What is research?
- What is clinical research?
- What is basic science research?
- What is translational research?
Publications
- What constitutes authorship?
- What do the various authorships mean?
- What is the peer review process?
- What happens after you submit a manuscript to a journal? <- New (4/11)
Undergrad research opportunities
- How to set one up
- Will I publish?
Medical student research opportunities
- How to set one up
- Will I publish?
- How do I choose a project?
Year-off programs for medical students
- Links to various programs and their descriptions
- Some reviews by people in these programs
For most of the people reading this forum, "research" refers to the application of the scientific method to expand human knowledge. Wikipedia calls it a harnessing of curiosity. At the very least, this requires a hypothesis, an experiment that tests that hypothesis, and either the rejection, or acceptance of that hypothesis.
With respect to the health fields, this can range from detecting signaling molecules in cell culture, determining the efficacy of treatments in disease models, surveying patient populations for clinic usage statistics, injury threshold testing with cadavers, NIH funded Phase 3 clinical trials, and so on. The house of medicine is huge and there is a place for nearly every interest. Many different techniques are used and nearly every discipline can bring some new insight.
- What is clinical research?
Clinical research generally refers to research with human subjects. Many definitions will focus on testing the efficacy of a drug or treatment, and this encompasses a large part of the clinical research literature. But many cohort and cross-sectional studies don't generally involve treatments, but they are considered clinical research. I feel that if the project requires human subjects and IRB approval, then it can be considered clinical research. Much of the work is done in hospitals or clinics.
- What is basic science research?
Basic science research deals with the most fundamental components of observable phenomena. Just like Galileo rolling cylinders down inclined planes, basic scientists try to find the exact reason why something happens, and what parameters affect the outcome. It is effectively on the other end of the spectrum from clinical research. The drug used in a clinical trial is the product of years of work discovering and characterizing a cell receptor: How that that receptor is generated in-vivo, it's function, what increases it's function, what decreases it's function. These are the questions a basic scientist pursues. Much of medical basic science research is done in labs (A.K.A. bench research) manipulating cells and organic molecules.
- What is translational research?
Translational research has become more of a buzzword with the NIH. This came about because while the US had developed a great deal of medical knowledge over the last 50 years, relatively few new treatments have resulted. It occupies the Gulf
between the extremes of basic science and clinical research. Translational research strives to apply basic science findings in the clinic. Or take clinical findings and figure out what it going on. Due to being sort of a grab-bag middle man, where translational research is conducted depends on the focus of the project.
Most of the posters on this board won't use legal definition of a publication; rather we're talking about a significant contribution to the scientific literature. We're talking about a full-length, peer reviewed journal article. These generally include an explicit description of a series of experiments, their results, and the interpretation of those results, showing how they relate to the field. You must also justify your experiments. There are specifics for each journal, and a guide can be found here. They are usually about 3500 words long and follow the Intro, Methods, Results, Discussion (IMRAD) format. Results and experiments must be unique, new, and generally positive. Negative results (e.g. "no correlation found," "X does not effect Y") are much more common than positive because there are many ways not to make a lightbulb, but only one way to make one that works, so they don't get the same amount of press.
- What constitutes authorship? or
- What does 1st, 2nd, etc. author mean?
Authorship means that an individual had a significant contribution to the completion of a published or publishable research project.
People starting in research are commonly frustrated by this - they will often state that they took all of the data for the project, did a lot of work, and yet, are not named an author. By contrast, the lab PI, who "didn't do anything," is given an authorship. It is understandable that this situation is frustrating, mostly because much of the work that goes into a project takes place before any data is taken. The idea behind the research must come from somewhere. In basic science bench work, there must be funding to pay for lab space, hire workers, pay for equipment, and supplies. In clinical research, you have to write a proposal and get IRB approval. The experiments must be designed to illuminate the one property you wish to examine.
With these ideas in mind, you can understand how authorships are generally awarded.
1st author: The "man on the ground," the one who ran the experiments and managed the day-to-day aspects of the study. Often the person who interprets the results and writes the majority of the final article. They will write the proposals and get permission from the host institution and gather subjects. Hour-by-hour, they put the most time and effort into the project. As a result, they get the honor of being named first, which is reflected in how papers are generally referenced (e.g. Smith, et al, Cell). Students working towards a graduate degree often fill this role.
2nd author: If there was someone who also put in a great deal of effort, but not as much as the first author, they are named second. In two-author papers, they are actually the last author.
