How to Read a Scientific Paper Dr. Talal Aburjai

Anatomy Lesson (The Components of a Research Paper) Before we dig into the specifics of analyzing a research paper, let's take a look at how scientific reports are organized and how the information is presented. 2Prof. Talal Aburjai

Usually, the basic structure of a scientific paper is the same, whether it's about AIDS or nuclear physics. Roughly speaking, you can always expect to find these sections in a paper: 3Prof. Talal Aburjai

the abstract, the background and rationale, a description of the methods used, the actual results, and finally the discussion -- the author's interpretation of the results. Hopefully the discussion makes sense of the results within the context of the issues that were raised in the background and rationale. Let's take a closer look at each of these sections. 4Prof. Talal Aburjai

The Abstract The abstract isn't technically a part of a paper, rather it's the "Reader's Digest" version: a short synopsis that summarizes the key points. These key points should give you a brief recap of each part of the paper listed above. Generally when one consults Medline, AEGIS, or other on-line information sources, an abstract is all that's available. 5Prof. Talal Aburjai

The abstract is an invaluable tool that can help you decide which papers are worth getting and reading in their entirety. As a tool for fully understanding the research, abstracts have substantial limitations. Specific details beyond those necessary to convey the main finding are scarce. 6Prof. Talal Aburjai

Often the description of methods is cursory or missing, making it hard to assess the scientific rigor of the study. Only the primary results are summarized, omitting potentially valuable supporting data. Still, abstracts play an indispensable role by allowing you to quickly extract the gist of a paper. 7Prof. Talal Aburjai

Introduction: Background and Rationale The background and rationale section tells you the reasons why the paper was written. It describes previous related research, identifies the questions that are still unanswered and proposes exactly what the paper will address. 8Prof. Talal Aburjai

For the purposes of this article I will refer to an imaginary antiretroviral drug I call "X-100" to provide examples. (X-100 does not exist, and all the data relating to X-100 is for illustration purposes only( 9Prof. Talal Aburjai

In a paper describing the usefulness of X-100 for patients who have previously failed a protease inhibitor (PI), the background and rationale should explain why the X-100 experiments were done in the first place. It might discuss the rate of virologic failure in patients treated with PIs, the clinical implications of virologic failure, and why new therapies like X-100 are needed. 10Prof. Talal Aburjai

Next, it might give us some background on X-100 itself: its basic chemistry and research results, including in vitro (in the laboratory) activity, animal studies, and any human research to date. 11Prof. Talal Aburjai

The background and rationale is exactly what it sounds like. It provides you with the basic context of the research, and offers the rationale (reason) why this particular study is needed. It should also describe the primary hypothesis (the key question that drives the research) as well as any secondary objectives 12Prof. Talal Aburjai

Materials and Methods The methods section is one of the most important, and also most neglected, parts of a scientific paper. Here the investigators describe exactly how they did the research: how they set it up, what measurements were taken, what mathematical methods were used to analyze the data, etc. 13Prof. Talal Aburjai

The methods section is where eligibility criteria (who was, and was not, allowed in a clinical trial) and endpoints (the exact definition of what is to be measured, and why) are defined. It is also in the methods section that the primary hypothesis and secondary objectives (introduced in the rationale) are specified in full detail. 14Prof. Talal Aburjai

In the case of our fictional "X-100" trial, the hypothesis might go something like this: "In adults with CD4 counts between 50 and 300, who have HIV RNA (viral load) of over ten thousand while on a protease inhibitor containing regimen, X-100 provides a greater and more prolonged decrease in HIV RNA compared to an optimized regimen using approved agents, guided by genotypic resistance testing." 15Prof. Talal Aburjai

The study then attempts to prove (or disprove) this hypothesis. Secondary objectives might compare X-100 with standard treatments on the bases of toxicity, quality of life, or other important considerations. 16Prof. Talal Aburjai

Results The heart of a paper, the results section presents the actual findings of the study. You also will read a description of what the conditions were at the start of the trial. In our fictional X-100 trial, we might see a summary of the patients' baseline (at the beginning) CD4s, their viral loads, their history of AIDS-related conditions, and, since this is a salvage trial, probably a summary of their previous treatment histories. In terms of the actual results themselves, we might expect to see the average viral loads of the group who got X-100 compared to those who didn't. 17Prof. Talal Aburjai

We also might see information about the duration of response, relative rates of clinical disease, toxicities, and other objectives of the trial. We can certainly expect to see all the data relating to the objectives described in the methods section. 18Prof. Talal Aburjai

Editorializing about the meaning and implications of the results is supposed to be restricted to the discussion section. Rarely are things divided this neatly, though, and the results section can contain a fair amount of analysis and sometimes, spin. 19Prof. Talal Aburjai

