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2023 Neuroscience Handbook

The Neuroscience Graduate Degree Program at Penn State College of Medicine is a campus-wide program coordinated by various faculty located at the Hershey campus. The program is administered through the Office of Graduate Education. Information on Neuroscience faculty members based in Hershey, and throughout Penn State, and their research projects can be found at

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Learning Objectives Expand answer

The program learning objectives reflect the Graduate Council Scholarly and Professional Goals for All Graduate Students.

The learning objectives are:

  • Understand current technology and experimental approaches used to study the central and peripheral nervous systems.
  • Understand the molecular, biochemical and anatomical organization of the central and peripheral nervous systems.
  • Conduct neuroscience research by developing and testing scientific hypotheses and reporting the results in both oral and written formats.
General Expectations for Student and Faculty Expand answer

Students are expected to conduct themselves professionally at all times, showing respect to faculty and to their fellow students. It is expected that students will be active learners who take responsibility to further their education. Equally, the faculty members are expected to conduct themselves professionally at all times, showing respect to students and to their fellow faculty members (see Appendix).

Competency in Written & Spoken English Expand answer

The Graduate School requires that all PhD candidates demonstrate high-level competence in the English language, including reading, writing and speaking. At Hershey, competence is assessed in the Qualifying Examination. Passing the exam satisfies this requirement. In the event of failure, the option director will recommend a program for improvement and subsequent re-examination.

Grade-Point Average Expand answer

Credit hours are earned only for the grades A, B, and C. However, all D and F grades are included in the computation of the grade point average.

Grade points are assigned as follows:

A= 4 (above average graduate work)
B = 3 (average graduate work)
C = 2 (below average graduate work)
D = 1 (failing graduate work)
F = 0 (failing graduate work)

Grades D and F are not acceptable for graduate credit. If a course is repeated, then both grades are used in computing the cumulative grade-point average.

Responsible Conduct of Research Expand answer

All new students in the Neuroscience graduate program must complete an online Responsible Conduct of Research (RCR) training course during their first year. The online course is offered through the CITI (Collaborative Institutional Training Initiative) Program and supplements the in-class, discussion-based RCR training provided in BMS 591, Biomedical Research Ethics, a required 1-credit course typically taken during the second year. Together, these two courses satisfy RCR training requirements mandated by Penn State’s SARI (Scholarship and Research Integrity) Program, an RCR initiative organized through the Office for Research Protections.

First year students should register for the online CITI RCR course as soon as possible in the Fall semester. To register, go to the Academic and Research Integrity page and follow the instructions. Select Pennsylvania State Univ – Hershey as the participating institution and register for Biomedical Responsible Conduct of Research Course 1, RCR.

All modules must be completed by the end of the first Fall semester; and a copy of the student’s Completion Report must be submitted to the Program administrative office before January 15th.

Unsatisfactory Scholarship Expand answer

Students are required to have a minimum grade-point average of 3.0 to be eligible for the doctoral qualifying examination, admission to the comprehensive examination, thesis defense and graduation. One or more failing grades, a cumulative grade-point average below 3.0, or failing any of the examinations may be considered evidence of unsatisfactory scholarship and be grounds for dismissal from the University (see full policy).

Lab Rotations/Advisor

First-Year Faculty Advisor Expand answer

The Program Director serves as the faculty advisor for students entering the program. The Director is available for specific questions about the program and for more general discussions of a student’s progress. The Director also signs course registration forms during the first year. After a student has selected a thesis adviser, that faculty member will assume these responsibilities.

Lab Rotations Expand answer

Students undertake three, six-week laboratory rotations in their first year. Timing of the rotations is flexible and can begin in the fall semester, although most students do not begin their first rotation until spring. The purpose of lab rotations is to provide students with the opportunity to become acquainted with different projects, laboratory environments and techniques to allow an informed choice of a thesis project and advisor. The rotation advisor will provide the student with a defined project and clear expectations as to the amount of work involved and the work schedule. The student should also meet regularly with the advisor to discuss the progress of the rotation. More than one rotation can be carried out in the same lab if the student has committed early to that lab for their thesis project (but this is at the discretion of the Program Director). Rotations often continue through the summer.

If research in a particular faculty member’s lab interests you, make an appointment to discuss the possibility of rotation in their lab. The Program Director will be available to provide guidance to narrow your choices.