Last author: Generally the person overseeing the project. They make sure that #1 is doing good science. They also are the one who secured the funding to support #1. Often the PI of the lab or the graduate student's advisor. While they didn't necessarily "do all the work," they make the work possible by providing infrastructure and expert guidance, and so they deserve to be recognized on any work that is produced in their lab.
Everyone else: They are the pinch hitters, the guys called in on a afternoon to do a statistics consult or collect data. They did an important part of the work, they just didn't do much compared to everyone else involved. A lot of undergrad students will get their first publication by helping write up a project completed by someone else, and will be recognized as a 3rd or 4th author.
The process of peer review is one of science's method of self-policing, one of the hallmarks of a profession. When papers are submitted to a journal for publication, they are scrutinized by experts in the same field. In an ideal situation, these experts have no ties to, or no conflicts of interest with, the authors of the submission. In general, these experts evaluate the merits of the submission and either reccomend it for publication, reject it completely, or reject it with revisions. The required revisions can be as simple as word and graphic changes, or they can be as complex as requiring a whole new set of experiments. The authors have to fufifll these revisions (and any new data aquired) in order for the submission to be accepted by that journal. The process from beginning writing to publication can take years.
The insights and advice in this thread are provided courtesy of Tildy, a practicing physician scientist who is also a journal editor in his field.
Introduction:
I’ve been asked to describe a bit about how biomedical articles get edited from the editor’s perspective. That is, to remove a bit of the mystery from the process for those submitting their first paper(s). I thought I’d do so via a thread so that questions can be asked directly.
Below, I will trace the typical course of a biomedical research article from hitting the on-line “submit” button, to appearance. This is not about how to write a good article, pick the right journal for it, etc. This is about how your well-written, brilliant contribution to human knowledge gets annihilated by a bunch of ignorant reviewers and editors and what you should do about it to get it published.
Remember that, similar to an article about the course of medical education that talks about the preclinical first two years of medical school while ignoring the fact that the preclinical part isn’t two years everywhere, this article is about the TYPICAL course used by primary journals within a discipline. In other words, not about “Science” or “NEJM” or, on the other end some 4th tier (there are no true tiers by the way…) journal, but about good primary journals that reject more papers than they accept and that practioners, physicians and scientists often read to keep up with a field. Of course, there are variations in the theme and details of the process. However, like medical education, there are more things in common than different between these journals.
1. Article goes to journal where it is logged in and screened by a technical editor.
2. If within the basic scope of the journal, close to being understandable in English, and basically follows the format of the journal, it is sent to the Editor-in-Chief of the journal.
3. The editor will either handle it as the “primary editor” or send it to an associate editor who may or may not be especially knowledgeable about the specific research topic. Journals with associate editors often have 1 to 10 of them who serve as the “primary editors” for manuscripts. They will review any difficult decisions with the editor in chief, but the workload for major journals is huge and associate editors are generally fairly autonomous.
4. The “primary editor” (henceforth, editor) will look at the article briefly, especially the abstract and decide if the article merits further scientific review. This review is based on the topic – does it really fit the journal, the scientific method – is it up-to-date, etc? For clinical studies, the editor will consider the study design. For example, some journals do not publish many or any retrospective reviews. Finally, the editor may do a scan of the literature to see if this study is novel or if the authors have published some of it before.
5. If the paper is deemed very unlikely to be acceptable for publication for any reason, most commonly it just isn’t “novel” or “important” enough for that journal, the editor will send it back to the author with a rejection letter. The letter may briefly describe the reason or simply say that the study would not be likely to clear peer review. Total time from submission for this process is often about a week or two. Appealing a rejection like this is essentially futile for the authors. Move on and resubmit elsewhere. Remember that the editor is doing you a FAVOR here with the quick rejection. If they send out for peer review a paper that they have already decided won’t be accepted, they are delaying you by a month or more on resubmission of the paper elsewhere. Journals have relatively fixed numbers of papers they can accept. The editors can’t accept all papers even all of the good ones. So, sending out for peer review a paper that is, for example, a case report or a retrospective review that the editor knows won’t be something they can accept for this journal is not being nice to the authors. You can think of analogies here to the med school admissions process….
