CNUP: Center for Neuroscience

PhD 02-03 Guidelines

1. Overall Objectives of the Graduate Program

The predoctoral training program of the Center for Neuroscience at the University of Pittsburgh (CNUP) has been designed to accomplish several objectives:

  • To develop competence in conducting laboratory research; to plan, execute, report, and defend an original piece of research in the field of neuroscience.
  • To develop general competence in neuroscience and specific expertise in one or more areas of neuroscience such as cognitive neuroscience, developmental neurobiology, homeostatic regulatory systems, membrane biophysics, modeling of neural circuits, molecular neurobiology, neuroanatomy, neurochemistry, neuroendocrinology, neuropharmacology,and neurophysiology.
  • To develop a general professional competence in oral and written expression, in the critical analysis of primary scientific articles, and in teaching.

In formulating the graduate training program, the faculty have been guided by several principles. First, the program should aid each student in the development of an individualized training program based on the student's background and interests. Second, research experience should form the core of each student's training and as such should not be postponed by a lengthy period of time devoted exclusively to course work. Third, students should be able to complete the program in five to six years. Fourth, students should be evaluated in terms of those competencies that are important to a research scientist: designing, conducting and evaluating research, both their own and that of others. Thus, the progress that a student makes in the program is considered primarily in terms of the student's performance as an investigator.

2. Purpose of this Document

"Guidelines and Regulations for Doctoral Study in the CNUP Graduate Training Program" is a document written by the CNUP graduate training faculty in consultation with the graduate students. The Guidelines are meant to supplement the Regulations Governing Graduate Study at the University of Pittsburgh and thereby provide a complete handbook for students concerning the Program's rules, expectations, and recommendations for each aspect of the graduate program. Questions regarding specific issues of the graduate program should be directed to the Co-Directors of the CNUP Graduate Program (see below).

2.1. Changes to the Guidelines

Each graduate student will be given a copy of the Guidelines when they enter the program. To ensure that students are given an up-to-date version of the Guidelines, a new edition of the Guidelines will be dated and printed at the beginning of each fall term. Each summer, the Co-Directors of the CNUP Graduate Program will oversee the editing of the Guidelines. Student input will be solicited. Any proposed changes will be circulated among the faculty and students for comment. It is expected that this annual revising of the Guidelines will not result in any substantive change in the graduate program. Rather, this process is expected to update or clarify aspects of the previous edition. Major substantive alterations in the Guidelines (e.g., a change in the format of the Comprehensive Exam) would require additional discussion by the faculty and students.

During their progress through the Program, each student should refer to the Guidelines that were current when they entered the Program.

3. Advisors

To aid the student in attaining the objectives outlined in this document, the faculty have created separate mechanisms for providing academic and research advice. Upon entering the Program, each student will select a research mentor for their first laboratory rotation. It is expected that the research mentor will also serve as a general advisor to the student (see below). Further advice regarding research projects is the function of research committees. At all stages of their graduate training each student must have a research advisor and an active research committee. Advice on academic issues and other issues relating to graduate education will be handled formally by the Co-Directors of the Graduate Program.

3.1. Co-Directors of the Graduate Program

The Co-Directors of the CNUP Graduate Program (Drs. J. Patrick Card and John P. Horn) have the primary responsibility for ensuring that the graduate program is running effectively. Students who have questions related to required coursework, curriculum development, or completion of Program milestones should consult with either of the Co-Directors on these matters. The Co-Directors are responsible for approving student registration forms, approving the composition of student evaluation committees (i.e., Reprint Exam, Comprehensive Exam, and Dissertation committees), and may at their discretion approve minor modifications in Program academic requirements for students on an individual basis.

The Co-Directors of the CNUP Graduate Program are also responsible for the annual evaluation of each student (See Yearly Evaluations - Section 7) and they serve as Co-Chairs of the CNUP Student Evaluations Committee. This committee consists of six members of the training faculty in addition to the Co-Directors of the Graduate Program. The major function of this committee is to facilitate the students' progress through the Program by providing students with thorough yearly evaluations and advice regarding their development. This committee will also serve as an advisory committee for the Co-Directors of the Graduate Program.

The Co-Directors of the CNUP Graduate Program will be assisted by CNUP administrative staff. These staff (Joan Blaney and Patti Argenzio) will be responsible for maintaining student folders, notifying students of upcoming deadlines, scheduling exams and committee meetings, and monitoring the status of students.

3.2. Research Advisor

At all times during their graduate training, students will be engaged in laboratory research. While a student is working within a faculty member's laboratory, that faculty member will serve as the student's research advisor. Research advisors are limited to CNUP training faculty members, except during the second and third rotation periods or apprenticeship, during which students may choose to work with graduate faculty members outside the CNUP.

Students and their research advisors should discuss the nature of their interactions so that each has a full understanding of what they should, and should not, expect from one another. The students should understand that different faculty members have different styles of interacting with students. New students are encouraged to consult with senior students to obtain student perspective concerning the mentoring styles of different faculty members.

4. Graduate Program

The following sections outline the academic courses, the research experiences, and the oral and written examinations (herein referred to as "milestones") that the student must successfully complete prior to being awarded the doctoral degree. A calendar listing the deadlines associated with these milestones is included at the end of this document. These requirements are described in terms of the academic and research accomplishments expected during each year of the student's progress through the Program. Deviations from the outlined sequence and time schedule must be approved by the Co-Directors of the Graduate Program.

