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Background  Successful implementation of new clinical programs depends on effectively establishing, reorganizing, or enhancing team structures and processes to coordinate the work of individuals who are interdependent in their tasks, manage relationships, and share responsibility for outcomes. However, a one-size-fits-all approach is rarely effective. In partnership with VA national clinical leaders and local clinical champions, the Optimizing Function and Independence VA Quality Enhancement Research Initiative program (Function QUERI) will evaluate efforts to implement team-based clinical programs for Veterans at risk for functional decline and disability.    Methods  Function QUERI will implement and evaluate three innovative, evidence-based clinical programs in VA medical centers: (1) a group physical therapy program for knee osteoarthritis (Group PT); (2) assisted early mobility for hospitalized older veterans (STRIDE), a supervised walking program for hospitalized older veterans; and (3) implementation of helping invested family members improve veteran experiences study (iHI-FIVES), a skills training program for caregivers of disabled Veterans. A common reason for clinical care gaps in these populations is poor communication and coordination among the many interdisciplinary providers involved in their care. To facilitate the implementation of the clinical programs, Function QUERI will evaluate the impact of complexity science-based implementation intervention to promote team readiness (CONNECT), an implementation intervention designed as a bundle of interaction-oriented activities to promote team function and readiness for change, on the implementation of clinical programs across multiple sites. The evaluation will use a mixed methods design. Group PT is a local, single-site quality improvement project where a modified CONNECT intervention will be tested to inform the remaining program implementation projects. For STRIDE and iHI-FIVES projects, we will randomize participating sites to implement the clinical program, with the CONNECT intervention or not, and will use a stepped-wedge cluster randomized trial design.    Discussion  Function QUERI will translate its findings across its projects to identify the contextual factors and components from CONNECT that improve team processes and function to optimize effective implementation for future rollout of VA clinical programs. Synthesizing findings within and across projects, we will specify dimensions of team characteristics and function that enhance capacity for clinical innovation and uptake of evidence-based programs.    Trial registration   NCT03300336  Registered September 28, 2017,  NCT03474380  Registered March 15, 2018.    Electronic supplementary material  The online version of this article (10.1186/s13012-018-0748-3) contains supplementary material, which is available to authorized users.

Supporting teams to optimize function and independence in Veterans: a multi-study program and mixed methods protocol