6. If the paper is deemed worthy of peer review, the editor will select the reviewers. This is the key step of the whole process. If the authors have suggested reviewers, these will be seriously considered. In general, the reviewers suggested by authors are not more positive to papers than non-suggested authors. If the authors have given the name of someone they do not want to be a reviewer, the editor probably won’t send it to them. But, they can send it to anyone they want, with the understanding that the editor has been warned of a potentially biased review. Certainly any editor brings their own scientific biases into selecting reviewers and that is inevitable. Clearly, the editor can select reviewers that they think will be easier/harder, etc. In general though, editors are seeking the most knowledgeable and unbiased reviewers they can find. They also are going to look at the reviewer’s history with their journal. Is the reviewer usually on-time with reviews, do they accept review assignments or complain?
7. Peer review occurs by the reviewers. This is the LONGEST step of the process. If the reviewers initially chosen by the editor decline to do the review, then the editor may need several tries to find reviewers. In general, it is considered nice to review a paper within 2 weeks of receiving it. But this often doesn’t happen. A range of 2 to 6 weeks is common. Some journals are notoriously slow. The editors can prod reviewers, but can’t force anything since being a reviewer is a voluntary, unpaid task. Reviewers are usually scientists and physicians with patients to see, their own papers to write, and grants to prepare. A thorough peer-review can take 2-20 hours for a reviewer and that is totally unreimbursed time. Peer reviewers are making a significant effort and sacrifice to look at YOUR science. Keep this in mind. A brief review is not a favor. A thorough review is best, even if it seems like a lot of work to rewrite the paper. In a sense, a good peer reviewer is acting as a mentor. Of course, some reviews are unkind and inaccurate, but most are pretty accurate and well-done.
8. The reviews are sent back to the editor who must make a decision. With some variation on the theme, one of three decisions is possible:
a. Accept the paper (very rare to be accepted at this point for original science papers)
b. Accept the paper if the author can respond appropriately to the reviewers comments/criticisms.
c. Reject the paper
Of these, within the middle category, there can be various ways by which the editor can indicate the likelihood of ultimately accepting a paper and convey this information to the authors. The editor could send the author a decision letter saying “This is the best thing every written about the topic, but answer the reviewers about why you did X,Y and Z before I can accept it.” They could send the author a letter saying “This is awful, but maybe we are missing a key point, so look at what the reviewers say and tell us why they are wrong.” Or, most commonly, they’ll simply say “Respond to the reviewers and we’ll relook at it.”
9. The editor will send this letter back to the authors, potentially adding their own personal comments and/or note some technical issues (e.g. please double space) that need to be fixed on resubmission. The editor may point out the most important points they need to have answered or they may provide some commentary to help the author with the revision. Pay very close attention to what the editor says in their letter. It is not inappropriate to communicate with the editor directly on these points, although this is uncommonly done. You may not, as the author, gain direct access to the reviewer except for those journals that do open review (few at present time).
10. The authors must decide if they are willing to revise the manuscript based on the reviewers’ and editor’s comments. They must respond with a revised manuscript, specific rebuttals, and a very nice letter that ALWAYS starts with (give or take a few words) “We appreciate the reviews sent to us regarding our paper. We have enclosed our revised manuscript in which we have responded to each comment by the reviewers.” Do not ever, ever send a hostile letter back to the journal. Even if you (or the PI) decide not to revise the paper for that journal, you may submit to that journal a different paper sometime and don’t want to make enemies.
After your first Nobel Prize you can become a prima donna and blast the reviewers for their ignorance of your brilliance. For now, eat crow and respond nicely to each point the reviewers’ make, even the ones that are clearly based on a lack of understanding of what you’ve done and written. That doesn’t mean you MUST agree with the reviewers and make EVERY change they suggest. You can decide not to make any given change the reviewer wants. But, you must explain to the editor clearly why you disagree with the reviewer. Remember the reviewer will see this again, especially if you pick a battle here. If the reviewer wants small changes that you don’t think are worth it, generally, do what the reviewer wants. Save the battles for key issues. If there are (as there almost always are) multiple authors on your paper, make sure that the co-authors see both the revised manuscript and your letter of response before submitting these. Above all, ALWAYS respond professionally to EVERY point in EVERY review. Don’t just ignore a comment by any reviewer – give a response to everything that is said. Please, remember to keep it polite and collegial. The reviewer could be your future boss, colleague, or mentor. Express your anger at the unfairness of the review to your friends and teddy bear.
11. The editor will look at the authors’ response and make a new decision. The choices are:
a. Accept the paper
b. Accept the paper IF the authors make a few more small changes
c. Send the paper BACK to the original reviewers to see if they agree or at least will accept the authors responses
d. Reject the paper.
