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San Fran gets the breezes blowing in from the ocean and not a lot of heavy industry.
Chicago has wind blowing in off the lake, or in the summer it blows in from the west with nothing to stop it. Everything just blows away. Also a great deal of public transit usage.
Minneapolis doesn't have a lot of industry, and it's a fairly windy city.
Boston is probalby the lack of heavy industry, the fact it is on average more windy than Chicago (which is the windy city, even though it's nowhere near the top US city as far as wind), and tends to have a higher usage of public transit.
-7 Pittsburgh is often ranked right up there with LA
The wind brings it in from other areas.
American Lung Association:*SOTA05 Best and Worst Citites (http://lungaction.org/reports/sota05_cities.html - broken link)
I'd give Baton Rouge a 4.5-5 (10 being good in my ranking). We have ozone issues, but not nearly as bad as say Houston. We also have Exxon-Mobil in our back yard which doesn't help and they mainly contribute to said ozone issues. More times than not our AQ isn't as bad as I'm sure it could be.
Oh, I forgot, sugarcane harvest season. Now I give BTR a 3. (but only during the harvest season)
Last summer during one of my runs the smog was so bad that I coughed my Propel back up all over the roadway. There have been many times where we can't utilize our rear patio in the summer due to the diesel exhaust fumes from the adjacent freeway. I worry all the time about developing asthma. Being so near to the BosWash Corridor has its advantages, but air quality is certainly not one of them.
Tri-Cities, WA is normally clean. Wind often keeps smog away. But its a valley, and as a developing metro on stagnant days it gets dirty and after a couple weeks it can start to resemble LA! Also there are forest fires in the summer but overall its a 7-8, on stagnant days a 4 and forest fire days a 2.
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(but only during the harvest season) 
