Student Research Resources

In general, one topic is appropriate for the thesis, but it is recognized that some students may have performed several projects in parallel under the supervision of their mentor. If the student elects to include more than one study in the thesis, it is recommended that an attempt be made to integrate the topics into one coherent presentation. In rare cases where this goal cannot be achieved, it may be acceptable to divide the results section into different portions (or “chapters”). However, to be consistent with Yale formatting requirements, a thesis may not contain more than one abstract, introduction, statement of purpose, methods, results, and discussion section. It is not acceptable to submit a published or submitted manuscript in lieu of the thesis requirement. The formal thesis is presented as a digital document (PDF) during the graduation year. It must adhere to the following formatting and content requirements. These aspects of research are critical in making the work sound, error-free, and impactful for communities of interest. Recognizing that students may have uncertainly regarding how these guidelines relate to their thesis, OSR will be happy to answer any questions that may arise. Additionally, students may find it useful to consult the Equator reporting guidelines to enhance the quality and transparency of their theses. The Yale MD Thesis is a doctoral thesis that assesses research competencies as the basis for the conferring of a doctoral degree. Therefore, a minimum requirement of 30 pages (exclusive of title page, abstract, acknowledgements, table of contents, figure legends, references) is considered the minimum acceptable length.

1. Font: 10-12-point font should be used.
2. Line spacing: Body paragraphs and tables should consist of double-spaced text. Single spaced text may be used within block quotations, footnotes, and bibliography.
3. Margins: 1.5-inch margins on the left with one-inch margins on the remaining three sides. These margins apply to text, full-page images and illustrations, and tables.
4. Figures: Illustrative information, schematics, and representative data should be included as figures. Each panel in a figure should be labeled. Legends should describe each panel in detail in a 9-point font or greater and positioned below the figure to which they refer. Figure legends do not count towards the 30-page minimum.
5. Page Numbers: Each page in the thesis should be numbered except the title page, abstract, acknowledgements, and table of contents. The numbering should start at page 1 of the first page of the instruction be placed either at the top or bottom center, or at the top or bottom right-hand corner, at least 1/2 inches from any edge.
6. Minimal page requirement: Most Yale MD theses average 40-80 pages of text. A minimum of 30 pages of text excluding title page, abstract, acknowledgements, table of contents, figures, legends, and references is required. Tables may count towards the minimum page requirement.

