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Selecting another target spike train and repeating the calculation of the influence strengths from the reference spike trains enables researchers to find all functional connections among multiple spike trains.
We computed cISI as follows: for each reference spike (x), the closest subsequent spike (y) is considered; if it falls before a new reference spike, then cISI is computed as their time difference, otherwise it is not accounted.
Cross-Correlation computed on two neurons is essentially proportional to the amount of spikes present in a time window around a reference spike.
However, by evaluating MI of time-delayed time series (e.g. by taking X as the reference spike train and Y as the delayed spike train), we build a MI function of the time-shift, thus providing information both on the synaptic strength and on causality [17], [37].
The reference spike mix was a mixture of 500 pg of each RNA.
In this method, exact coincidences (within the time resolution h = 0.1 ms of the data) are detected for a range of shifts between − b and + b of the second spike train against the first (reference) spike train.
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A related reference (spiking neurons with partial reset) is [38].
Despite other approaches are also possible (e.g. when two reference spikes are followed by just one spike two cISIs could be computed), the method we used yielded the best results.
Two-color Agilent protocols were used for all samples, with Cy3-labeled reference produced from total RNA from Stratagene Universal Human Reference (spiked 1 1000 with MCF-7 RNA and 1 1000 with ME16C RNA to increase expression of breast cancer genes) and Cy-5 labeled patient specimens.
Cy3-labeled reference was produced from total RNA from Stratagene Universal Human Reference (spiked with 1 1,000 with MCF-7 RNA and 1 1,000 with ME16C RNA to increase expression of breast cancer genes) following amplification with Agilent Quick Amp labeling kit following the manufacturer's protocol with minor modifications as described in Hu et al. [ 19].
A fast-isotope switching capability has been incorporated in the system, allowing flexibility in isotope selection and for the quasi-continuous normalization to a reference isotope spike.
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