Thesis Advisor Expand answer

It is the student’s responsibility to identify a thesis adviser and permanent laboratory home by the end of the first academic year. Students should consult the First-Year Faculty Advisor with any questions about this process. A student may choose any member of the Neuroscience Graduate faculty, provided that the faculty member is willing to accept the student and that there are space and resources available to the student. Usually, the student will have rotated with this faculty member and will be familiar with their laboratory and researc.h

Doctoral Students

Academic Requirements Expand answer

The coursework in the Neuroscience Graduate Program consists of required courses and electives. This website lists all the required courses that the students need to take during the first two years (numbers in parentheses indicate the credit hours).

In addition to the required courses, students also need to take a minimum of five credits of elective courses during the second year. PhD students may take no more than 12 graded credits (A-F) of NEURO 600 Thesis Research, and master’s-level students may take no more than six such graded credits.

Publication requirement

A further program requirement is that the candidate must submit at least one 1st-author paper for publication in a peer-reviewed journal before the thesis defense.

Qualifying Examination Expand answer

As prescribed by the Graduate School, students must have a minimum GPA of 3.0 to be eligible to take the Qualifying Examination (QE). The purpose of the QE is to establish that a student is adequately proficient in the critical thinking skills needed to qualify for admission to the Doctoral Degree in Neuroscience. The qualifying exam is composed of written and oral components addressing a scientific “proposition” selected by each student from a list. Each student will address a different proposition, thus avoiding collaboration. The QE is taken at the end of the first year (usually completed by the end of May).


A list of scientific propositions is given to the students on a specified date in May. Each student must state which proposition they will address within 24 hours and submit the finished paper to the Office of Research Affairs by 5 p.m. twelve (12) days later. The oral component of the examination will be held ten (10) days after the written component is submitted.

(Note: The precise timeline and number of days allowed for each component of the QE may differ slightly each year to accommodate faculty schedules and other calendar variations.)


Format of the Written Component: The written component (Proposition Part A) is a paper that should rely heavily on primary (peer-reviewed) literature to defend or refute the chosen proposition. The written paper must be 4 pages long, including title and abstract, but not including the references. Text should be 11-point Arial font, single-spaced and contain 1-inch margins. The document must be submitted electronically to the Office of Graduate Student Affairs. The written paper will be graded by at least 3 (three) faculty members. Plagiarism is unacceptable and will result in a failing grade.

The format of the paper is as follows:

  1. Title: The Proposition Statement chosen by the student (verbatim).
  2. Abstract: A short abstract (200 words or less) detailing a concise overview of the subject in question and the broad conclusion of the paper.
  3. Body of paper: May be organized into subsections as appropriate, and must contain citations to primary literature. A figure may be included (no more than 25% of one page) if it is directly pertinent to the subject. References to textbook chapters, websites, and other non-peer-reviewed literature is not appropriate.
  4. Bibliography: All cited literature must appear in a bibliography at the end of the paper, using the Journal of Neuroscience format. There is no limit to the number of references. Use of a proper citation manager (e.g. EndNote or equivalent) is highly recommended.

Format of the Oral Component: The oral component (Proposition Part B) is designed to test the students’ knowledge and ability to think on their feet in a meeting with a committee of program faculty. The student will design and present a series of experiments to test a hypothesis related to the written component. Students will be expected to explain their reasoning, experimental design, and anticipated results; while demonstrating detailed knowledge of the neuroanatomy, cellular, molecular, and systems neuroscience, as well as technical approaches employed in their experimental design. Students should not prepare a PowerPoint presentation and will be asked to use a whiteboard or chalkboard to help explain their plan and answer questions from the examining committee. Students may also bring a single page of notes to be given to the examining committee members, which they can refer to if needed.

Clinical and Translational Science (CTS) dual-title program Qualifying Exam

This dual-title program is designed to complement and expand the student’s major area of study by instilling knowledge and skills needed to transform findings from the laboratory into clinical settings and community practices to improve human health.

The written and oral components of the Qualifying Exam will use the same format as above, but the content will be expanded to include at least one clinical or translational element relevant to the proposition statement. For example, this may take the form of a critical evaluation of a pertinent clinical trial or translational study in the published literature, development of a new clinical or translational hypothesis accompanied by a brief description of a study design to test the hypothesis, or identification of a potential barrier to translation of a novel discovery and a proposed solution to overcome the barrier.


