Explain what it means to say, variables must vary.? List and define the four levels of measurement (using examples) discussed in this weeks introduction and res

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Rev Clin Esp. 2015;215(7):401—404

www.elsevier.es/rce

Revista Clínica Española

SPECIAL ARTICLE

Research: Why and how to write a paper?

R.W. Light

Vanderbilt University, Nashville, TN, USA

Received 26 April 2015; accepted 27 April 2015 Available online 6 June 2015

KEYWORDS Research; Publishing; Scientific writing

Abstract In this article, an internationally renowned pulmonologist with extensive experience in teaching and publishing gives practical advice to young physicians and/or residents on the importance of doing research, the steps for planning a project and also some do’s and don’ts of writing and publishing a scientific paper. © 2015 Published by Elsevier España, S.L.U.

PALABRAS CLAVE Investigación; Publicación; Escritura científica

Investigación: ¿por qué y cómo escribir un artículo?

Resumen En este artículo, un neumólogo internacionalmente reconocido, con amplia expe- riencia académica e investigadora, da consejos prácticos a residentes y médicos jóvenes para llevar a cabo proyectos de investigación y publicaciones científicas. © 2015 Publicado por Elsevier España, S.L.U.

I have been involved in medical research for more than 50 years.1 During that time I have both directed the research myself and also mentored many young researchers. The fol- lowing is a summary of what I have learned during this period.

Why do research?

The first question that one might ask is why anyone, par- ticularly you, should ever want to do research. There are several possible reasons. One might want to become famous,

E-mail address: [email protected]

but only rarely does this happen. One might want to get rich, but most researchers do not end up that way. Without question, the income of practicing physicians in the United States is higher than those in private practice.2 One might want to get a free trip. Certainly, if you perform research and your abstract is accepted for presentation, you might win a free trip to an interesting place. One might want to obtain a good professional position. Certainly a background in research with publications might help in that regard. One might want to answer a question about a diagnosis or treat- ment for a disease that one of your patients has. This a rational reason to perform research. One might want to help patients. Again, this is a valid reason to perform research. Lastly, one might want to discover something new. The main

http://dx.doi.org/10.1016/j.rce.2015.04.007 0014-2565/© 2015 Published by Elsevier España, S.L.U.

© 2015 Elsevier España, S.L.U. and Sociedad Española de Medicina Interna (SEMI). All rights reserved.

© 2015 Elsevier España, S.L.U. and Sociedad Española de Medicina Interna (SEMI). All rights reserved.

© 2015 Elsevier España, S.L.U. y Sociedad Española de Medicina Interna (SEMI). Todos los derechos reservados.

402 R.W. Light

reasons that I have performed research are the last three possibilities.

What is necessary to perform research?

Do you need a genius intelligence quotient (IQ) level, a lot of money, an inquisitive mind, dedication, persistence, or organization? In my opinion, the most important element is persistence. I have worked with many individuals who have started a project, but never completed it. They may likely stop at any stage from initially writing the proto- col, doing the research or, most commonly, while writing the paper itself. To be a successful researcher one must be persistent and finish the research. In my opinion, the second most important element is organization. By organi- zation I mean arranging one’s life so that time is not wasted. Have things organized so you do not spend an hour looking for a paper. Do not waste time complaining about things. I keep a list of things that I need to do on my computer. When I have a certain number of minutes free, I look at the list and see what I can accomplish in that period of time. I believe that dedication is the third most important ele- ment. If you are not dedicated to your research and prefer instead to watch football games or go to movies, you are less likely to be successful. The fourth most important element is to have adequate money. Without adequate resources to perform your research, it will obviously fail. Even so, it should be noted that many of the research projects that I have completed did not require any money (e.g., the paper describing Light’s criteria1 and the one describing parap- neumonic effusions).3 The fifth most important element is to have an inquisitive mind. This is important to aid the researcher in formulating the research and analyzing the data. Lastly, one need not have a genius IQ level to perform research. It helps to be smarter than the average person, but being a genius is not necessary.

What are the different types of research?

Case reports are frequently the type of research that one starts with. However, it is difficult to get case reports pub- lished unless the case is distinctly unique. Medical journals do not like to publish them because they decrease their impact factor. Reviews of the literature are worthwhile but, again, are hard to get published unless one is invited to write the review. Retrospective reviews of case series generally do not cost any money and are certainly useful. However, their downside is that important data are frequently miss- ing. Prospective reviews of case series do not cost any money either and, if they are organized, missing data should not be a problem. Be aware that it may take time to accumulate the appropriate number of patients. The evaluation of new diagnostic tests is an important part of medical research, when comparing them with the test that has previously been used as the gold standard. The sensitivity, specificity, and receiver-operating curve for the new test should be com- pared with those of the previous one which was the gold standard. The evaluation of new therapies is one of the most commonly performed types or research. Ideally, it should be done with randomized, double-blind controlled studies. If the study is not blinded, the researcher may be biased in

evaluating results. The evaluation of new medical devices is important in advancing medical science. Again, it is best to do randomized controlled studies, but it is frequently difficult to design medical device studies which are blind. Lastly, a large percentage of medical research has to do with basic science. I performed no basic science or animal studies until 1988. When I started doing animal studies I found that they were much easier than patients to recruit. Subsequently, I found that cells were easier to obtain. How- ever, basic science research requires more resources than do many types of human research.