1. Title page: Title should not exceed 100 characters including spaces between words. The title page is not included in the 30-page minimum.
2. Abstract page: As described below. The abstract is not included in the 30-page minimum.
3. Acknowledgements: Personal and faculty acknowledgements, grant support, departmental support, etc. The acknowledgements page is not included in the 30 page minimum.
4. Table of Contents: with page numbers for each section. The table of contents is not included in the 30-page minimum.
5. Introduction: A thorough, complete, detailed, critical review of the literature that contextualizes and cites the work of previous investigators. This section should describe the state of the existing knowledge, provide rationale for the study, identify knowledge gaps, and frame the contribution of the thesis to medicine. The introduction is included in the 30-page minimum.
6. Statement of purpose: Specific hypothesis if appropriate, and specific aims of the thesis. The statement of purpose is included in the towards the 30-page minimum.
7. Methods: Thorough description of valid and rigorous study design. The methods are included in the 30-page minimum.
   1. Student Contributions: Describe in detail exactly which procedures, methods and experiments were conducted by you and which procedures, methods and experiments, generation of data, or production of reagents, were performed by other members of the study team. It is not sufficient to state that this information may be mentioned elsewhere. It must be summarized here. It is recognized that students may often be completing a portion of a larger work. A statement detailing precisely what was done by the student and what was done by others does not detract from the thesis but is necessary for academic honesty.
   2. Ethics Statement: Include information regarding the ethical and responsible conduct of research.
   3. Human Subjects Research: If relevant, include explicit information regarding Institutional Review Board approval and informed consent. If the study had a waiver of consent, this exception must be clearly stated. Information regarding inclusion of historically vulnerable populations as research participants should be included here.
   4. Laboratory Animals: For studies involving laboratory animals, include an explicit statement regarding study approval from the Institutional Animal Care and Use Committee. Include information regarding the species, strain, sex, and age of laboratory animals in this section as well.
   5. Methods Description: Provide information regarding the materials and methods used in the study. Each method should consist of its subheading and paragraph and be described in detail that is sufficient to allow its replication by an investigator who did not participate in the study.
   6. Statistical Methods: The last paragraph in this section should present the methods used to derive results. As needed, describe any data preprocessing such as transformation and normalization. Describe how outliers were defined and handled and present descriptive statistics as appropriate. The number of sampled units (ie, “n”) and significance (ie, “P”) should be reported for each statistical comparison. Continuous variables that are normally distributed may be presented as mean + standard deviation. Continuous variables that are asymmetrically distributed should be presented as median + interquartile range. All statistical tests should be clearly described and include information regarding testing level (alpha) and one- or two-sided comparisons. Corrections for multiple testing should be addressed and reported. Any novel or complex data algorithms should be clearly described and appropriately referenced.
8. Transparent reporting of results: All primary data related to the thesis topic should be presented. Important data should be enumerated in figures or tables. For ease of review, it is preferred that figures and tables be included in proximity to their callout in the text. Alternately, tables and figures can be presented separately after the discussion but, if possible, it is advantageous to the reader to include these components in the body of the results section, as occurs in research publications. The results section is included in the 30-page minimum.
9. Discussion: This section presents thorough and detailed interpretation and analysis of data, conclusions drawn, and framing of observations with the larger scientific literature. Limitations should be addressed, as should alternate interpretations and how the thesis may inform future studies in the field. Whenever relevant, a discussion of how the thesis may or already has meaningfully impact(ed) communities of interest should be included here. The discussion section is included in the 30-page minimum.
10. Challenges & Limitations: A brief discussion of methodologic, operational, and other challenges relevant to the research presented in the thesis. Please also include a brief discussion of how these challenges were addressed. Recognizing that all research projects have important limitations that readers should consider in interpreting the results, please include a brief discussion of the limitations relevant for your research. This section is included in the 30-page minimum.
11. Dissemination: Please include efforts made to share findings with the scientific community (through oral presentation, peer-reviewed publications, and other venues) and the larger community including patients. This section is included in the 30-page minimum.
12. Figure References and Legends: Figures must be cited sequentially in the text using Arabic numerals (for example, “Fig. 7”). Provide a short title (in the legend, not on the figure itself), explanation in sufficient detail to make the figure intelligible without reference to the text, and a key to any symbols used. Figures and legends are not included in the 30-page minimum.
13. Tables: All tables should be double-spaced, self-contained, and self-explanatory. Provide brief titles and use superscript capital letters starting from A and continuing in alphabetical order for footnotes. Tables and their legends are included in the 30-page minimum.
14. References: We strongly recommend the use of bibliography software such as Endnote for managing the references. References should be formatted according to New England Journal of Medicine Style. References are not included in the 30-page minimum.

It is acknowledged that theses in the area of medical humanities, ethics, history, and related fields may not obviously adhere to the above requirements. In this case, the thesis will likely replace the “hypothesis” with a “claim” based on evidence gleaned through literary, historical, and ethical research. The first paragraph of the Methods should still contain information about the student’s contribution. The subsequent paragraphs should describe the artistic, literary, or historical databases and methods used to gather the “evidence” presented in support of and contrary to the central claim. The discussion and remaining sections are the same and the 30-page minimum applies. If you have questions about how to best frame your thesis, please contact OSR.

Standardized format for the abstract of each MD thesis is required. This format must be followed for all abstracts published in the Yale Medicine Thesis Digital Library. These abstracts will not be reviewed for content. It is the responsibility of the student investigator and the faculty advisor to prepare the abstract. Faculty sponsors provide approval of the abstract when they approve the final version of the thesis. These abstract instructions are to be used for the digital library submission.

