Autologous Mesenchymal Stem Cells in Multiple Sclerosis DQ

Randomized Placebo-Controlled Phase II in Multiple Sclerosis Sara Llufriu,#1 María Sepúlveda,#1 Yolanda Blanco,1 Pedro Marín,2 Beatriz Moreno,1 Joan Berenguer,3 Iñigo Gabilondo,1 Eloy Martínez-Heras,1 Nuria Sola-Valls,1 Joan-Albert Arnaiz,4 Enrique J. Andreu,5 Begoña Fernández,1 Santi Bullich,1 Bernardo Sánchez-Dalmau,1,6 Francesc Graus,1 Pablo Villoslada,1 and Albert Saiz1,* Tim Friede, Editor

Slightly Modified from John W. Little and Roy Parker–University of Arizona

http://www.biochem.arizona.edu/classes/bioc568/papers.htm

The main purpose of a scientific paper is to report new results, usually experimental, and to relate these results to previous knowledge in the field. Papers are one of the most important ways that we communicate with one another.

In understanding how to read a paper, we need to start at the beginning with a few preliminaries. We then address the main questions that will enable you to understand and evaluate the paper.

Organization of a paper

In most scientific journals, scientific papers follow a standard format. They are divided into several sections, and each section serves a specific purpose in the paper. We first describe the standard format, then some variations on that format.

A paper begins with a short Summary or Abstract. Generally, it gives a brief background to the topic; describes concisely the major findings of the paper; and relates these findings to the field of study. As will be seen, this logical order is also that of the paper as a whole.

The next section of the paper is the Introduction. In many journals this section is not given a title. As its name implies, this section presents the background knowledge necessary for the reader to understand why the findings of the paper are an advance on the knowledge in the field. Typically, the Introduction describes first the accepted state of knowledge in a specialized field; then it focuses more specifically on a particular aspect, usually describing a finding or set of findings that led directly to the work described in the paper. If the authors are testing a hypothesis, the source of that hypothesis is spelled out, findings are given with which it is consistent, and one or more predictions are given. In many papers, one or several major conclusions of the paper are presented at the end of this section, so that the reader knows the major answers to the questions just posed. Papers more descriptive or comparative in nature may begin with an introduction to an area which interests the authors, or the need for a broader database.

The next section of most papers is the Materials and Methods. In some journals this section is the last one. Its purpose is to describe the materials used in the experiments and the methods by which the experiments were carried out. In principle, this description should be detailed enough to allow other researchers to replicate the work. In practice, these descriptions are often highly compressed, and they often refer back to previous papers by the authors. Autologous Mesenchymal Stem Cells in Multiple Sclerosis DQ

The third section is usually Results. This section describes the experiments and the reasons they were done. Generally, the logic of the Results section follows directly from that of the Introduction. That is, the Introduction poses the questions addressed in the early part of Results. Beyond this point, the organization of Results differs from one paper to another. In some papers, the results are presented without extensive discussion, which is reserved for the following section. This is appropriate when the data in the early parts do not need to be interpreted extensively to understand why the later experiments were done. In other papers, results are given, and then they are interpreted, perhaps taken together with other findings not in the paper, so as to give the logical basis for later experiments.

The fourth section is the Discussion. This section serves several purposes. First, the data in the paper are interpreted; that is, they are analyzed to show what the authors believe the data show. Any limitations to the interpretations should be acknowledged, and fact should clearly be separated from speculation. Second, the findings of the paper are related to other findings in the field. This serves to show how the findings contribute to knowledge, or correct the errors of previous work. As stated, some of these logical arguments are often found in the Results when it is necessary to clarify why later experiments were carried out. Although you might argue that in this case the discussion material should be presented in the Introduction, more often you cannot grasp its significance until the first part of Results is given.

Finally, papers usually have a short Acknowledgements section, in which various contributions of other workers are recognized, followed by a Reference list giving references to papers and other works cited in the text.

Papers also contain several Figures and Tables. These contain data described in the paper. The figures and tables also have legends, whose purpose is to give details of the particular experiment or experiments shown there. Typically, if a procedure is used only once in a paper, these details are described in Materials and Methods, and the Figure or Table legend refers back to that description. If a procedure is used repeatedly, however, a general description is given in Materials and Methods, and the details for a particular experiment are given in the Table or Figure legend.

Variations on the organization of a paper

In most scientific journals, the above format is followed. Occasionally, the Results and Discussion are combined, in cases in which the data need extensive discussion to allow the reader to follow the train of logic developed in the course of the research. As stated, in some journals, Materials and Methods follows the Discussion. In certain older papers, the Summary was given at the end of the paper.

The formats for two widely-read journals, Science and Nature, differ markedly from the above outline. These journals reach a wide audience, and many authors wish to publish in them; accordingly, the space limitations on the papers are severe, and the prose is usually highly compressed. In both journals, there are no discrete sections, except for a short abstract and a reference list. In Science, the abstract is self-contained; in Nature, the abstract also serves as a brief introduction to the paper. Experimental details are usually given either in endnotes (for Science) or Figure and Table legends and a short Methods section (in Nature). Authors often try to circumvent length limitations by putting as much material as possible in these places. In addition, an increasingly common practice is to put a substantial fraction of the less-important material, and much of the methodology, into Supplemental Data that can be accessed online.

Many other journals also have length limitations, which similarly lead to a need for conciseness. For example, the Proceedings of the National Academy of Sciences (PNAS) has a six-page limit; Cell severely edits many papers to shorten them, and has a short word limit in the abstract; and so on.

In response to the pressure to edit and make the paper concise, many authors choose to condense or, more typically, omit the logical connections that would make the flow of the paper easy. In addition, much of the background that would make the paper accessible to a wider audience is condensed or omitted, so that the less-informed reader has to consult a review article or previous papers to make sense of what the issues are and why they are important. Finally, again, authors often circumvent page limitations by putting crucial details into the Figure and Table legends, especially when (as in PNAS) these are set in smaller type.

Reading a scientific paper Autologous Mesenchymal Stem Cells in Multiple Sclerosis DQ

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.