morphometric analysis was used to measure their total area in each of the 16 36 cells per Cx group that were derived from two independent cultures.
From raw files, MS/MS spectra were exported as dta (text format) files using the script extract_msn.exe (Thermo Fisher Scientific) under the following settings: peptide mass range: 500 3500; minimal total ion intensity threshold: 1000; minimal number of fragment ions: 15; precursor mass tolerance: 1.4 amu; group scan: 1; minimum group count: 1.
From raw files, MS/MS spectra were exported as individual files in DTA format using extract_msn.exe program contained within Bioworks v3.2 software (Thermo Electron) under the following settings: peptide mass range: 500 4000; minimal total ion intensity threshold: 10000; minimal number of fragment ions: 15; precursor mass tolerance: ± 1.4 amu; group scan: one; with a minimum group count of one.
For the analysis, the user can specify both a general signal intensity threshold and a minimal number of pixels required above that threshold for positive counts.
In clinical practice and in scientific studies, corticospinal excitability is estimated objectively by examining the cortical motor threshold (or resting motor threshold, RMT), which is the minimal intensity of motor cortex stimulation required to elicit a MEP of minimal amplitude in the relaxed target muscle.
Once this site was identified the resting motor threshold was determined as the minimal intensity of stimulation that produced MEPs larger than 50 µV in 50% of the stimulations delivered to this site.
Motor threshold was defined as the minimal intensity of stimulation capable of inducing MEPs of more than 50 uV in at least six out of ten trials, during which the subjects maintained complete muscle relaxation, as documented by the electromyogram recording from at least 200 ms prior to TMS.
In Exp1M1right and Exp2M1left, the intensity of magnetic pulses was set at 125 % of the resting motor threshold (rMT), defined as the minimal intensity of stimulator output that produces MEPs with an amplitude of at least 50 μV from the muscle with 50%% probability (using about 20 pulses).
The Otsu method objectively estimates the intensity threshold from the histogram of all intensities to get minimal variance both above and below threshold.
The Otsu method estimates the intensity threshold from the histogram of all intensities to get minimal variance both above and below threshold.