Students are judged on their combined performance in the written and oral components of the exam. Each component is assigned a percentage grade and the combined performance is the average of those grades. An average score of 70 percent or above is considered a pass. In the event of failure, the Neuroscience Curriculum Committee will determine whether the student may take another examination, which must be administered within four weeks. If the student fails a second examination, they shall be terminated from the program.

Doctoral Committee Expand answer

According to the Graduate Degree Programs Bulletin published by the Graduate School regarding Doctoral Committees, the Doctoral Thesis Committee should have:

  • A minimum of four members of the PSU Graduate Faculty.
    • Two members must be faculty members in the Neuroscience Graduate Program, including the thesis adviser
    • One member must be from a disciplinary field outside neuroscience (Outside Field Member)
    • One member must be outside the home department of the thesis adviser (Outside Unit Member)

The Outside Field Member represents a field outside the candidate’s major field of study and is expected to provide a broader range of disciplinary perspective and expertise.

A person not affiliated with Penn State may be added as a special member (beyond the four members of the approved Penn State Graduate Faculty) upon recommendation of the head of the program and approval of the graduate dean.

In addition to the above requirements:

  • The doctoral candidate and three committee members must be physically present for the comprehensive exam and defense. No more than one person may be present via telephone or videoconference, and the Dean of the Graduate School must approve this arrangement. A form letter is available for this special request.
  • Approval of two-thirds of the committee members is required to pass the comprehensive exam and dissertation defense.
  • The student must submit paperwork three to four weeks prior to scheduled comprehensive exam and defense to:Ms. Kathy Shuey, H170, Penn State College of Medicine; 717-531-8982;

Please note these regulations may be temporarily suspended during epidemic quarantine, and remote video conferencing may be used by all committee members.

Doctoral Thesis Committee Meetings

Progress on the doctoral research project should be periodically monitored by the thesis committee, which is required to meet with the student at least once a year but more frequently is recommended, at the discretion of the committee.

The format of these meetings is also at the discretion of the committee but usually involves private discussion between the committee members (while the student waits outside the meeting room) followed by student presentation of data, questions and discussion, and agreement on future directions. It is recommended that the student present the committee members with brief data summaries or a meeting agenda about a week before each committee meeting. It is also recommended that the student provide the committee with a brief written summary after the meeting, detailing the discussion and future directions agreed upon by the committee.

Provision of refreshments during committee meetings and oral exams

In the past some students have provided food and drink for their committee meetings at their own expense, especially during the holiday seasons. It should be made clear that this practice is not a requirement or expectation and is discouraged.

Comprehensive Examination Expand answer

The Comprehensive Exam is designed to test the student’s maturation “from a consumer of knowledge to a generator of knowledge” and is the final formal evaluation before the student advances on to focus entirely on thesis research. It is a test of their ability to present a logical experimental plan to adequately test a hypothesis.

The page limit for the Research Strategy is six (6) (with 0.5-inch margins, including top and bottom, single-spaced Arial 11-point font); and for the Specific Aims page it is one (1). You may use extra pages for the bibliography without limit. (see: Please adhere strictly to this format. Your committee will be instructed to ignore information that exceeds the strict page limit (just like a real grant application). The inclusion of preliminary data, however, is flexible and can include data from published sources if cited correctly.

This exam is usually taken at the end of the second year and consists of a written research proposal followed by an oral examination. The Comprehensive Examination is administered by the student’s doctoral committee. It is a rule of the Graduate School that students must have a minimum grade-point average of 3.0 to be eligible to take the Comprehensive Examination. The student must also have satisfied the English competence requirement and should have completed all required coursework. The oral examination must be formally scheduled by the Graduate School, which requires three weeks’ notice.

Written Proposal

The purpose of the exam is to test the student’s ability to develop a coherent research proposal that is supported by logical arguments and literature. The proposal may be on any topic, but will most likely be within the scope of the student’s prospective thesis research, and follows the format of a NIH Pre-doctoral Fellowship application (F31). The thesis committee must agree upon the topic of the proposal and the Specific Aims, usually by choosing between two draft Specific Aims pages submitted by the student. After agreeing to the topic and wording of the Specific Aims, the student’s adviser should not have any further role in preparation of the exam. This means no verbal or written communication about the exam, and the student should not have access to grant proposals previously written by the adviser.