4.1. Overview of Requirements

Students have a 24-credit course requirement covering fundamental material in cellular and molecular biology and systems neuroscience and several elective courses. A graduate-level course in statistics is also required. Graduate students must receive a grade of at least a B to pass a course (re-taking the course is not required with a grade of B-), and they must maintain a cumulative grade point average (QPA) of at least 3.0.

Students are also required to pass three milestones en route to the doctoral degree: the Reprint Exam, the Comprehensive Exam, and the Dissertation Defense.

Additional requirements of the Graduate Program are: attending pro-seminar during the first year, attending a departmental journal club every Fall and Spring term, attending research seminars on a regular basis, obtaining research experience in at least two separate laboratories (either done initially as research rotations or later as a research apprenticeship), serving as a Teaching Assistant for at least one term (or course), and completion of a 1 credit course in professional ethics.

Students should refer to the Regulations Governing Graduate Study at the University of Pittsburgh for additional details concerning University requirements.

4.2. Yearly Sequence of Requirements and Expectations

4.2.1. Entering Students:

Entering students should schedule a brief introductory meeting with the Co-Directors of the Graduate Program in order to discuss issues related to being a graduate student. The purpose of this meeting is to answer any questions that the student may have and to assist the student in getting settled in the program. Prior to the beginning of the student's first term, the student, with the aid of the Co-Directors, outlines a plan of study for the first two years.

4.2.2. First Year:

The major objectives of the first year are to select a laboratory for dissertation research, complete the core course requirements, and obtain sufficient experience through courses and research to pass the preliminary or "Reprint" Exam.

It is expected that students generally will participate in the following activities during the Fall and Spring terms of their first year: (a) laboratory research, typically consisting of laboratory rotations in at least two different laboratories (see section 5.1 on Research Rotations), (b) two courses of the core curriculum in neuroscience (either Cellular and Molecular Neurobiology or Foundations in Biomedical Science, and Systems Neurobiology, with associated conferences), (c) pro-seminar, (d) journal club, (e) research seminar, and (f) additional academic courses as appropriate. During the summer term at the end of their first year, students focus primarily on research, although some course work may be appropriate, as well; specifically, students may choose to take statistics (BIOS 2041) during the summer of the first year. During the first year, students typically register for 3-6 research credits as Directed Study (MSNBIO 2690 or NROSCI 2902) per term.

Towards the end of their first year of study, each student takes the preliminary or "Reprint" Exam (see Section 9.1).

4.2.3. Second Year:

The major objective of the second year is to begin work toward a dissertation project. By the beginning of the second year, students should have selected a dissertation advisor; this might have been done as early as June 1 of the first year, but must be done by the end of the Fall term of the second year.

During the Fall and Spring terms students will generally participate in (a) research (registered for as 6-9 credits, MSNBIO 2690 or NROSCI 2990, pass/fail), (b) one elective course each term (c) statistics, (d) journal club, and (e) research seminar. A list of elective courses currently offered can be obtained from a CNUP administrative office.

It is expected that most students will complete the Program's teaching requirement during their second year (see Section 6).

The annual evaluation at the end of the second year includes a research presentation to the student's research committee (see section 7.4).

4.2.4. Third Year:

The Comprehensive Exam (see section 9.3) must be completed by January 31 of the third year.

In this and subsequent years graduate students are expected to be involved in research, to participate in journal club and research seminars, and to take additional courses as necessary. By the end of the third year, they also should have submitted a proposal for a research apprenticeship if the research rotation requirement was not satisfied earlier (see Section 5.9).

4.2.5. Subsequent Years:

The major objective of the remainder of a student's graduate program is to complete the doctoral dissertation (see Section 9.4). Students continue to attend journal club and research seminar for each Fall and Spring term they are enrolled in the Program.

4.3. MD/PhD Students

MD/PhD students are expected to follow an accelerated schedule for passing each of the milestones; they should aim to complete the program in 3 years. The requirements for MD/PhD students are identical to those of PhD students, except that MD/PhD students are not required to take the two core neuroscience courses (Foundations in Biomedical Sciences or Cellular and Molecular Neurobiology, and Systems Neurobiology) and the associated conferences. MD/PhD students are required to complete at least 6 hours of elective courses and a graduate-level course in statistics.

Research requirements for MD/PhD students are the same as those for PhD students. MD/PhD students should consider completing one of their laboratory rotations during either the summer prior to beginning medical school or the summer between the first and second year of medical school. The teaching requirement is optional for MD/PhD students.

5. Components of the Plan of Study

In developing a plan of study, students are expected to strike a balance between breadth in neuroscience and depth in their area of specialization. Students are encouraged to be innovative in designing their graduate training experience. Thus, courses are defined as any accredited interaction between a student and one or more faculty members. This includes formal lecture courses (usually but not always at the graduate level), seminars, or tutorials at the University of Pittsburgh, CMU, or at other universities, research institutes, or special study programs.