How do you get started to do research?

The first thing you need to do is to develop an idea including a hypothesis. How do you develop the idea? It can be a ques- tion raised when taking care of a patient. It can be a question raised by an associate, an attending or a subordinate. It can be a question raised while attending a lecture or while read- ing the medical literature. It can also be a question raised while dreaming or even while drinking.

Once you have posed the question, it is important to review the literature. It is best not to embark upon a project that has already been done and you need to review the lit- erature to determine if this is the case. Medline is a good place to start. On Medline you should narrow your search as far as is practical. One should obtain a copy or download all pertinent reference papers. Do not rely on review papers. Do not use Wikipedia.

It is important to organize the pertinent references. I rec- ommend transferring all abstracts to your computer. Keep them organized by putting them in alphabetical order by the first author’s last name. Make notes on the abstracts as pertinent. Make an outline of what you have found in your review.

Once you have your idea formulated and have reviewed the literature, then discuss the proposal with your asso- ciates. In addition, you should evaluate the resources necessary to complete your project. How many patients do you need to answer your question? How much money will it take to conduct the study? Take into account money for personnel, ELISA kits, animals, pharmaceuticals, pipettes, etc. What personnel are needed for the study? What space, including for both the office and laboratory, is necessary for the study? How long will it take to complete the project? In general, it is a good idea to multiply your estimate of required time by a factor of at least two.

Is the research ethical?

For human subjects, the question I ask myself is as follows: would I volunteer for this project if I were qualified to partic- ipate? If your answer to this question is no, then the research should not be performed.

Writing the protocol

Before the research can be conducted, a research protocol needs to be written. You should start with the specific objec- tives and hypothesis. Then, set the stage for your protocol by writing the background information, which is essentially

Research: Why and how to write a paper? 403

a review of the literature in the context of your research. Next, describe the actual research protocol. Make this very detailed. Do not leave anything open to question. Include the statistical method of analysis and perform a power anal- ysis. Include references in the protocol.

Necessary approvals before research can begin

If the project involves humans, approval must be obtained from the Institutional Review Board (IRB) before the study can be started. If blood or tissue is obtained for present or future studies, a written informed consent is required. IRB approval is necessary even if you are simply doing a chart review, but this does not require a written informed con- sent. Most journals will not accept a paper for publication if the project has not been approved by an IRB. If animals will be studied, the animal studies committee must approve the project. If radioisotopes are used in the study, the radioiso- tope committee must approve the project. If biohazards are being used, e.g. Staphylococcus aureus or asbestos, the biohazard committee must approve the project. If you are studying a new drug or an old drug for a new indication, you may have to submit your proposal to the National Health Service (NIH in the United States).

Eliciting cooperation of collaborators

In order to elicit the cooperation of collaborators, one needs to create a win—win situation. By this I mean you need to cre- ate a situation in which you win (your project gets done), but the collaborator also needs to benefit. The main difficulty is creating the win portion for the collaborator. This can be in the form of a co-authorship on the manuscript, saving the collaborator work, a dinner, a book or money. It is best to avoid the following: direct payment for patient referred is unethical, competition for patients that the collaborator wants to study, and making extra work for the collaborator where nothing in return is received.

Performing the research

Before you actually start the research, have everything orga- nized. Effort is wasted if everything is not done on the first patients. It is best to develop forms for all the data which will be collected. They should be such that the data is easily transcribed to a computer. Alternatively, you can enter the data directly on spread sheets on the computer. The respon- sibilities of all co-investigators and collaborators should be well defined. Once the research is started, one should be patient, persistent, and compulsive. If the research is going poorly and the chances for success appear minimal, the research should be stopped.

Reasons for failure of research projects

The most common causes for failure of a research project are a lack of persistence or organization. Other reasons for failure include an inadequate literature review — after the research has been started it becomes apparent that

the study has already been done or that the hypothesis is completely different from what is accepted in the medi- cal literature. It is also possible that someone completes an identical project before yours is completed, but this is uncommon. Inadequate numbers of patients can lead to fail- ure of a project as can a lack of required cooperation. In some instances, there is not enough time to complete the project. This is particularly likely to happen when residents, fellows or visiting researchers are primarily responsible for the project. And lastly, and very importantly, the research is done but the paper never gets written. This has happened to me numerous times in my career.