Obviously, the student is free to utilize any published (or in press) papers that are available, but the logic, experimental design, and writing must belong entirely to the student. The written proposal must be completed and delivered to the members of the doctoral committee at least one week before the oral examination. It should be emphasized that this proposal need not correspond to the student’s intended dissertation research, although it usually does.

Oral Examination

The student is responsible for organizing the date and venue of the comprehensive exam. This includes scheduling the time and date with all committee members. During the oral examination students are expected to present the hypothesis, rationale and approach of their proposal through a power point presentation (approx. 20 minutes). Students should be prepared to address extensive questions from the thesis committee both during this presentation.


Students are judged on their combined performance in the written and oral portions of the exam. A favorable vote of at least two-thirds of the committee is required to pass. In the event of failure, the examining committee will determine whether the student may re-take the examination. A second failure will result in termination from the program. Successful students may be encouraged to convert their Comp Exam to an actual fellowship application, based on guidance from their committee.

Dissertation and Final Oral Examination Expand answer

The research project that a student performs in partial completion of a PhD should be original work that was performed primarily by the student. Chapters taken directly from manuscripts published by the student as first author should be adapted to conform to the thesis format. Repetition of methods sections is discouraged.

Students must present their thesis in accordance with the Penn State University guidelines as described in “Requirements and Guidelines for the Preparation of Master’s and Doctoral Dissertations.”

Current copies can be obtained from the Thesis Office:

115 Kern Building
University Park, PA 16802

It is recommended that the student will organize a “penultimate” committee meeting to decide the timeline for completion of the thesis. Once the committee agrees that the student should write up a thesis, they should agree on a time frame. It is typical for the committee to recommend a four- to six-week period for the student to complete the thesis. The final draft should be submitted to the committee at least two weeks before defending, but longer is recommended since they will need time to read it and make corrections. Many faculty still appreciate a hard copy of the draft thesis, so they can write corrections directly on the page as needed before and during the thesis defense.

Thesis Preparation

The research project that a student performs in partial completion of a PhD should be original work scholarship that was performed primarily by the student. Chapters taken directly from manuscripts published by the student as first author should be adapted to conform to the thesis format. Repetition of “Methods” sections is discouraged. The thesis may contain unpublished as well as published data and may even contain data from failed experiments and pilot studies in the main text or as appendices, if considered appropriate by the student and thesis committee. Students are encouraged to end their thesis with a “Future Directions” section, in recognition of the scientific process. In some cases, the “thesis by publication,” is acceptable, in which the student uses several published papers as individual chapters, and a general introduction and discussion are added to complete the thesis. However, only papers in which the candidate is the 1st author are eligible to be used in this way and the candidate must clearly identify in the thesis any parts of the paper that they did not generate.

The Graduate School has strict guidelines for the preparation and format of the written thesis; see the Graduate Programs Thesis and Dissertation guidelines for details. Extensive consultation with the thesis committee is strongly encouraged. The draft dissertation should be complete and properly formatted before the oral examination.

Thesis Defense

The thesis defense consists of a public seminar presentation of the thesis research, followed by a closed meeting with the student’s doctoral committee. The examination should be scheduled after the student has fulfilled all of the Graduate School requirements for the degree; three weeks notice is required by the Graduate School for scheduling this examination. The dissertation should be delivered to the members of the doctoral committee two weeks before the defense. A favorable vote of at least two-thirds of the thesis committee is required for passing the final oral examination. A favorable vote of at least two-thirds of the thesis committee is required for passing the thesis defense examination.

Thesis Acceptance

This is the final step of the process: the thesis must be accepted, as indicated by the signatures of two-thirds of the doctoral committee and the program director.

Activate Intent to Graduate Expand answer

At the beginning of the semester in which the student intends to defend their thesis, the student must apply for graduation via LionPATH.

Master's Students

Courses Expand answer

Master’s students must have a minimum of 30 credits and a 3.0 overall GPA (see the MS Requirements Graduate Degree Programs Bulletin).