5.1. Research Rotations and/or Apprenticeships

Each student is required to spend at least one term conducting research in a laboratory other than the laboratory in which they do their dissertation research. This will typically be done as research rotations during the first year. The first year is divided into two research rotation periods with additional rotation periods during the summer before or the summer after. Rotations officially begin on the first day of classes and end on the last day of classes each term (see University calendar for specific dates). Students are required to begin their first research rotation no later than the first day of the Fall Term. The first rotation must be with a member of the CNUP Graduate Training Faculty. This research rotation is set up by arrangement between the student and the specific training faculty member, who serves as the student's research mentor during that rotation period. In addition, the student must establish a research committee consisting of the research mentor and two other members of the training faculty (although, with permission of the Co-Directors of the Graduate Program, one of these members need not be a member of the CNUP training faculty). The student will need to fill out a "Research Rotation Form" listing the research mentor and the other members of the research committee; this form must be submitted to a CNUP administrative office within one week of beginning the research rotation. By the last day of each of the first two laboratory rotation periods, the student must submit a rotation report to his/her committee and also a copy to a CNUP office (see description of the Rotation Report below). The research mentor will receive a form to fill out and return to the CNUP office, evaluating the student's performance during that rotation. Rotations are graded satisfactory/unsatisfactory. Unsatisfactory rotations will not count toward the required two and will result in the student being placed on probation.

At the end of the student's first rotation, the student will typically move to a second laboratory to complete a second research rotation. (Although the research mentor will change, it is not necessary for the other members of the research committee to change.) At the end of the second research rotation, the student may elect to remain in the same laboratory, return to the initial laboratory, or move to a third laboratory for an additional research rotation. Rotation reports are required only for the first two rotation periods; if a student chooses to do a third rotation, a report is not required.

Some students may choose to spend the entire first year in a single laboratory and remain in that laboratory for dissertation research. In such cases the student must petition the Student Evaluations Committee at the end of the Spring term of the first year to opt out of the laboratory rotation requirement. The petition must include the reasons for the request, and a statement of support from the mentor. Each case will be considered on an individual basis. If a student starts their dissertation research without first rotating through at least one other laboratory, that student will need to fulfill a research apprenticeship under the direction of a faculty member other than his/her major research advisor. This research apprenticeship is a period of at least 3 months during which a student works in a different laboratory. A proposal for satisfying the research apprenticeship requirement must be submitted by the end of Spring term of the third year. During this apprenticeship the student is expected to acquire both experience with a research technique different from those available in the laboratory of his/her major research advisor, and experience with another investigator's perspectives on neuroscience research and approach to designing specific projects. Under certain conditions a clinical apprenticeship in the Departments of Psychiatry, Neurology, or Neurosurgery may serve as a research apprenticeship. All research apprenticeships must receive prior approval from the Co-Directors of the Graduate Program. Students should register for the research apprenticeship as a course (MSNBIO or NROSCI 3001) and receive a grade (pass/fail).

5.1.1. Rotation Report:

The main goal of the rotation report is to produce a scholarly account of the research activities undertaken by the student during that rotation period. In general, the report should include 5-8 pages of double-spaced text and any useful figures. It may utilize the standard format of scientific journals (i.e., Introduction, Methods, Results, Discussion) or instead have a more narrative style in which the research problem, the methods, and the outcomes are described and discussed much like a seminar presentation. Copies of the report are given to the research mentor, other members of the research committee, and a CNUP administrative office. Rotation reports are due on the final day of the rotation period.

5.2. Core Curriculum in Neuroscience

The core curriculum consists of two courses, designed to be taken during the first year. The first core course deals with issues of cellular and molecular biology. Either Cell & Molecular Neurobiology (MSNBIO/NROSCI 2100) or Foundations in Biomedical Science (INTBP 2000) can be used to fulfill this requirement. Each of these courses will be offered during the Fall term. The second core course is Systems Neurobiology (MSNBIO or NROSCI 2102). It focuses on the functional anatomy of the mammalian brain and is offered during the Spring term.

5.3. Electives and Tutorials

Students must also take elective courses in order to further their expertise in neuroscience. Students may also establish tutorials in specialized areas for which formal courses are not available. In such cases, a student (or group of students) identifies a faculty member willing to serve as a tutor and develops a syllabus, including a mechanism by which competency in the area will be assessed. The syllabus should be approved in advance by the CNUP Curriculum and Education Programs Committee. The subject matter of these tutorials usually will be "academic" in nature; i.e., with a focus on the reading of primary and secondary literature. It also may involve learning new laboratory techniques.

5.4. Statistics

Students are expected to obtain a background in statistical and quantitative analysis of data that is appropriate to their area of research. Students are required to take a graduate level course in statistics. While any graduate-level statistics course may be used to fulfill this requirement, Intro to Statistical Methods 1 (BIOS 2041) is specifically well-suited for most CNUP students. This course is offered during the Summer and Fall terms, which fit well into most students' schedules.

5.5. Pro-Seminar

The Pro-seminar is a required two-term course taken during the Fall and Spring terms of the first year of graduate study. The course meets once weekly, during which one or two members of the training faculty present an overview of their research.

