This touches on my area of research. The 'pyramid' idea of brain function is essentially a straw man to jazz up the Science Daily article. It's been known for a long time (a century) that recurrent loops occur throughout the brain. The mystery is what these loops do, given the apparent hierarchical buildups of representation that seem to occur in sensory systems, particularly the visual system. (Also in the hippocampus, e.g. place cells, and other areas in all likelihood.)

I haven't read the paper thoroughly (http://www.pnas.org/content/early/2010/07/28/1009112107), but looks like the authors are using a strategy of systematic and tightly circumscribed injections of anterograde & retrograde tracers to map out, with unusually high precision, the inter-areal projections for a particular circuit they're interested in. This mapping of inter-areal connectivity is a little different from what I'm interested in, which is to understand how the many-to-many anatomical wiring diagram between individual neurons in a neuronal network relates to the transformation of information carried out by that network. In other words, they are mapping connections between areas, but I think it's likely that an additional level of resolution -- the mapping of connections at the level of individual neurons -- will likely be necessary (and probably insufficient) to crack brain circuits.