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Susan should approach her advisor again in efforts to learn more about the publication expectations. Engaging in further discussion with the advisor is the ideal way to resolve the issues. The power dynamic between advisor and student may make Susan reluctant to go against lab practices.  If the advisor refuses to address the matter, Susan can seek assistance from various resources on campus. 

Yes, this situation could be considered research misconduct. Falsification or fabrication of data, such as manipulating raw images without clear explanations or misrepresenting findings, falls under the SCRM definition of research misconduct.

Ideally, she would approach her advisor again to review the significance of the changes, impact on the manuscript and explore opportunities to correct the error. Many journals now require authorship contributions to be noted and require all authors agree to the content of the manuscript prior to acceptance.  Should the advisor not be welcoming, she can speak with trusted faculty, the department chair, or the office of research integrity for guidance.  If this was an NIH or NSF sponsored research award, she should also review her Responsible Conduct of Research notes as these provide guidance and resources for related concerns.

Susan could formalize a complaint by reaching out to the Research Integrity Officer (within ORI). If she feels uncomfortable due to the nature of her relationship with her advisor, she has a few options:

• Anonymous Complaint: Susan can submit an anonymous complaint, ensuring that her identity remains confidential.
• Trusted Faculty or Department Chair: Alternatively, she can ask a trusted faculty member or the department chair to make the complaint on her behalf. This way, she can be considered a witness to the procedures and receive protection from reprisals while discussing her concerns related to the manuscript.

No, there is no strict requirement to file a formal complaint. It is often more effective and efficient to address these concerns within the lab and with the assistance of co-authors. Corrections, such as issuing an erratum or retraction, can be made by the journal. However, if Susan chooses not to act, there is always the possibility that someone else may discover the issues and file a formal complaint. In such a scenario, Susan could become a respondent, potentially impacting the success of the manuscript and her educational process. (COPE) is a non-profit either group committed to educating and supporting editors, publishers, universities, research institutes, and all those involved in publication ethics.