Not sure I follow. But If I got this correct you ssh into a university server to view journals. Are these on the server? if they are on the server that you ssh into then you can use the scp command.
scp <file path>/<filename> username@remotehost:<directory path>/<filename>
scp /home/jstephens84/article.pdf firstname.lastname@example.org:/home/someuser
that would copy the article.pdf from the local server to a remote server.