It's good that UP is doing things to clean up diesel emissions.
About a year or two ago I was on the hunt for vintage phono radio consoles. One of them was in West Oakland downwind from the railyards and the port. I was appalled at how bad the air was compared to my home's location, which was only about 10 miles away. I figure a lot of the pollution is from the trains as well as from trucks idling as they wait to pickup containers etc. Maybe some from the ships as well.
On another train related note, I understand that Santa Clara County voters have very narrowly approved the latest funding measure to ensure that BART is extended into San Jose. This is an important milestone; I commuted from the East Bay down to Milpitas/San Jose for eight years and it became a real horror story trying to fight traffic. Some Fridays after work it would take me 2 hours to go 25 miles. I finally started riding my bicycle five miles to the Hayward Capitol Corridor station, and then another three miles from the Great America station to my workplace, just to avoid the commute drive. Great exercise, 16 miles a day, but not exactly the safest (along expressways, etc, and at one point I would have to carry the bike along a dirt path under an overpass by the Guadalupe). The biggest problems were the late CC trains, overcrowded cars, no place to put the bikes, and surly conductors. The last BART stop in Fremont was too far away to make a bike commute feasable, and after I got laid off in 2002 I refused to look for work in the area, but I would consider working down there again if BART ran into downtown San Jose.