5.6. Journal Club

Each student is required to attend a weekly journal club during each Fall and Spring term. Each term, students will be randomly divided into groups of 10-14, and each group will be assigned a faculty supervisor and a weekly meeting time. If a student has a conflict with their assigned time, they should contact the faculty supervisor for their group to get reassigned. Each student is required to present a paper in journal club at least once each term, and it is expected that the more senior students will make their presentations earlier in the term whereas the more junior students will make their presentations later in the term. At the initial meeting each term, each student will sign up for a week that they will be responsible for selecting and presenting the journal article. The presenting student is also responsible for selecting another faculty member to attend journal club that week in order to provide particular expertise for the paper. Presentations will be critiqued by students and the faculty supervisors. Presentations that are not considered acceptable by the faculty supervisors must be repeated. In addition to presenting a paper once during the term, each student is required to read the selected paper each week and be prepared to discuss it. Active participation in journal club is viewed by the faculty as an important component of the graduate training program.

5.7. Seminar Series

Each student is required to attend research seminars on a regular basis. Each Fall and Spring term that the student is enrolled in the graduate program, they must register for Seminar Series (MSNBIO 2660 or NROSCI 2106, pass/fail). This "course" requires that the student attends at least 10 relevant research seminars during the term. For each seminar that a student attends, he/she must send an e-mail message noting their attendance to the seminar coordinator of the course for which they registered.

5.8. Professional Ethics and Practices

All students are expected to show ethically appropriate behavior with regard to the conduct of their research and mastery of safe laboratory practices. These competencies extend to the treatment of laboratory animals, publication of data, and the use of references to previous literature. Further, all documents submitted to satisfy curriculum or research requirements of the program should be free of plagiarism and conform to the rules defined in the University of Pittsburgh Honor Code. As part of their orientation to the University upon first entering the program, all students must attend training sessions in Radiation Safety, Laboratory and Formaldehyde Safety, and Library usage. All students are required to familiarize themselves with the NIH "Guide for the Care and Use of Laboratory Animals" (1996), the "Handbook for the Use of Animals in Research, Testing, and Teaching at the University of Pittsburgh", and "Guidelines for Ethical Practices in Research" (University of Pittsburgh, May 1997); each are available on web-sites. In addition, students should familiarize themselves with acceptable publication practices, as described by the Society for Neuroscience (Journal of Neuroscience, January, 1999 and Handbook for the Use of Animals in Neuroscience Research. All students using animal subjects in their research must attend the appropriate training session(s) conducted by the Division of Laboratory Animal Resources.

All Students are required to complete a formal training program on research ethics during their first year in the program. This requirement will be fulfilled by taking a 1 credit course in Scientific Ethics (INTBP 2290) during the summer term.

6. Teaching by Graduate Students

Teaching is seen as an integral part of the graduate training program. It provides experience in classroom instruction as well as an opportunity to obtain a broader perspective of neuroscience. In general, second-year students serve as teaching assistants to members of the training faculty for one term or one full course. As such they are typically responsible for conducting recitation sections, teaching laboratory exercises, holding office hours to answer questions of class members, and helping to prepare, proctor, and grade exams.

Some students may elect to become more involved in teaching. Certain faculty allow graduate students to give classroom lectures in their undergraduate courses. Students wishing to obtain this experience should contact Dr. Pat Card.

7. Evaluation of Graduate Students

7.1. Yearly Progress Reports

By June 15th of each year all students must submit a brief progress report summarizing their activities during the past year and their plans for future study. This report will serve as the focal document for the annual student evaluation by the CNUP Student Evaluations Committee, although reports from the student's research advisor, committee chairpersons, course instructors, teaching supervisors, etc. will also be incorporated into the evaluation. Therefore, the progress report should incorporate everything the student wishes the faculty to know at the time of the evaluation. It should be organized as follows:

  1. a statement of last year's goals and the extent to which they have been achieved,
  2. a list of the courses taken and the grades attained,
  3. a summary of research efforts,
  4. a list of Program "milestones" completed,
  5. a list of any awards or honors attained,
  6. a list of manuscripts and abstracts published,
  7. attendance and presentations at scientific conferences, and
  8. a statement of specific objectives for the coming academic year.

The length of the progress report can vary from 2 to 10 pages (double-spaced). Relatively long reports from first- and second-year students are particularly important because the faculty generally know less about them than about more senior students.

These reports should be submitted to the CNUP Graduate Administrators (Joan Blaney, 446 Crawford, and Patti Argenzio, E1448 Biomedical Science Tower).

7.2. Yearly Evaluation

All students are evaluated by the CNUP Student Evaluations Committee each year beginning at the end of June. Results of these evaluations are reported to each student in a letter from the Co-Directors of the Graduate Program. This letter may be supplemented by a discussion between the student and a member of the committee to clarify the letter, if necessary, or to discuss additional aspects of the student's progress. Students are also encouraged to discuss this evaluation with their research advisor. In evaluating students, the committee considers performance in laboratory research, course work, teaching, journal club, mastery of the relevant scientific literature, and any major examinations that have been taken during the past year. Copies of the yearly evaluation letter are sent to the student's research advisor, and become a part of the student's file.

7.3. Mid-year Evaluation of First-Year Students

The progress of first-year students in laboratory research, together with their classroom performance, will be reviewed by the CNUP Student Evaluations Committee at the beginning of the Spring term. This early evaluation is to provide feedback to the students on their progress, while also allowing any problems that might have arisen to be identified, so they can be corrected promptly. Following this evaluation students will be given a brief written statement summarizing the committee's perception of their progress.