If pursuing a master’s thesis option, up to six 600-level credits from relevant departments may be A-F graded and 12 credits need to be in the major at the 400-600 level. The students select a thesis committee (upon consultation with faculty adviser), write a thesis, and defend their work.

See the course list here.

Thesis Expand answer

Students must present their thesis in accordance with the Penn State University guidelines as described in “Requirements and Guidelines for the Preparation of Master’s and Doctoral Dissertations.”

Current copies can be obtained from the Thesis Office:

115 Kern Building
University Park, PA 16802

Miscellaneous Expand answer

Students accepted into the master’s program should not assume that successful completion of the master’s thesis entitles them to transition into a PhD position, even if they complete the master’s track within 6 semesters and have completed all academic requirements. Transition may be possible under exceptional circumstances but is at the discretion of the program director under the advisement of the associate dan of graduate education.


Assistantships and Student Status Expand answer

Students must be registered as full time students to maintain stipend eligibility. Full time status is considered either a minimum of nine credits each fall and spring semester (pre-comprehensive exam) or NEURO 601 for zero credits (post-comprehensive exam).

Career Services Expand answer

Career services are available to all graduate students through a full-time career services coordinator, Jessica Kirkwood. Services include frequent training events, workshops, industry job fairs, outside speakers, and in-person guidance on CV and resume construction. More information is available at the Career Services page.

Employment Expand answer

Fulfilling the requirements for a degree (MS, PhD, or MD/PhD) from the Neuroscience Graduate Program requires extensive time and effort. In most cases, this undertaking is incompatible with additional employment either within or outside the University. Thus, students appointed to a graduate assistantship or fellowship typically are not permitted to hold any additional employment. Per University Policy, any additional jobs (PT wage payroll, etc.) must be officially approved before starting. These are the steps for p/t wage positions that students need to follow:

  1. Written approval from PI which must include: hours per week/semester, duration of position and source of funds
  2. Submit PI approval and Job Posting to Rachel Reager and Becky Yockey in Graduate Education
  3. Rachel Reager/Becky Yockey review and submit all information and recommendations to Dr. Daniela Zarnescu, associate dean for graduate education and postdoctoral training, for approval

For international students: Employment for F-1 and J-1 students is limited, and working without permission is a violation of status and a deportable offense. F-1 and J-1 students may not work off-campus without permission from International Student and Scholar Advising (ISSA). On-Campus Employment is permitted with certain restrictions. Students must complete employment paperwork with ISSA in order to work on-campus. A Social Security number is required for anyone receiving payment. ISSA can assist you with this process. ISSA offers workshops every semester which explain the different types of off-campus work permission available to F-1 and J-1 s Only in very rare circumstances will exceptions be granted. Students on assistantships must receive written permissions from the research adviser, the Chair of the Program, and other individuals designated by the Graduate School prior to seeking concurrent employment.

Governance Expand answer

The NEURO Program is governed by the Neuroscience Advisory Committee, which typically meets once per month.

The Advisory Committee for this academic year is listed below.

Internships Expand answer

The internship experience is optional. Typically after the second year in residence, students can spend a summer in an internship at a medical center, government laboratory or in an industrial environment. The time frame for the internship is negotiable with the Thesis Adviser and Co-Director (see further details under General Information).

Library Services Expand answer

Graduate students are encouraged to use the services and study spaces of the Harrell Library. Group and individual spaces are available throughout the library (open 24 hours with ID for general access).

During staffed hours, students may borrow current books and materials on reserve, including whiteboard markers. Most of the group study rooms have digital screens for collaborative work and are available by reservation.

The library provides 3D printing services and an audio/ video recording studio (called the One-Button Studio) available to all College of Medicine faculty, staff and students.

The library website has up-to-date information on upcoming workshops, events and technology support and resources. Additionally, students are welcome to schedule appointments with faculty librarians and staff for training on literature searching, bibliographic software management, technology training or other related topics.

Safety Training Sessions/Examinations Expand answer

Within the first semester of residence, all students are required to complete all necessary safety-training courses. These are generally offered during Orientation, before the start of the first semester.

Neuroscience Student Seminars Expand answer

Students beyond their first year in the program are required to give one presentation of their research each year in the Neuroscience Student Seminar series. This is an informal 50-minute PowerPoint presentation with opportunity for questions from the audience.

