"We feel that this validates the work that we do here: high expectations in academic achievement and behavior for every single student," Japzon said. He said, however, that "our staff views the MSA and meeting AYP as minimal standards, and as one snapshot to measure the success of our students."
State officials identify special education as Maryland's biggest challenge. And a small number of special-education students caused several of the city's highest-performing schools to fall short of the goal. Among them was Roland Park Elementary/Middle School, which also noted 100 percent proficiency in two grade levels this year.
Alonso said that he believed the district's stepped-up test monitoring after recent cheating investigations could have been a factor in some schools failing to make AYP in special education. Those students are allotted special accommodations, such as verbatim reading of the tests or extra time.
"In an area where there may have been room for accommodations," he said, "we created this environment that we were so conscious about that line, people didn't go to it."
Despite the flaws of NCLB, city school leaders take the missed targets seriously.
"It only took one or two children not doing as well as we had hoped, but we're looking at the whole picture," said Edna Greer, principal of Leith Walk Elementary, which did not make AYP in special education. "We do not get to pick and choose, and we don't differentiate between children. We have to make sure all of our children are at the levels they should be."
Leith Walk, which tests and serves one of the largest general and special-education populations in the city — the overwhelming majority of whom are poor and minority — has consistently posted high proficiency marks. This year, the scores were in the 80s and 90s.
Greer said her staff has begun to pull students' individualized education plans and will comb through the data to figure out where special-education students fell short.
"It just means we have to go back to the drawing board," Greer said. "We get all bent out of shape about test scores sometimes, but the main thing is that the kids are learning."
While Alonso says that's the kind of philosophy he wants to see adopted throughout the district, he added that there are still a number of schools that will continue to be negatively affected by the AYP pressure.
"There will always be a set of consequences related to this, but we have always tried to be incredibly flexible," Alonso said. "When the standard labels a school as not achieving, and that school is actually making progress for kids, it can be incredibly harmful to the culture of the school."
As a result of this year's results, the city now makes up 40 percent of the state's school improvement list. Schools on the list have not met AYP for two years in a row. There are 77 city schools on the list, 31 of which could be subject to radical reforms in the coming years, such as overhauling their curriculums and staff.
Five city schools went into the MSA tests knowing that their staffs' jobs and their schools' structures were on the line. The city school board voted in March to approve drastic improvement plans for the schools to begin implementing this year if they didn't make AYP. None did.
The decision sparked a debate among school board members about whether the district will be in complete unrest by 2014 as more schools are targeted for mandated interventions.
City school board Commissioner David Stone recommended during the debate that the city reject the federal dollars — about $133 million, which accounts for 13 percent of the school system's $1.2 billion budget — to be exempt from requirements of the No Child Left Behind law.
"I think that the important thing is that the system be the main judge of whether schools are successful, not one test from 50 miles down the road," he said.
"We can't be held hostage on goals that are unachievable. I know there are schools on that list that did many of the things who anyone in education would say were best practices, so to say they're not doing their job is just a shame."
Baltimore Sun reporter Liz Bowie contributed to this article.
Number of city schools missing academic targets surges
Highest achieving schools in the city among those that fell short of controversial AYP standards
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