Cis and trans electrodes
Sometimes authors use buzz words in their paper in order to make their work novel or fancier than it should be. However, such newly coined terms never get popular and vanish with the author into oblivion. No, cis and trans can never mean cathode or anode. It refers to the chambers in which the electrode is place.
I looked up the Oxford's Latin Dictionary:
cis has three meanings

(in time) before, within
(in space) on the near side of, on this side of
(expressing motion) to the near side of

trans

to the other side of

Now look at the cell configuration in your link. The very first lines of the paper you linked says

DNA translocation through protein or synthetic solid state nanopores
is a two stage process that involves capture of a DNA coil by the pore
including its delivery to the pore and insertion of one of its ends
into it, followed by its motion through the nanochannel. The process
may be driven by voltage $\Delta$V typically a few hundred millivolts
applied between two macroscopic electrodes positioned on both sides of
the partition separating the cis where DNA is initially placed and the
trans to where it translocates through the pore chambers, as shown
schematically in Fig. 1