7.4. Second Year Research Evaluation

The evaluation at the end of the second year includes a specific evaluation of research progress. As part of their Annual Progress Report at the end of the second year (submitted by June 15th), the student submits a written description of their research progress during their time in the graduate program, focusing primarily on what had been accomplished since selecting a laboratory for dissertation research. This research report should be approximately 8-10 double-spaced pages of text, plus figures and tables describing the results of experiments. The report must also include the date that the committee meeting is scheduled for; this meeting must occur before July 31. It is the student's responsibility to circulate their research progress report to their committee.

At the Second Year Research Evaluation meeting, the student presents a 20-30 minute overview of their research following which the student is asked questions pertaining to the research project. The student is expected to be generally knowledgeable in the area in which he/she is working and to be able to defend specific aspects of their research project.

Based on the student's research and the student's ability to discuss the research, the research committee provides an evaluation of the student's research progress (i.e., either acceptable or unacceptable). If the student's research progress is viewed as unacceptable, they will be given one term to improve their research progress to an acceptable level. However, if a student is already on probation, they may be terminated from the Program (at the discretion of the CNUP Student Evaluations Committee).

7.5. Termination of a Student from the Graduate Program

Students may be terminated from the Graduate Program for failure to pass two required core courses or one of these courses on successive occasions, failure to pass the Reprint Exam, Comprehensive Exam, or Doctoral thesis examination, failure to make adequate progress in laboratory research, or breaches in ethical conduct such as plagiarism. Except for instances involving breaches in legal or ethical behavior, students will not be terminated from the Program without first being notified in writing that they have been placed on probation. This written communication will include a detailed description of the reason(s) for placing the student on probation, and the goals that the student must accomplish in order to be taken off probation. Students will typically have one term to resolve their problems and get off probation or they will be terminated from the Program. This "Program Probation" is different from "University Probation" (see below) in that it does not preclude financial support from the University.

When a student who is not on probation fails one of the major examinations listed above, the student will be placed on probation and given a second opportunity to pass that examination. This second examination must be taken within three months of the first examination. Failure on the second examination shall result in termination from the Program. When a student who is already on probation fails one of the major examinations, they may or may not be given a second opportunity to pass that examination, at the discretion of the CNUP Student Evaluations Committee.

When a student is informed that his/her laboratory research progress has been determined not to meet program standards, the student will be given one term to improve laboratory skills and productivity before being reevaluated. A second determination that laboratory performance is substandard, at this time or during any subsequent evaluation, will result in the student's termination from the program.

In all cases, the termination of a student requires a decision by the CNUP Student Evaluations Committee and cannot be made by an individual faculty member or examination committee. Terminations are final.

7.6. University Probation

The University requires that all graduate students maintain a QPA of 3.0 or above to undergo the preliminary evaluation, to take the comprehensive examination, to be admitted to candidacy for the PhD degree, and to be graduated. Students whose QPA falls below 3.0 must be put on "University probation" and cannot be awarded financial assistance from the University (e.g., teaching assistantship) until they have re?established a QPA of 3.0 or above.

7.7. Terminal Masters Degree

If students leave the program, whether voluntarily or not, after having completed the following requirements, they may write to the CNUP Graduate Student Evaluations Committee petitioning to receive a Masters Degree. Students wishing to receive such a degree must fill out appropriate forms, as mandated by the University. The requirements for a Masters degree include: passing the two required core neuroscience courses, at least one elective course, and the Reprint Exam, Proseminar, at least two terms of journal club, at least two terms of research seminar, and at least four terms (including summers) of laboratory work. Students must also submit and defend a Masters thesis and publicly present their Masters research. The format for the Masters thesis is as specified in the University's Style and Form Manual, which can be obtained from the Office of the Associate Dean for Graduate Studies.

Students wishing to obtain a Masters degree en route to the PhD, and working under the direction of a faculty member in the Department of Neuroscience, may apply for the degree through the Faculty of Arts and Sciences. The requirements for the degree are the same as stated above for a terminal Masters degree.

8. Special Status

8.1. Leave of Absence

Students may request a leave of absence from the Program. Such requests should be made in writing to the Co-directors of the Graduate Program. Requests should include the reason for the request and the duration of the requested leave. Leaves of absence are subject to the approval of the Associate Dean for Graduate Studies of the appropriate school (i.e., depending upon the student's current mentor). Students considering taking a leave of absence should consult the Regulations Governing Graduate Study at the University of Pittsburgh regarding policies on leaves of absence.

9. Examinations

Note: Specific forms are required in association with the different milestone exams. The relevant forms, and their filing procedures, should be obtained from the appropriate CNUP Graduate Office.

9.1. First Year Preliminary Exam (Reprint Exam)

During the first year students are expected to obtain experience in the critical evaluation of original research reports. This training is provided in part by the conference sections associated with the core courses, which is typically supplemented by a program of supervised reading with their research advisor. Students are strongly encouraged to discuss this issue with their advisor. It is required that the preliminary or "Reprint" Exam will be taken by May 31 of the first year. By May 1, the student must submit the completed Reprint Examination Form stating the committee members and the date on which the exam is scheduled. Students wishing to postpone this exam past May 31 of the first year must receive approval from the Co-Directors of the Graduate Program.