Analyzing the data

Once the research project is finished, it is time to analyze the data. Most physicians are frightened by statistics. How- ever, analysis of the data is easy if it is organized. The actual statistical analysis will depend upon the design of the project. In general, one desires to discover whether the results in two groups differ significantly. Basic terms in statistics are the mean (the average value), the median (the value with an equal number of observations above and below), and the variance, which is a measure of the vari- ability of the results in one group. Most studies involve comparing the mean levels in two or more different groups.

Minimize the variance

The formula for the variance is shown in the following equa- tion:

Variance = Sum(xi − xmean) 2

n − 1

where xi is the value of the ith observation, xmean is the average of all observations and n is to total number of observations in the group. The standard deviation (SD) is the square root of the variance. The standard error of the mean (SEM) is the SD divided by the square root of n. In order for two means to be different with a probability (p) value less than 0.05, the two means need to be separated by 2 SEMs. From the above discussion, it is apparent that if the variance is minimized, the two means are more likely to differ significantly. In performing research, it is important to do everything possible to minimize the variance. This means paying careful attention to details to decrease the randomness of the results.

Writing the manuscript

The main sections of the manuscript are the abstract (sum- mary), the introduction (why?), the materials and methods (how?), the results (what you found), and the discussion (so what). When I write a manuscript, I write the sections in the following order. First, I write the material and methods section. This section is the easiest to write — just cut and paste from the protocol (remember to change tenses from future to past). Then, I write the results with the liberal use of tables and graphs. I next write the introduction while

404 R.W. Light

relying heavily on the protocol. I do not write the introduc- tion initially because the results of the study may alter it somewhat. Afterwards, I write the discussion. Lastly, I write the abstract so that it will be consistent with the remainder of the paper.

Writing the discussion

Without a doubt this is the most difficult part of the paper to write.4 Before I start writing the discussion, I always make an outline of what I want to include. In the outline, the first paragraph is a brief summary of the results of the study and the last paragraph is the conclusion. The other para- graphs in the discussion should compare the results of the present study with those reported previously, the clinical implications and limitations of the study.

Tips on writing

Write in a simple manner. Keep sentences short. The first sentence in each paragraph should say what that paragraph is going to say. This makes it easier for the reader to speed read the paper. If the reader agrees with and knows about what is said in the first sentence, he/she can skip the rest of the paragraph. If you have difficulty in writing one para- graph, go to a different one. Writing the manuscript is a big task. Count your successes as paragraphs, not entire papers. If you write one paragraph per day, you will have at least 12 manuscripts per year.

Submitting the paper

Before you submit the manuscript, have someone whose first language is English and has some knowledge about medicine, review the manuscript and edit it. Make certain that all the co-authors review the manuscript. Consider their sugges- tions, but remember that you do not need to accept all of them. Next, you need to choose the journal to submit your manuscript to. One should look at previous editions of the journal to see if they have accepted similar papers on simi- lar subjects.5 It is best to select a journal with a high impact factor. After it has been selected, read the instructions to the authors carefully and follow them. Abide by any word limits that have been established (i.e., if the journal states that the upper limit is 2500 words, do not submit a paper with 3500 words). If they say that they do not accept animal experiments and your research involves animals, do not sub- mit it to that journal. If you do not follow the directions, the reviewers will think that you are not a careful researcher.

When paper is accepted provided revisions are done

The goal of revising the paper is to get it accepted for publication. A rebuttal letter should be written where the critiques of each of the reviewers is addressed. List each

criticism by reviewer and then formulate a response. It is best to use different fonts when listing criticisms and making responses. When the reviewer requests an explana- tion of something, he wants it explained in the manuscript — not only in the rebuttal letter. Make simple requested changes without argument. Remember, the reviewer is try- ing to make the paper better. Thank the reviewers for their constructive criticisms whether or not you like them.

When the paper is rejected

If the paper is rejected, do not give up but rather plan on resubmitting. Remember that submitting a paper is a lit- tle like playing the lottery — sometimes you get favorable reviewers and sometimes you get unfavorable reviewers. Note that reviewers frequently do not agree—maybe you were just unlucky or, alternatively, maybe the paper is really bad. There are many medical journals and some have higher standards than others. Before you submit to another jour- nal, look carefully at the criticisms of the reviewers from the first submission and answer as many as possible. You may get the same reviewer upon resubmission and nothing irritates a reviewer more than seeing the same paper again without any changes.

Conclusions

Persistence and organization are the most important fac- tors for success when doing research. Before the research is started, review the literature and write a detailed protocol. Create win—win situations to elicit cooperation of collabo- rators. Write the paper one paragraph at a time. Respond to reviewers and change the paper as suggested.

Conflict of interest

The author declares that he has no conflicts of interest.

