Tier 1: Scientific Paper Review

The purpose of the Tier 1 qualifying exam is to demonstrate whether a Ph.D. candidate has mastered basic knowledge in the biological sciences and has developed the critical thinking skills to evaluate various aspects of a research project that are necessary to complete a Ph.D. degree.

Scientific Paper Review format: The exam is delivered as a manuscript critique and will be administered at the end of fall semester of your second year in the program. One week before the exam, students will be provided with a PDF of a published research article and any supplemental materials associated with that article. Students will have the opportunity to read this article and research background information about prior studies that lead to the current paper, technical aspects of the methods used in the paper and aspects of the findings of the paper and their translational potential.

Exam Administration:  The test is closed book, invigilated and access to the internet is not allowed. Students are permitted to use personal computers as well as make appropriate supplemental diagrams outlines or drawing on paper to compose responses. The exam will be limited to three hours. Test questions are designed to assess the following aspects of the selected paper:

1. Hypothesis: What is the central hypothesis that is tested in the research study?
2. Background: The background basic knowledge and specific prior finding upon which the current hypothesis is based.
3. Research methodology. a) What are the basic scientific principles that underlie the research methodology that were used? b) What are the specific technical principles of the methods that were used in the study? c) What are supporting methods and data in the study that validate specific experimental findings? d) What are potential methodological deficiencies and alternative approaches necessary to validate the findings of the study?
4. Basic and Translational Significance: Do the results of the study yield information that advances the basic understanding of a biological process/ technical approach to address a medically relevant problem? How could findings be translated into therapeutic or diagnostic/prognostic strategies and/or interventions?
5. Understanding Limitations Deficiencies and Alternatives: a) What are strengths of the paper? Are the results novel or incremental? b) What are weaknesses of the paper? Are the findings supported by persuasive evidence? How would you judge the quality of the data? c) What are alternative explanations for the results? Are there issues or perspectives that were not addressed by the authors?
6. Forward Thinking: Where do these studies go? What questions could next be addressed in further the studies?

This exam is graded on a 100-point scale with a pass achieved at 80 percentile. Prior to the exam, a question key is developed on which the major elements of the 6 parts of the exam are defined.  Upon completion of the exam your written answers are independently read and graded by the Chairman of the committee, the Program Chairman, and one outside reader. The answer key may be provided on request as a basis for performance comparisons.

The Tier 2 qualifying exam is designed to evaluate a student’s ability to develop a scientific hypothesis and design critical experiments to test this hypothesis. In order to examine these abilities, students will be required to write a research proposal in the area of study that they have chosen for their dissertation research. Tier 2 exams will be evaluated on both the quality of the written document and the oral presentation of the proposal.

Role of the Research Mentor (Primary Thesis Advisor): The student’s advisor may provide guidance in development of the overall hypothesis and specific aims of the proposal as well as technical advice in the design of experimental approaches.

Example grants from the mentor are also allowed. The Program will provide additional examples of prior successful F31 grants. The Mentor may not contribute to the writing or editing of the proposal. The mentor is also not allowed to provide answers or any other guidance (e.g., leading questions) during the oral portion of the exam.

Requirements and assessment criteria for the written element of the proposal:

The Tier 2 exam is in the format of a NIH-style pre-doctoral grant proposal, and should be formatted using single spacing, 11 size Arial font, with 0.5 inch margins and include the following elements:

1. Title page: including a Title, Student name, Name of the Mentors

2. Abstract no more than 30 lines (1 page)

3. Specific aims page stating the hypothesis and specific aims (1 page) 4. Research Proposal including Figures and Figure legends (6 pages).

It should be formatted as an NIH F31 pre-doctoral proposal. (Significance and Approach). Documents failing to adhere to page limits and formatting restrictions are ineligible for submission.

4. References (no page limits)

5. All preliminary data and figures are ascribed to a source. If it’s from the student’s lab indicate courtesy of “lab members name”. If it’s from the literature they need to reference the figure. If it is adapted from the literature students also need to reference the source material. Any results generated by that student can be indicated as such.

Specific elements of the proposal (written and oral) which are assessed:

1. State a defined hypothesis

The student should indicate the central question of their proposal in the form of a hypothetic statement.

2. Defining Specific Aims

The aims should be independent, identifying any elements of the hypothesis that are being tested. They should be included an abbreviated description of the experimental design and outcome variables.

3. Background significance and innovation

Students need to provide context for how the proposed studies address a biological problem. This context may be from the published literature or from their own lab’s data. Students provide a section that describes what is novel and innovative about these studies. This section describes how the proposed studies move the field forward, how they apply existent methodology in a unique way, or how they develop new methodology that is applied in the studies.

4. Experimental design or Approach

Students must present experimental methods with enough detail so that the study is clearly understood. Students should present what the controls are for a given experiment and describe anticipated results. Students may use preliminary data as examples to the methods they are proposing to present the approach.

5. Potential experimental pitfalls, unanticipated results and alternatives

Students must present what they anticipate as results, as well as how unanticipated findings will influence the design and interpretation of the study as a whole.

6. The proposed experiments must be robust and reproducible

This means students clearly state the numbers of replicates (technical and biological) for a given method that is standard to their field. Students may reference studies from the field to show what’s standard. If they are using animal studies students need to present either a power analysis or an explanation of numbers of specimens and/or animals used to obtain meaningful results. Similarly, if students are using human materials, they must provide either a power analysis for their numbers or a reference of a comparable study from the field.

7. The written elements must be presented in a professional, grammatically correct manner without spelling errors and use of common lab lingo

Requirements and grading criteria for the oral presentation of the proposal:

Students should prepare a presentation of their proposal that can be delivered in no more than 30-40 minutes. Students may contact the Chair to review their slides prior to the presentation.

Committee members will interrupt with multiple general knowledge questions, proposal-specific questions, and clarification comments throughout the exam.

a. During the oral exam questions will be asked that are related to specific elements of the proposal as well as questions that test general knowledge of the medical science concepts and techniques.

b. The student needs to be able to accurately convey their proposal, including the general knowledge of their selected field of research, the reasoning and background for the development of the hypothesis and the methodology that will allow them to test their hypothesis.

c. Importantly, the exam is not designed to be an assessment of the preliminary data or quality of the experiments performed to date that support the stated hypothesis. The preliminary data can be derived from the literature, prior work in the mentor’s laboratory as well as any experiments that are completed by the date of the exam. All work that is not generated by the student must be appropriately referenced.

Outcome:

1) Pass. Students form and convene their first dissertation committee advisory (DAC) meetings.

2) Pass with remediation. Students may proceed to their first DAC. A detailed remediation plan intended to address identified areas of encouragement will be delivered to the student, mentor and DAC Chair to assess progress and completion.

3) Fail. Students can fail both parts and one part of the exam and will be required to address either based on the recommendation of the Qualifying Exam Committee.