1. Abstracts should be formatted with 1.5-inch margins on the left and 1-inch margins on the remaining three sides. All text, including title page, must be double-spaced.
2. Abstracts may be no more than 800 words in length, not including title and author information.
3. Titles should be brief, clear, and carefully chosen. The title should not exceed 100 characters including spaces between words. Capitalize the entire title, using no abbreviations.
4. Authors’ names are to be written in full, omitting degrees. The student author's name shall be first. If the faculty sponsor also qualifies as an author, their name should be last. If the faculty member has been only a sponsor, his or her name should appear in parentheses after the name(s) of other authors as follows: "(Sponsored by...)". Other collaborators should be listed after the student's name and before the faculty sponsor's name. Immediately following the faculty sponsor's name, designate section (if any), departmental affiliation, institution, city, and state (Yale University School of Medicine, New Haven, CT) (see examples in the Thesis Guide).
5. For thesis work performed at another institution, designate the senior author's departmental and institutional affiliation. In parenthesis, indicate the Yale faculty sponsor and institutional affiliation with the phrase: "Sponsored by..." (see examples).
6. Organize the body of abstract as follows:
   1. A statement of the hypothesis or goals and specific aims of the study.
   2. A statement of the methods used.
   3. A summary of the results presented in sufficient detail to support the conclusions. Include actual values with statistics, if appropriate.
   4. A statement of the conclusions reached.
   5. Do not use subtitles, e.g., methods, results.
7. Do not include graphs, references to other publications, or acknowledgement of any research grant support. A single short table of results can be used if appropriate.
8. Abbreviations may be used in text only if defined initially by placing them in parentheses after the full word (or phrase) first appears in the text. Abbreviations may not be introduced in the title.
9. Non-proprietary (generic) names are required the first time a drug is mentioned, written in small letters. Proprietary names are always capitalized, e.g., acetazolamide (Diamox).
10. Completed abstracts must be approved by faculty advisor.

The thesis assessment will assess student performance on the following domains using a 1-5 Likert Scale.

Domains:

• Significance
• Innovation
• Rigor of Prior Research
• Methodologic Rigor
• Responsible Conduct of Research
  
• Organization and Clarity of Text
• Presentation of Data
• Interpretation of Data
• Student Effort
• Dissemination to Communities of Interest

Likert Scale:

1. Excellent
2. Very Good
3. Good
4. Fair
5. Not Acceptable

The vast majority of YSM students receive scores of 2-3 across these domains. Scores of 1 are considered truly outstanding. Scores of 5 are highly unusual and indicate the presence of critical deficiencies. Students receiving a score of “5” in any domain will be referred to OSR and the Progress Committee for remediation in order that they may stay on track to graduate.

1. Yalow, R.S., and Berson, S.A. 1960. Immunoassay of endogenous plasma insulin in man. J. Clin. Invest. 39:1157-1175.

2. Gardner, W., and Schultz, H.D. 1990. Prostaglandins regulate the synthesis and secretion of the atrial natriuretic peptide. J. Clin. Invest. In press.

3. Myant, N.B. 1981. The Biology of Cholesterol and Related Steroids. London: Heinemann Medical Books. 882 pp.

4. Innerarity, T.L., Hui, D.Y., and Mahley, R.W. 1982. Hepatic apoprotein E (remnant) receptor. In Lipoproteins and Coronary Atherosclerosis. G. Noseda, S. Fragiacomo, R. Fumagalli, and R. Paoletti, editors. Amsterdam: Elsevier/North Holland. 173-181.

5. Standardized format for the abstract of each MD thesis is required. This format must be followed for all abstracts published in the Yale Medicine Thesis Digital Library. These abstracts will not be reviewed for content. It is the responsibility of the student investigator and the faculty advisor to prepare the abstract. Faculty sponsors provide approval of the abstract when they approve the final version of the thesis. These abstract instructions are to be used for the digital library submission.

Your MD Thesis represents an academic milestone. The protection of your thesis copyright exists from the time your work was created in digital form. Every article, book, or web page you used in conducting research and writing your thesis is also protected by copyright. When you download a single personal copy of a research article or cite a short passage, this scholarship is protected by the legal concept of fair use. A basic understanding of copyright protections and fair use is found at www.copyright.gov. Yale University also provides a guide to copyright protection and fair use: http://ogc.yale.edu/legal_reference/copyright.html.

Section 107 of the U.S. Copyright Law describes how to determine if a particular use of copyrighted material is fair. However, the distinction between what is fair use and what is infringement is not always clear or easily defined. Copying an image from an academic e-journal and citing the source does not substitute for obtaining permission to reproduce the image. Many publishers use www.copyright.com to grant reproduction rights of their articles to authors.