Discussion This is where the authors try to wrap up the whole package. The findings are discussed in the context laid out in the background and rationale, and the significance of the results is established. In general, this is the most editorial section of the paper, where authors not only discuss the raw data, but attempt to generalize (extend) these findings to groups of people who were not in the trial. 20Prof. Talal Aburjai

By nature, some speculation is not only tolerated but expected, even if it's as bland as "X-100 holds great promise for the treatment of HIV-infected individuals failing existing therapies." 21Prof. Talal Aburjai

Now that we have discussed how a paper is constructed, we can get to the interesting stuff -- the actual contents of the paper. Of the thousands of papers published every year, some are far more reliable and relevant than others. There are certain specific characteristics you can look for when deciding which papers to trust and use for making important decisions. 22Prof. Talal Aburjai

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2. Reading a scientific paper Although it is tempting to read the paper straight through as you would do with most text, it is more efficient to organize the way you read. Generally, you first read the Abstract in order to understand the major points of the work. The extent of background assumed by different authors, and allowed by the journal, also varies as just discussed. 24Prof. Talal Aburjai

One extremely useful habit in reading a paper is to read the Title and the Abstract and, before going on, review in your mind what you know about the topic. This serves several purposes. First, it clarifies whether you in fact know enough background to appreciate the paper. If not, you might choose to read the background in a review or textbook, as appropriate. 25Prof. Talal Aburjai

Second, it refreshes your memory about the topic. Third, and perhaps most importantly, it helps you as the reader integrate the new information into your previous knowledge about the topic. That is, it is used as a part of the self-education process that any professional must continue throughout his/her career. 26Prof. Talal Aburjai

If you are very familiar with the field, the Introduction can be skimmed or even skipped. As stated above, the logical flow of most papers goes straight from the Introduction to Results; accordingly, the paper should be read in that way as well, skipping Materials and Methods and referring back to this section as needed to clarify what was actually done. 27Prof. Talal Aburjai

A reader familiar with the field who is interested in a particular point given in the Abstract often skips directly to the relevant section of the Results, and from there to the Discussion for interpretation of the findings. This is only easy to do if the paper is organized properly. 28Prof. Talal Aburjai

Codewords Many papers contain shorthand phrases that we might term 'codewords', since they have connotations that are generally not explicit. In many papers, not all the experimental data are shown, but referred to by "(data not shown)". This is often for reasons of space; the practice is accepted when the authors have documented their competence to do the experiments properly (usually in previous papers). 29Prof. Talal Aburjai

Two other codewords are "unpublished data" and "preliminary data". The former can either mean that the data are not of publishable quality or that the work is part of a larger story that will one day be published. The latter means different things to different people, but one connotation is that the experiment was done only once. 30Prof. Talal Aburjai

3. Difficulties in reading a paper Several difficulties confront the reader, particularly one who is not familiar with the field. As discussed above, it may be necessary to bring yourself up to speed before beginning a paper, no matter how well written it is. Be aware, however, that although some problems may lie in the reader, many are the fault of the writer. 31Prof. Talal Aburjai

One major problem is that many papers are poorly written. Some scientists are poor writers. Many others do not enjoy writing, and do not take the time or effort to ensure that the prose is clear and logical. Also, the author is typically so familiar with the material that it is difficult to step back and see it from the point of view of a reader not familiar with the topic and for whom the paper is just another of a large stack of papers that need to be read. 32Prof. Talal Aburjai

Bad writing has several consequences for the reader. First, the logical connections are often left out. Instead of saying why an experiment was done, or what ideas were being tested, the experiment is simply described. Second, papers are often cluttered with a great deal of jargon. 33Prof. Talal Aburjai

Third, the authors often do not provide a clear road-map through the paper; side issues and fine points are given equal air time with the main logical thread, and the reader loses this thread. In better writing, these side issues are relegated to Figure legends or Materials and Methods or clearly identified as side issues, so as not to distract the reader. 34Prof. Talal Aburjai

Another major difficulty arises when the reader seeks to understand just what the experiment was. All too often, authors refer back to previous papers; these refer in turn to previous papers in a long chain. Often that chain ends in a paper that describes several methods, and it is unclear which was used. Or the chain ends in a journal with severe space limitations, and the description is so compressed as to be unclear. More often, the descriptions are simply not well-written, so that it is ambiguous what was done. 35Prof. Talal Aburjai

Other difficulties arise when the authors are uncritical about their experiments; if they firmly believe a particular model, they may not be open- minded about other possibilities. These may not be tested experimentally, and may even go unmentioned in the Discussion. Still another, related problem is that many authors do not clearly distinguish between fact and speculation, especially in the Discussion. This makes it difficult for the reader to know how well-established are the "facts" under discussion. 36Prof. Talal Aburjai