The Student Seminar series has two main goals:

  1. provide an opportunity for every student to practice delivering a professional research seminar and answer questions about their research;
  2. provide all students and faculty with the opportunity to learn about research being conducted by others in the Neuroscience program.

Student seminars are generally held on Thursdays at noon in C3700, although other times may be scheduled. Students can request two faculty members to give written feedback on their
performance. but they are not graded. Students are advised to inform their doctoral committee members about the date and location of their seminar since the committee may use this opportunity to meet with the student after the seminar.

All students are required to attend and participate in the Neuroscience Student seminar series. Excuses should be obtained by emailing either Kathy Shuey or the program director. As a general rule the presenting student is responsible for room setup prior to giving their seminar.

Attendance at NBS Department Seminars

To encourage good practice in collegiality and self-directed education, it is a program requirement that all pre-comprehensive exam students attend the NBS Department seminars, which are often given by excellent invited external speakers as well as internal Penn State faculty. For the same reason, it is recommended that all post-comprehensive students also attend NBS seminars on a regular basis. Furthermore, students are encouraged to be aware of other seminars and research meetings occurring on campus (e.g., BMS program seminars and guest speakers). Students in the Neuroscience graduate program students are also highly encouraged to attend the Annual Graduate Student Forum and present their research each year.

Teaching Expand answer

Teaching experience is available but is not required by the Neuroscience program. Students who have successfully taken NEURO 511 have the opportunity to develop teaching skills in a classroom or laboratory by taking teaching assistant positions in the neuroanatomy laboratory sessions of the medical school course NBS 725.

Students interested in this opportunity should initiate discussion early on with their adviser and the graduate program. Students may also take the Graduate School Teaching Certificate.

Thesis Submission and Exit Interview Expand answer

Upon completion of the degree, students are to provide the Graduate Program with a copy of their thesis. Students also participate in the University Exit Interview Process.

Use of Artificial Intelligence Expand answer

Computer-assisted information processing has become an essential part of academic and scientific investigation, including simple writing tools such as spelling and grammar checkers, keyword database search tools (PubMed, Google Scholar, etc.), image analysis, and a wide variety of advanced bioinformatics tools. These digital tools all employ some degree of artificial intelligence (AI) and their use is entirely legitimate in conducting and reporting scientific investigations. However, the advent of more sophisticated “generative” AI tools that are designed to generate a detailed product based on a set of command inputs by the user demands a preemptive policy on the use of these new and rapidly evolving tools in graduate school.

It is the policy of the Graduate Program in Neuroscience that the use of “generative” AI tools (such as ChatGPT, StabilityAI, SimplifiedAI, Google Docs GhostWryter, etc.) is not a legitimate method to generate written work or oral presentations that were assigned to assess academic aptitude (such as course papers and presentations, qualifying exams, comprehensive exam, etc.). Essentially, “generative” AI must not be used to generate graded work of any kind. Students may use AI to generate artistic illustrations, but not images that could be construed as scientific data. Students found to have used “generative” AI to write a graded assessment will receive a failing grade for the assignment. This includes the use of “generative” AI to write any part of a research thesis. Separate from this policy, the use of “generative” AI is permitted in the conduct of research designed to test specific AI-related hypotheses, under the purview of the research advisor.

Vacation/Sick Leave Expand answer

Full time graduate students in the Neuroscience Graduate Program who receive stipends are permitted two weeks of vacation per academic year (July 1 to June 30).

Leave should be arranged at least two weeks in advance with consent of the Program Chair (first-year students) or dissertation/thesis adviser (second year and above students). Students will not be routinely granted vacation leave while enrolled in class work. For extenuating circumstances, special arrangements may be made for additional vacation days. Such arrangements need approval of the Program Chair (first-year students) or the dissertation/thesis adviser (advanced students). Vacation leave days do not accrue from year to year. Holidays designated by The Pennsylvania State University are separate and in addition to vacation days.

No sick leave is formally assigned or earned, but may be used as necessary with approval of the Program Chair (first-year students) or the dissertation/thesis adviser (advanced students). Under normal circumstances, up to five days of sick leave per calendar year will be granted, when necessary. Sick leave in excess of five days will be recorded as vacation time. It is the student’s responsibility to contact the Program Chair or dissertation/thesis adviser when he/she is absent from the classroom or laboratory due to illness.