References

1. Light RW, MacGregor MI, Luchsinger PC, Ball WC Jr. Pleural effu- sions: the diagnostic separation of transudates and exudates. Ann Intern Med. 1972;77:507—14.

2. Singh VK, Giardiello FM, Singhal S, Badreddine RJ. Life after fellowship: private practice versus academics — the low down. Gastrointest Endosc. 2014;79:327—31.

3. Light RW, Girard WM, Jenkinson SG, George RB. The inci- dence and significance of parapneumonic effusions. Am J Med. 1980;69:507—12.

4. Cals JW, Kotz D. Effective writing and publishing scien- tific papers, part VI: discussion. J Clin Epidemiol. 2013;66: 1064.

5. Cals JW, Kotz D. Effective writing and publishing scientific papers, part X: choice of journal. J Clin Epidemiol. 2014;67:3.

Editing Graphs

Video Title: Editing Graphs

Originally Published: 2012

Publishing Company: SAGE Publications Ltd

City: Brighton, United Kingdom

ISBN: 9781473995628

DOI: https://dx.doi.org/10.4135/9781473995628

(c) Andy Field, 2012

This PDF has been generated from SAGE Research Methods.

ANDY FIELD: When I came to the idea of doing these little presentations to show various things in

SPSS, I thought, well, they're going to be much more interesting than reading the book. And it'd be

a nice little thing that people could go and watch and keep themselves entertained on those lonely,

cold nights. But I've just been kind of looking over

ANDY FIELD [continued]: some of (LAUGHING) the ones I've already done, and they're all terrible!

Really, really, really unbelievably boring. However, this one– this one is going to be fantastic. And the

reason for that is because it's all about graphs.

ANDY FIELD [continued]: And graphs are the most exciting thing in the universe. Really. So sit down

with a nice, big syringe of heroin, and off we go into the exciting world of graphs. Now in the book

chapter I spend quite a lot

ANDY FIELD [continued]: of time telling you how to draw different types of graphs. And that's all well

and good, but one of the things that it did mean is that I didn't really have a lot of space to talk about

how you can edit graphs in SPSS. And editing graphs can be quite a useful thing to do, because the

graphs that pop out of SPSS don't always look how you want them to look.

ANDY FIELD [continued]: Now one of the kind of quite tragic things about– [LAUGH] being me is that

you can get really quite excited [INAUDIBLE]. Perhaps that's the wrong word. But in a way excited

about a good graph. A good graph says a million words. And, you know, it's like looking at, I don't

know,

ANDY FIELD [continued]: a nice Picasso or something. It's just– they're things of great beauty. But

when they're pink, they can be things of hideous ugliness. So edit your graphs to present your data

well. In the chapter I've gone for bloody pages about this, about how graphs should look and how

they should do this and they shouldn't do that.

ANDY FIELD [continued]: And that's because I really am quite sad. However, so that you can all

impress me with your graphs– in fact, I expect every single person watching this– [LAUGH] it'll one

person, then– that'll be my mother– to email me your beautiful graphs.

ANDY FIELD [continued]: And there'll be a cash prize of zero pence– or that's "dollars," for the

American– to the best graph that I receive. Although if you can get SPSS to make your graphs look

like a cat, then, well, I might send you something nice.

ANDY FIELD [continued]: Anyway, in the book chapter we use an example, and I'm going to use that

example here, of men and women watching different types of films and looking at how aroused they

get by those films. And that arousal is supposed to indicate how much they like the film. And we used

two films– Bridget Jones' Diary, which is supposed to appeal to women.

ANDY FIELD [continued]: It's, uh– well, I don't know if this is a British thing, but it's known as a "chick

flick." Whereas Memento is– well, it's kind of gender-nonspecific, really, so it should appeal equally, I

think, in theory. So we have these data. These are up on the screen now. And, to draw graph of them,

all we

ANDY FIELD [continued]: do is use SPSS Graph Menu and then the Chart Builder. Now the Chart

SAGE

2012 SAGE Publications, Ltd. All Rights Reserved.

SAGE Research Methods Video

Page 2 of 7 Editing Graphs

Builder gives us a nice little window like this. And basically we have this canvas, here. "Canvas"

makes it sound like you're making a painting, which I kind of like. So you have a canvas on which to

create your masterpiece.

ANDY FIELD [continued]: And it also gives you– unlike if you were a great artist, they don't have

a number of templates that they can pick, but maybe they should. I don't know. You know, here's

template for a vase of sunflowers or whatever. But in SPSS it gives you some templates for graphs.

ANDY FIELD [continued]: There are bar charts. You can see there's a whole variety of bar charts

here, line charts, and so on and so forth, all explained in the book. All of it. Every single one. Now

we want to do a bar graph, so we go to the Bar menu. And what we end up wanting to do is what's

known as a "clustered bar chart." So we double-click on this. And, lo and behold, we get a nice little

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