This is part of our year-end series, looking at where things stand in each of our major investigations.

For the past two years, ProPublica and NPR have collaborated on an investigation that looks in-depth at the military's handling of traumatic brain injuries, a signature wound of the conflicts in Iraq and Afghanistan.

More than 115,000 soldiers have sustained mild traumatic brain injuries, also called concussions, in the wars when shock waves from bombs rippled through their brains. Most have recovered quickly, but some have suffered lasting cognitive problems, from headaches and dizziness to problems with memory and reasoning.

As a result of our work, Congress and government investigators have pressed the Defense Department to fix flaws that have prevented troops with TBIs from being properly diagnosed and treated.

In January, Sen. Claire McCaskill, D-Mo., questioned the Pentagon's decision to deny cognitive rehabilitation therapy to troops with brain injuries. Her inquiry came after a story we did about how the Pentagon based its decision not to pay for such care on a much-criticized report from the ECRI Institute. Following the story and McCaskill's inquiry, the Pentagon solicited the help of the Institute of Medicine, which released a report in October urging the Defense Department to do more research on the therapy before offering it more broadly.

Investigators at the U.S. Government Accountability Office have also scrutinized military programs developed to address brain injuries. In a February report, the GAO said that the Pentagon's Defense Centers of Excellence was plagued by weak leadership, uncertain priorities and flawed accounting. The DCOE, which was created after a 2007 Washington Post series exposed the poor living conditions of concussed troops at Walter Reed Army Medical Hospital, couldn't explain exactly how much taxpayer money it received or how it was spent, the GAO report said.

In March, the Army responded to a story we published last year about how soldiers had been denied Purple Hearts after suffering concussions on the battlefield. The Army issued new guidance, making it easier for brain-injured soldiers to get recognition.

Among the reasons the military has struggled to treat brain-injured troops, one of the most obdurate is a lack of neurologists, according to interviews and documents we obtained earlier this year. Policies issued in June 2010 requiring soldiers to receive a comprehensive evaluation when they suffer three or more mild traumatic brain injuries in one year have intensified the need for qualified doctors.

Plus, as we reported in May, more than half of all Iraq and Afghanistan veterans treated in Department of Veterans Affairs hospitals since 2002 have been diagnosed, at least preliminarily, with mental health problems.

One such veteran is Brock Savelkoul, a troubled young man who survived a blast in Iraq. Back home in North Dakota, he embarked on an equally harrowing journey that ended in an armed standoff with local law enforcement officers, who spent hours persuading him not to commit suicide.

Savelkoul, who we featured in a Kindle Single earlier this year, was one of about 300 troops examined in a study conducted by then-Lt. Col. Mike Russell, the Army's leading neuropsychologist. Russell presented his findings in November 2009 and concluded that a computer test being used to evaluate whether soldiers had suffered concussions was "only slightly better than a coin toss."

Russell was referring to the Automated Neuropsychological Assessment Metrics, or ANAM, which the military has given to 1 million troops since 2008 in response to an order from Congress.

Last month, we published a story about how the military came to spend $42 million on the ANAM program, despite the fact that the test was never scientifically proven to detect brain injuries. As part of our investigation, we released a withering report on the ANAM that Russell delivered to members of Congress, which was not previously available to the public. In his critique, Russell lambastes nearly every aspect of the program, saying that "the selection of ANAM was nepotistic, and the long delay in examining alternative instruments is baffling."

Following our story, McCaskill began an investigation into contracts surrounding the ANAM program. Rep. Bill Pascrell, D-N.J., co-chairman of the Congressional Brain Injury Task Force, proposed an amendment to the 2012 National Defense Authorization Act to help fix the beleaguered testing program, but it was pulled from the legislation. Pascrell is now pushing for a large increase in funding for the military's TBI services in this year's appropriations bill.