12. In theory, the cycle of 7 through 11 can be repeated a few times. In general, it is not done more than twice (two revisions) except in rare circumstances or related to some trivial changes that lead to a third or fourth revision. Typos and the like can usually be handled after acceptance. It is uncommon for an unsolvable conflict between author and reviewer to exist. Usually reviewers will accept the authors’ answers but may ask for some “hedge words” or explanations of the limitations of the study in return. These types of trade-offs make editors satisfied that a balance of perspective has been achieved. In the uncommon situation of a true stalemate, it is up to the editor to make a decision. Don’t worry, they won’t be afraid to do it. But, they would much rather that the author and reviewer are in reasonable agreement. As a last resort, the editor may offer the reviewer the option of writing an editorial commentary or a letter to the editor in rebuttal of a paper. This is unlikely to occur for studies done by post-docs and junior faculty.
13. Eventually, the paper is accepted by the editor and the author is sent a letter that includes the phrase “Your manuscript has been accepted”. At this point, and not before then (e.g. not when the letter says “we expect to accept” or “if you respond to these minor issues we will accept”) can the authors list the paper as “In Press” on their CV.
14. The manuscript as accepted is now sent to the publisher and leaves the hands of the editorial office. Whether it is technically edited by hand, by computer, by the journal, or by the publisher for grammar, style and spelling is highly variable, but somehow it will get edited and your typos fixed. It is the publisher that will determine when the paper actually appears and send out page proofs.
15. About 2 months before the paper appears in the written journal, you will be sent, usually electronically as pdf files, what are called page proofs. This is the paper as it will look in the journal with everything except the actual final page numbers since they don’t know them yet. You will be given 48 hours to review these. It really behooves you to spend a few HOURS poring over these. Have someone who isn’t familiar with the paper do this too. Amazing how often tables are messed up (data columns transposed!), words and sentences deleted, etc. Much better to catch these mistakes now than after publication and be forced into a correction. You cannot rewrite anything in the paper now except for making corrections of mistakes. You could be asked to pay if you insist on substantial changes. Your paper could be delayed as well. Rarely, if you ask to make a real change, the editor could be informed and decide if they agree to this change. Be cautious here. Fix actual mistakes but don’t try to change what you’ve written based on more recent data, new publications in the field, etc.
16. Finally, the paper is published. If an on-line version was published earlier, it will usually be replaced with the final version which will now appear in pubmed as a final version.
17. Congratulations! Now, just do this another 20-50 times and you’re ready to be promoted!
- How do you set up a research opportunity as an undergrad?
Talk to your professors. If you have a favorite, ask them after class if they are looking for help. Most profs will be receptive and see it as a compliment. If they can't take you on, they may be able to give you the name of some one who can. Many profs will offer class credit, work study, or an hourly wage in exchange.
At this stage, you don't have many skills to offer the PI, so you will probably wash a lot of glassware and/or work with a lot of mice. Or rats. It's boring being a lab monkey, but you have to start somewhere. Just like any job, if you're hard working, attentive, and enjoyable to work with, you'll be given more responsibility, namely allowed to run some of the experiments. This may sound cool, and sometimes it is when you're doing SEM or using a motion-capture suite, but all of that is window dressing to the real crux of research: learning how to refine a hypothesis, design an experiment that tests that hypothesis, and including good controls. Being able to critically appraise your results is also important. A good mentor and PI will introduce you to these concepts.
- Will I be able to publish as an undergrad?
Do not expect to publish - most undergrads don't. However, it is feasible to present some results at a local/college research conference. The most important things are to learn and to see if the field is a good fit for you.
- How do you set up a research opportunity as a medical student?
The only real time for medical students in regular MD programs to do research is during their first summer (~10 weeks) after MS1. Their next summer is filled with USMLE
prep, MS3 runs through the summer after that, and the summer of MSIV...you're either moving, sleeping, or waiting for intern year to start.
Similar to undergrad, talk to your professors. Many profs will present aspects of their research in their lectures, so if you like a particular lecture, talk to them. Many schools have summer research fellowships which can get you a stipend for the summer. Most run $2500-5000 for the 10 weeks.
There are a number of formal summer research programs that medical students can apply for.
See the list of institutions.