ProQuest/UMI and the Yale Medicine Thesis Digital Library may elect not to distribute your thesis in the absence of evidence that permission or reproduction rights have been secured. Providing evidence of permission or reproduction rights is a student author responsibility. Examples encountered in MD Thesis research that require documentation of reproduction rights include but are not limited to:

• Sections of published survey instruments or questionnaires.
• Complete journal articles or other complete scholarly works [Note: The publisher Elsevier does allow graduate student authors of a journal article prior to graduation to reproduce their article in a thesis].
• Image, graphic, or pictorial works from publications where the author has transferred copyright to the publisher, a common occurrence.

The safest course to avoid a delay in thesis is to avoid using published images without obtaining permission. It is almost always possible to cite a source and expect that readers can find the figure, chart, or image in the published version of the referenced work. Research faculty who transfer copyright to a publisher of their article are no longer the copyright holder and are unable to grant permission for reproduction. To circumvent this issue, the student or mentor may be able to offer unpublished images from their group’s image collection.

When it is impracticable or prohibitively expensive to obtain permission through the publisher or the Copyright Clearance Center (www.copyright.com), students should avoid using that the material, unless they have obtained a written legal opinion that fair use would apply to the situation. Neither the Office of Student Research nor the Yale Library can supply legal advice on copyright and fair use. If there is any doubt, it is advisable to consult the Yale University Office of the Vice President and General Counsel at 432-4949. If a student is unable to obtain permission to use their previously published work in their MD thesis, they may place a permanent embargo on their thesis at the time it is uploaded into the Yale Medicine Digital Thesis Library (see below).

Upon receiving notification that the MD thesis has been approved as meeting graduation requirements, students should upload the thesis to the Yale Medicine Digital Thesis Library.

Starting with the YSM class of 2002, the Cushing/Whitney Medical Library and OSR have collaborated on the Yale Medicine Digital Thesis Library (YMTDL) project, publishing the digitized full text of medical student theses as a durable product of Yale student research efforts. Digital publication of theses ensures access for all scientists to a summary of such work, provides students with a formal citation for their thesis, and demonstrates the exceptional quality of student research and student-faculty cooperation at Yale. In 2006, the digital copy became a graduation requirement. Starting in 2012, alumni of the Yale School of Medicine were invited to participate in the YMTDL project by granting scanning and hosting permission to the Cushing/Whitney Medical Library, which digitized the Library’s print copy of their thesis or dissertation.

The Office of Student Research and Yale School of Medicine require that the MD thesis be submitted to the YMTDL. This submission should be accompanied by a completed “Yale School of Medicine Digital Thesis Depositor’s Declaration Form.”

Logging In

Detailed instructions on how to submit a thesis via the ProQuest website will be provided to students at the time they receive notification of formal YSM thesis approval and feedback from the Office of Student Research.

The electronic thesis submission process in ProQuest is organized into three major categories: Publishing information, About my dissertation/thesis, and Submission & payment. The system will walk you through the submission process step-by-step.

A few things to note: the ETD Administrator software is a 3rd party product that YSM licenses from ProQuest. Because this vendor is unaffiliated with Yale, OSR and Yale University Libraries do not have control over its policies or processes. The ProQuest Dissertations and Theses Global database is a subscription resource that collects dissertations and theses from multiple countries and a range of academic specialties. This collection is then made available to subscribers. When students choose to make their thesis publicly available, the full-text will appear in this database and users will be able to read, save, and download the text.

EliScholar is a digital platform for scholarly publishing provided by the Yale University Library (YUL). While it is supported by third party software, EliScholar is maintained by YUL and offers more flexibility in uploading and managing theses. The option selected for thesis release in the ETD Administrator system will apply to both ProQuest Dissertations and Theses Global and EliScholar. All theses are available to the Yale community (individuals with a NetID and password and users physically present at a library facility on campus) upon publication. A limited release of approved theses to the awarding institution’s user community is common practice.

YSM requires a Thesis Publishing Agreement Form, previously known as a Thesis Deposit Declaration Form, to be submitted in conjunction with your final thesis to ProQuest. For reference, you can find a copy of the form at this link.

We urge your participation in evaluating your experience with your thesis advisor at this Qualtrics link. The results will be kept anonymous, and any feedback to the individual faculty member will be made over a three- to four-year interval and will be a summarized statement, not involving reproduction or direct quotes from this form.

We will file these evaluations for future use by first and second year students who are looking for a project and research advisor. These evaluations have been immensely valuable to students initiating thesis projects. Thank you for your cooperation in this effort.