The Exam primarily serves to set a standard of competency in the critical evaluation of research articles and in oral expression, a standard which students are expected to attain early in their graduate career. In addition, it helps the faculty to identify areas of weakness in this skill.

To begin the process, the student writes a brief description of the general area from which he/she would like an article to be selected. A Reprint Exam committee, consisting of three CNUP graduate training faculty members, is selected by the student with the assistance of the research advisor. A fourth member of the committee from outside the CNUP training faculty may be added for a particular area of expertise. Typically the current research advisor serves as the chairperson of this committee. The composition of the committee must be approved by the Co-Directors of the Graduate Program. Two weeks before the exam, the committee selects a suitable paper and provides a copy to the student. At the examination the student briefly presents some background material and then discusses the paper's major points, analyzing the rationale for the research, the methodology chosen, the validity of the evidence obtained, and the conclusions. Thirty minutes are provided for this presentation. The student then is questioned on the presentation. At the conclusion of the presentation, the committee selects one of two options: pass or fail. If the student fails, then the exam may be taken a second time provided that the student was not already on probation. If the student is already on probation, then failing the Reprint Exam may, at the discretion of the CNUP Student Evaluations Committee, result in termination of the student from the program. Failing the Reprint Exam, or any other program milestone, results in the student being placed on probation. A failed Reprint Examination must be retaken within three months; the exam will follow the same procedure and format as the first exam but with a new article selected by the exam committee. It is expected that the exam committee will remain the same, though students may petition the CNUP Student Evaluations Committee to request that one member of the committee be changed.

9.2. Comprehensive Examination

The Comprehensive Examination is the major requirement that a student must pass before being admitted to candidacy for the doctoral degree. This exam provides the student with an opportunity to master a literature that is relevant to their research interests and ultimately to demonstrate that the needed competency has been achieved.

The specific educational goals of the Comprehensive Exam are to test the student's ability to:

  • independently evaluate and critique a body of neuroscience literature
  • integrate the acquired information into broad conceptual schemes
  • develop testable hypotheses
  • devise experimental approaches and thereby evaluate hypotheses
  • demonstrate the communication skills required to present and defend scientific ideas in oral and written formats

The topic of the Comprehensive examination is expected to overlap with the student's research interests and general dissertation goals. In addition, it is expected that the proposed plan be original in its conception and scholarly in its execution. This means that the research proposal submitted for the comprehensive examination must be demonstrably different from work that has been previously designed and discussed or written up in any form by either the student or the research mentor.

Students are required to complete the Comprehensive Exam by January 31 of the third year in the graduate program. Any requests for a delay in this schedule should be made in writing to the Co-directors of the Graduate Program; such requests should include a reason for the delay, as well as the time when the student plans to take the exam. Note that although the exam does not need to be started until December of the third year (in order to be completed by the end of January), the student must establish their Comprehensive Exam committee and set up a tentative time frame for the exam by July 1 of their second year.

9.2.1. Committee:

The Comprehensive Exam committee is selected by the student, but must be approved by the Co-Directors of the Graduate Program. This committee must be established by the end of the second year (July 1). The committee consists of at least four members, and must contain at least four members of the CNUP graduate training faculty. The research advisor is generally a member of the committee but cannot serve as its chairperson. Prior to its first meeting the student should select a chairperson.

9.2.2. Initial Proposal and Meeting:

Prior to the first meeting, students submit to their committee a brief description of three research topics (approximately one paragraph for each area) from which they would like their exam topic to be chosen. Then they meet with their committee. At this meeting a general agreement is reached as to the specific research topic on which the student will be examined, with the committee selecting from one of the three topics the student has provided, or a modification of one of these areas. The committee will ensure that the topic that is agreed upon does not overlap excessively with the student's dissertation project.

9.2.3. Written Exam:

After receiving the specific research topic students have 5 weeks to write a "grant application" based on this problem. Thus, students will need to evaluate the literature in this area, formulate a significant and relevant hypothesis, and devise experimental strategies to test their hypothesis. The written report should follow the basic form of an NIH RO1 application, and should be a realistic proposal for 3 years of research. It should include all of the sections characteristic of a research grant proposal. Specific Aims: This section should include a statement of the hypotheses to be tested and the goal or objectives of the proposal (1 page). Background: Concise presentation of pertinent literature in the chosen area of interest, setting the appropriate context of the proposed research plan (~5 pages). Significance: Brief summary of the broad significance of the research to the advancement of the relevant scientific field (1-2 paragraphs). Preliminary Data: This section should include a brief description of the types of preliminary data the student feels are necessary to support the proposal (1 page). Research Plan: Description of the methods and experiments that are proposed to achieve the research goals of the proposal. This section should place less emphasis on methodological details and more emphasis on anticipated outcomes and potential experimental pitfalls. (~8 pages). Literature Cited: Full citations of all referenced literature should be included. The entire document, not including references, cannot exceed 15 single-spaced pages. (For margins and font requirements, see instructions for preparing an NIH grant application.) Students are encouraged to look at actual grant applications submitted by their advisor or other committee members to get a sense of what is included in an application.