Bangalore
• Indian Academy of Science
• Indian Institute of Science
• Jawaharlal Nehru Centre for Advanced Scientific Research
• National Centre for Biological Sciences
• National Institute of Mental Health and Neuro Sciences
• National Tuberculosis Institute
Chandigarh
• Post Graduate Institute of Medical Education and Research
• Institute of Microbial Technology
Chennai (Madras)
• Indian Institute of Technology
Delhi
• All India Institute of Medical Sciences
• Council of Scientific and Industrial Research
• Defence Research and Development Organisation
• Indian Council of Medical Research (ICMR)
• Indian Institute of Technology
• Institute of Genomics and Integrative Biology
• International Centre for Genetic Engineering and Biotechnology
• National Brain Research Centre
• Science and Engineering Research Council
• National Institute of Immunology (NII)
Hyderabad
• Centre for Cellular and Molecular Biology
Jammu
• Regional Research Laboratory (Indian Institute of Integrative Medicine)
Kanpur
• Indian Institute of Technology
Kolkata
• Indian Institute of Chemical Biology (IICB)
Kharagpur
• Indian Institute of Technology
Lucknow
• Central Drug Research Institute
• Industrial Toxicology Research Centre
Mumbai
• Indian Institute of Technology
• Tata Insitute of Fundamental Research
Pune
• Agharkar Research Institute
• Bioinformatics Distributed Information Centre
Pilani
• Birla Institute of Technology and Science
Trivandrum (Thiruvananthapuram)
• Rajiv Gandhi Centre for Biotechnology
• Regional Research Laboratory National Institute for Interdisciplinary Science & Technology
• Sree Chitra Tirunal Institute of Medical Sciences and Technology
Indian council of Medical Research (ICMR)
• Central JALMA Institute for Leprosy
• Enterovirus Research Centre (EVRC)
• Genetic Research Centre, Mumbai
• Institute of Cytology and Preventive Oncology
• Institute of Immunohaematology
• Institute of Pathology
• National AIDS Research Institute (NARI)
• National Institute of Cholera And Enteric Diseases
• National Institute of Epidemiology (NIE)
• National Institute of Nutrition (NIN)
• National Institute of Occupational Health (NIOH)
• National Institute of Virology
• Research institute of Medical Sciences, Patna
• Tuberculosis Chemotherapy Centre (TCC)
• Vector Control Research Center
- Will I be able to publish as a medical student?
Yes and no. Most med students can get a few results if the spend their summer doing research, which may be enough for a poster, but most won't have enough to publish. Everyone will know someone who does - a buddy of mine got 2 papers for a summer's effort, but he was motivated and happened to join a very productive lab.
To publish something as a medical student, most folks will have to work over several years (maybe extending their summer work) or they will get some clinical research time during their 2nd two years. Your attendings will likely have several projects going at any time, so just ask to get involved. Many schools also allow for research rotations, which are prime time to get something written up or conduct a brief project.
- I like orthopaedics
, but there's no orthopaedics
research opportunities where I go to school - will it look bad to do research in a different field? OR
- How do I choose which research project to do?
Like most things, it will help if your interests all line up nicely together. Yes, it could help your chances of matching if can talk about your biomechanics research with the orthopaedics
attending during your residency interview. That being said, this is an unlikely scenario for most medical students since:
1) Many students don't know what they want to specialize in when they matriculate, and
2) Most will change their mind while earning their MD/DO.
Given this, it is unlikely that an orthopaedics
attending will look poorly upon the neurology project you did during you MS1 summer. If this is the first time a student has done any research, I urge you to treat it as a learning experience and use the opportunity to see if research is right for you. At this point you're 'kicking the tires' of the career path, and a mentor's job is to clear out the red tape so that you have as rich and educational experience as possible. Learn whatever tools you need to conduct your assays, or studies, or whatever, but focus on the process of refining a hypothesis, designing an experiment that tests that hypothesis, and including good controls. Knowing what your results mean (both what you expect to happen, and what your controls confirm or deny) is also very important, especially since it is excellent material for any subsequent interview. Other things like stats and protocol design sort of shake out of the process from there. So I suggest you choose a project based upon the interpersonal skills and mentoring ability of the project's PI. More important than a big name, or flashy project is doing quality work, and a good PI will get you there.
- But I still don't know what project to do!
If you're really stuck on a place to start, yet you're undecided on your career, then start by looking at diseases that effect systems. Examples include hypertension, inflammation, and diabetes. These are also extremely common conditions, and there is not a field of medicine that does not deal with these problems in some way or another. You can spin a project in hypertension, for example, to support an application to any residency.
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