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The Shaffer papers include ten document series including correspondence, diaries, scrapbooks, short publications, notes, and his Ph.D. dissertation. Major subjects are his research work in biochemistry and the administration of WUSM as dean and head of the Department of Biological Chemistry. His work with Barnes Hospital, St. Louis Children’s Hospital, American Society of Biological Chemists and the U. S. Army in World War I are also subjects.

In 2006, this collection contained many deteriorated brittle carbon copies on newsprint and newspaper clippings that chipped or fractured with minimal handling. The acidic newsprint had stained surrounding documents and was losing contrast due to browning. Archives staff made acid-free photocopies to preserve content and contrast for future use and preservation microfilming.

This collection includes items related to Barnes Hospital. From the bequest which funded the creation of the hospital; to the hospital’s opening at the end of 1914; and continuing up to and beyond its merger with Jewish Hospital in 1996, the history of Barnes Hospital is documented in a variety of material formats. The collection includes administrative records; staff correspondence; hospital publications; newspaper and magazine clippings; scrapbooks; photographs; VHS tapes; and artifacts. Of note is the collection of hospital publications (series 4), which includes serial magazines and annual reports of the hospital, as well as ephemera such as brochures and flyers. Also noteworthy is the hospital superintendent’s correspondence collection (series 3) covering the years 1913-1926; the hospital’s book of forms from the year of its opening (series 1); a scrapbook containing correspondence of Robert A. Barnes and the original trustees of Barnes Hospital (series 8); and the Hospital's Staff Register covering October 13, 1915 to January 13, 1958 (series 5).