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Bagian left NASA in 1995. He was elected to membership in the National Academy of Engineering and the Institute of Medicine. Bagian was the Veterans Health Administration (VHA) Chief Patient Safety Officer, and Director of the VA National Center for Patient Safety.

Bagian served as the Lead Mission Specialist on the crew of STS-40 Spacelab Life Sciences, the first dedicated space and life sciences mission, which launched from the Kennedy Space Center, Florida, on June 5, 1991. SLS-1 was a nine-day mission during which crew members performed experiments which explored how the heart, blood vessels, lungs, kidneys, and hormone-secreting glands respond to microgravity, the causes of space sickness, and changes in muscles, bones, and cells which occur in humans during space flight. Other payloads included experiments designed to investigate materials science, plant biology and cosmic radiation. In addition to the scheduled payload activities on STS-40, Bagian was successful in personally devising and implementing repair procedures for malfunctioning experiment hardware which allowed all scheduled scientific objectives to be successfully accomplished. Following 146 orbits of the Earth, Columbia and her crew landed at Edwards Air Force Base, California, on June 14, 1991. Completion of this flight logged him an additional 218 hours in space.

Bagian first flew on the crew of STS-29, which launched from Kennedy Space Center, Florida, aboard the Orbiter Discovery, on March 13, 1989. During this highly successful five-day mission, the crew deployed a Tracking and Data Relay Satellite and performed numerous secondary experiments, including a Space Station -heat pipe" radiator experiment, two student experiments, a protein crystal growth experiment, and a chromosome and plant cell division experiment. Bagian was the principal investigator and performed Detailed Supplementary Objective 470 which described, by the use of transcranial Doppler, the changes of cerebral blood flow and its relationship to Space Adaptation Syndrome (SAS) and Space Motion Sickness (SMS). Bagian was the first person to treat SMS with the drug Phenergan by intramuscular injection. This represented the first successful treatment regimen for SMS and has now been adopted by NASA as the standard of care for the control of SMS in Shuttle crews and is routinely used. In addition, the crew took over 3,000 photographs of the Earth using several types of cameras, including the IMAX 70 mm movie camera. Mission duration was 80 orbits and concluded with a landing at Edwards Air Force Base, California, on March 18, 1989. With the completion of this mission, he logged over 119 hours in space.

Bagian became a NASA astronaut in July 1980. He took part in both the planning and provision of emergency medical and rescue support for the first six Shuttle flights. He served as the Astronaut Office coordinator for Space Shuttle payload software and crew equipment, as well as supporting the development of a variety of payloads and participating in the verification of Space Shuttle flight software. In 1986, Bagian served as an investigator for the 51-L accident board. He was responsible for the development program and implementation of the pressure suit used for crew escape and various other crew survival equipment to be used on future Shuttle missions, and is in charge of Shuttle search and rescue planning and implementation for the Astronaut Office. Bagian was a member of the NASA Headquarters Research Animal Holding Facility Review Board. He has authored numerous scientific papers in the fields of human factors, environmental and aerospace medicine. A veteran of two space flights (STS-29 in 1989 and STS-40 in 1991), Bagian has logged over 337 hours in space. In 2003 Bagian served as the Chief Flight Surgeon and Medical Consultant for the Columbia Accident Investigation Board and currently serve as a member of the NASA Aerospace Safety Advisory Panel.

Bagian worked as a process engineer for the 3M Company in Bristol, Pennsylvania, in 1973, and later as a mechanical engineer at the U.S. Naval Air Test Center at Patuxent River, Maryland, from 1976 to 1978, and at the same time, pursued studies for his medical degree. Upon graduating from Thomas Jefferson University in 1977, Bagian completed one year of general surgery residency with the Geisinger Medical Center in Danville, Pennsylvania. He subsequently went to work as a flight surgeon and research medical officer at the Lyndon B. Johnson Space Center in 1978, while concurrently completing studies at the USAF School of Aerospace Medicine in San Antonio, Texas where he graduated first in his flight surgeons class. He was completing a residency in anesthesiology at the University of Pennsylvania when notified of his selection by NASA for the astronaut candidate program. Bagian received his Professional Engineers Certification in 1986, and was board-certified in aerospace medicine by the American College of Preventive Medicine in 1987. Since 1981, Bagian has been active in the mountain rescue community and has served as a member of the Denali Medical Research Project on Mt. McKinley. He has been a snow-and-ice rescue techniques instructor on Mount Hood during this period. Bagian is a colonel in the U.S. Air Force Reserve and is the pararescue flight surgeon for the 939th Air Rescue Wing. He is a USAF-qualified freefall parachutist, holds a private pilot's license and has logged over 1,500 hours flying time in propeller and jet aircraft, helicopters, and gliders.

Bagian graduated from Central High School in Philadelphia, Pennsylvania, in 1969; received a Bachelor of Science degree in mechanical engineering from Drexel University in 1973, graduating first in his class, and a Doctor of Medicine degree from Thomas Jefferson University in 1977, where he was a member of Alpha Omega Alpha.

James Philip Bagian, MD, PE (born 22 February 1952), is an American physician, engineer, and former NASA astronaut of Armenian descent. During his career as an astronaut, he logged 337 hours of space-flight, over two missions, STS-29 (in 1989) and STS-40 (in 1991). After leaving NASA in 1995, Bagian was elected as a member of both the National Academy of Engineering and of the Institute of Medicine. Bagian is currently the Director of the Center for Healthcare Engineering and Patient Safety at the University of Michigan.