While working on the written portion of the Exam, it is appropriate for students to discuss their ideas with their committee members as well as with other faculty and students. Students are encouraged to show their Specific Aims to their committee within the first two weeks of the 5-week period, so that they can receive feedback as to whether they are going in an appropriate direction. However, students are not allowed to receive assistance with written drafts of their Exam.

9.2.4. Oral Exam:

Approximately one week after the student submits the written "application" there will be an oral examination. The oral exam consists of a public presentation of the proposal (lasting ~ 45 minutes) followed by a private oral exam administered by the committee. At the oral examination students will be expected to defend their hypothesis and to address questions concerning all background information relevant to the topic, significance, and design of the experiments they proposed. It is expected that the entire oral exam (presentation and defense) will last 2-3 hours.

9.2.5. Evaluation:

At the end of the oral exam, the student will be excused from the room and the committee will evaluate the student's performance. The student will then be immediately informed of the decision of the committee. The possible outcomes are pass, partial pass, or fail.

Students may receive a partial pass if they were deficient in some but not most of the areas on which they were examined. Significant problems associated with either the written or oral portion of the exam, or both, that are not so severe as to result in a failing score may result in a "partial pass". If the committee decides on a partial pass, they must define those areas of the performance that were deficient, and provide specific criteria that must be met for the student to pass. For example, the committee might decide that experimental descriptions were poor throughout the written portion of the exam, and thus the student must submit revised descriptions of the proposed experiments. As another example, the committee might decide that some of the student's oral answers were unacceptable, and thus the student must retake the oral portion of the exam. Whatever the reason for the partial pass, the committee must present the student with a detailed description of what needs to be done to satisfactorily complete the exam. Partial passes must be remedied within 4 weeks of the initial oral exam, or the student will be considered to have failed the exam.

Students who fail the Comprehensive Exam will be allowed to take the exam a second time provided that they are not already on probation. The second exam must occur within 3 months of the initial exam. The exam must be passed before a student can apply for admission to candidacy for the PhD Once this examination has been passed, the program notifies the appropriate Dean of Graduate Studies of that fact.

9.3. Doctoral Dissertation

The dissertation is the culmination of the graduate program. The dissertation is intended to embody an extended original investigation of a problem of significance in the field of neuroscience. It must add to the general store of knowledge and to understanding in this field. And it must serve to demonstrate each of the competencies described at the outset of these guidelines.

9.3.1. Dissertation Committee:

After successful completion of the Comprehensive Examination, the student and his/her research advisor propose a doctoral committee for approval by the Co-Directors of the Graduate Program. The committee consists of at least 5 members. At least 4 of them (including the research advisor) must be members of the CNUP graduate training faculty and at least 3 of these must be from the school in which the student is registered (i.e., School of Medicine or Faculty of Arts and Sciences). At least one member of the committee must be from outside the school of the research advisor. All committee members from the University must be members of the Graduate Faculty. According to University Regulations, the research advisor must be a member of this committee; however, in the CNUP the research advisor retains his/her status as an advisor, both to the student and the committee, and does not chair the committee's meetings. The student should select one of the committee members from within the CNUP to serve as the chairperson. For the final thesis defense, an outside examiner is added to the committee. The outside examiner should be an expert in the area of the thesis, and should be selected by the committee in consultation with the student.

9.3.2. Dissertation Proposal and Overview Meeting:

A dissertation proposal and an overview meeting are University requirements, but their function is not in any way analogous to an examination. Instead they provide an opportunity for students to organize their thoughts concerning the anticipated dissertation, to obtain advice concerning these thoughts, and ultimately to receive some assurance that the broad outlines of the research are acceptable to the faculty. Thus, the proposal should not be prepared and distributed when the research is nearing completion but rather at a much earlier stage; in general, proposals should be submitted six months after completion of the Comprehensive Examination. As a general guideline, students should plan on submitting their dissertation proposal prior to the start of their fourth year. Delaying submission of the thesis proposal past the end of December of the fourth year requires written permission from one of the Co-Directors of the CNUP Graduate Program; the student must understand that delaying the submission of a thesis proposal past this date will necessarily extend the program beyond five years. Students should understand that they can revise their original proposal or submit an entirely new proposal when subsequent events warrant it.

The format for the proposal is that of the research plan portion of an NRSA predoctoral fellowship application, the guidelines for which should be examined. The proposal submitted to the committee should be divided into the following sections: Specific Aims (1 page), Background and Significance (5 pages), Preliminary Studies (variable, but not to exceed 5 pages including figures), Research Plan (5 pages). The page numbers listed are guidelines for each section, but the entire document cannot exceed 15 pages.

Approximately two weeks after distribution of the research proposal, the student has an overview or prospectus meeting with the committee. At this meeting (or at a subsequent meeting if necessary) the student and committee reach an agreement on the dissertation topic and research plan. When agreement is reached, this is reported to the Associate Dean for Graduate Studies. A brief written summary of this meeting (and subsequent meetings) should be prepared by the committee's chairperson and provided to a CNUP administrative office.

9.3.3. Admission to Candidacy for the PhD Degree:

After successful completion of the overview, the student files an application for admission to candidacy indicating the dissertation topic. This application must be approved by the Co-Directors of the CNUP Graduate Program and the Associate Dean for Graduate Studies of the school in which the student's mentor is appointed (i.e., FAS when the appointment is in the Department of Neuroscience, SOM when it is not). It is a university requirement that this be done at least eight months prior to the dissertation defense.

