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This investigation aimed to evaluate the influence of three different soft tissue environments on onlay bone graft incorporation into the craniomaxillofacial skeleton and to follow this process immunohistochemically by staining for some bone and cartilage matrix proteins and proteoglycans.Femoral and tibial bone grafts, either uni- or bicortical, were placed subperiosteally, submuscularly, and intramuscularly in 36 identically sized and aged isogeneic rats. The results were evaluated after 4, 12, and 20 weeks.Corticocancellous grafts showed a more extensive incorporation and more pronounced local resorption. Bicortical grafts produced more resorption of the recipient site, which oftentimes resulted in the graft being almost level with the surrounding bone. The marrow space of both graft types was sealed off by compact bone formation. Intense labeling of tested bone matrix proteins at various parts of the graft-host area was demonstrated. Ultimate graft height was significantly reduced for most groups, but no major differences between groups were registered. Intramuscularly positioned control grafts ultimately showed signs of lacking viability and reduced labeling of cartilage matrix proteins.These findings indicate that either type of graft had its drawbacks and that further studies to enhance integration and size maintenance are necessary to improve overall graft persistence. Immunolabeling may help to identify essential mechanisms in and find markers of graft incorporation.