At least, I think it's some kind of popup. Here's a screen shot, it's the box with the "MT" on the left.
The box is not really a popup, or at least doesn't behave like one--I can't close it and it stays always on top of any window. The story it displays does change. I'm running Chrome. I don't see anything that shouldn't be there in the extensions. I'm running Debian Jessie with Gnome 3.14.1. I don't see anything obviously fishy in running processes, though I'm no expert. I have restarted and it's still there. I believe it does not appear until I open chrome.
EDIT: In some respects the box behaves as if it's not there: if I click on certain parts of it, the click will act on whatever the box is covering. But if I click right on the text it opens a tab in chrome displaying the article that the box is previewing.