9.3.4. Data Meetings:

Students should schedule periodic meetings per year with their committee to discuss the progress of experiments and to review new data. Specifically, students should meet with their committee at least twice each year, but, at a minimum, must meet with their committee at least once each year. The committee must write a summary report of each meeting and submit it to the program administrators so that it can be given to the student and added to their file.

9.3.5. Dissertation:

The format for the written dissertation is as specified in the Style and Form Manual, which can be obtained from the Office of the Associate Dean for Graduate Studies. In addition to meeting these requirements, the student is encouraged to approximate the guidelines for the journal or journals in which the research results are to be published. The exceptions to this rule are (a) the introduction to the dissertation should include a more thorough review of the literature than usually is the case for a research article, (b) the methods section should include all necessary information concerning the conduct of the research, including procedural information already published, (c) the student may wish to include within the results section (or in an appendix) some data which, because they are confirmatory or incomplete, will not be published, and (d) there must be a general discussion section that is more broad than a discussion section associated with a single manuscript.

Manuscripts (including articles in any state of the publication process, e.g., published, submitted for publication, or completed but not yet submitted) authored or co-authored by the student and based on research conducted for the dissertation study may be included in the dissertation. To logically integrate this work into a dissertation, the student is required to write extensive introduction and discussion sections that give an overview of the objective or objectives of the research and draw general conclusions from the assembled data. If a manuscript is co-authored, the contribution of the student must be clearly delineated in the preface so that the committee can ascertain that the student's own work satisfies the requirements of a dissertation. The Style and Form Manual gives instructions on incorporating manuscripts into the dissertation.

A completed dissertation must be submitted to all committee members at least two weeks prior to the defense. The student can expect his/her advisor to read the dissertation prior to its submission, and submission of the dissertation implies that the student's advisor has approved the dissertation as ready for distribution to the committee.

9.3.6. Application for Graduation:

Candidates for graduation must file an official application for graduation in the Office of the Associate Dean for Graduate Studies in the first month of the term in which graduation is expected.

9.3.7. Announcement of Thesis Defense:

One month before the final examination, the student provides the CNUP administrative office with the title of the dissertation and the time and place for its defense. This information is to be published in the University Times and The Neurotransmitter, and is sent to all appropriate departments of the University. It is assumed that all graduate students, postgraduate fellows, and faculty within the CNUP will attend the dissertation defense.

9.3.8. Final Oral Examination:

The chairperson of the doctoral committee will oversee the examination and introduce the student. The student begins by making a public presentation of the research project. Approximately 45 minutes are allotted for this presentation. After a brief period for questions and discussion, the candidate, the doctoral committee, and any faculty who wish to attend move to a conference room to complete the oral examination. The research advisor does not participate in this examination and must remain silent throughout the process. When the questioning is complete, the candidate leaves the room while the committee evaluates the dissertation and its defense. The research advisor (and other faculty members in attendance who are not members of the examining committee) may be asked to leave for a portion of the committee's deliberation. The committee selects one of the following options: pass, revision of the written document and/or additional oral questioning at a later time, or fail. If the committee requires revision of the written document and/or additional oral questioning, this needs to be completed within a 3-month period. If the student fails the thesis defense, the student may take the exam again within 3 months. Failure to pass the thesis defense on a second occasion may result in the student being terminated from the program. At the conclusion of the defense, the student is provided with a verbal summary of the committee's deliberations. In addition, a report signed by all members of the doctoral committee, including the research advisor, is sent to the Associate Dean for Graduate Studies. When the decision of the committee is not unanimous, the matter is resolved by the Dean.

Calendar of Milestones and Deadlines

I. First Year

Select research rotation and initiate researchUpon entering program
Design a Two Year Program of StudyUpon entering program
Form Research Committee (submit Rotation Form)First week of Fall term
Submit first Rotation ReportEnd of Fall term
Evaluation Committee Reviews student progressBeginning of Spring term
Submit second Rotation ReportEnd of Spring term
Submit Reprint Examination FormMay 1st
Completion of Reprint ExaminationMay 31st
Submit Progress ReportJune 15th
Annual Review by CNUP Evaluation CommitteeJuly

II. Second Year

Select Dissertation Mentor & Advisory CommitteeEnd of Fall Term
Complete Teaching Requirement (flexible)Fall or Spring Term
Submit Annual Progress ReportJune 15th
Establish Comprehensive Exam CommitteeJuly 1st
Second Year Research Evaluation MeetingAugust 15th with Advisory Committee
Annual Review by CNUP Evaluation CommitteeAugust

III. Third Year

Complete Comprehensive ExamJanuary 31st
Submit Apprenticeship Proposal (if necessary)End of Spring Term
Form Dissertation CommitteeSpring
Submit Annual Progress ReportJune 15th
Submit Dissertation ProposalAugust 31st
File for Admission to CandidacyUpon approval of proposal
Annual Review by CNUP Evaluation CommitteeAugust

IV. Subsequent Years

Submit Annual Progress ReportJune 15th of each year
Annual Review by CNUP Evaluation CommitteeAugust
Data Meetings with Dissertation CommitteeTwo per year
Application for GraduationTerm of graduation
Announcement of Dissertation DefenseA month prior to defense