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Articles Guidelines for Writing Research Papers Received for publication, April 24, 2003 Perry A. Frey‡ From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53726 The preparation of reports is as important a part of doing research as the actual execution of the research itself. Until the work is written up in an informative paper, the research is not complete. Among the reasons for this are that research has little intrinsic value before it is dissemi- nated to the scientific community, and researchers, at least good researchers, often subject their findings to the most critical analysis at the time they are writing them up in research papers. Unfortunately perfectly capable re- searchers frequently find it difficult to write up their work. This is often all too obvious to their readers, and when a researcher’s problem with writing leads to a poorly written paper that is difficult to read or understand, the effect is to diminish the impact of the research itself. It is not possible in guidelines such as these to solve all writing problems that may be encountered. Skill in such things as writing style, grammar, punctuation, sentence and paragraph structure, and so forth can be acquired only through extensive practice and attentive reading. One pur- pose of these guidelines is to help smooth the way to such practice by discussing and perhaps eliminating the first hurdle that confronts anyone who undertakes to write a research report, the problem of organization. What infor- mation goes where? This question always arises. Another purpose is to give some guidance on the writing process. ORGANIZING THE PAPER Technical and scientific papers are organized in sections such as Theory, Introduction (or Introductory Statement), Results, etc. They also include data in the form of figures and tables, and they include detailed descriptions of the experimentation as well as an overall discussion of the significance of the experimental findings. Most journals specify the required sections while giving some leeway for including additional sections such as Theory or Appendi- ces. The traditional sections may be eliminated in short communications. Consult the Instructions for Authors pub- lished annually by the journal you choose before starting to write the paper. A full research paper should consist of a Title, an AB- STRACT (or SUMMARY), an INTRODUCTION (or INTRO- DUCTORY STATEMENT), and sections entitled EXPERI- MENTAL PROCEDURE (or MATERIALS AND METHODS), RESULTS, and DISCUSSION. Many journals allow some latitude in permitting additional sections as well as permit- ting RESULTS and DISCUSSION to be combined when convenient and appropriate. The section headings should not be numbered or carry subtitles. Each section may be subdivided into subsections, which are identified by de- scriptive titles that are underlined or italicized but not numbered. For example, subsections of MATERIALS AND METHODS might be Chemicals, Enzymes, Substrates, En- zymes and Coenzymes, Chromatography, Assays, etc. Subsections of RESULTS arise from the descriptions of several different experiments on the same system and so forth. Each major section has a specific function that is implied by its title. Readers have come to know what to expect in each section, such as RESULTS, and are confused when the information they are seeking is not where they expect to find it. The TITLE—The title creates a first impression that should be positive and by all means accurate. Never prom- ise anything in the title that you do not deliver in the paper. The title should be informative but not too long. It should convey a general idea of what the paper is about and, if possible, something but not too much about the main conclusion. Excessively detailed titles are clumsy and may not entice readers with peripheral interests. Many titles found in journals today are more detailed and longer than they need to be because authors often wish to convey as much as possible about their papers to attract readers. This sometimes works, it must be admitted, but such titles are nonetheless clumsy. And many readers may not bother to read a paper that has told them all they want to know in the title. It is often best to wait until a paper has been written before deciding on a title. This is because the content and significance of papers continue to evolve during the writing process, and so an author’s concept of the most funda- mental meaning of the work may continue to develop while the writing is in progress. The INTRODUCTION—The introductory statement in a paper has the limited purpose of informing the reader about the background for the work, including basic ques- tions being addressed in the research and why it would be important to obtain answers. The principal aims of the work should be straightforwardly stated as well as some indication of the experimental approach. The actual find- ings should be presented in later sections, although some ‡ To whom correspondence should be addressed: Dept. of Biochemistry, University of Wisconsin-Madison, 1710 University Ave., Madison, WI 53726. E-mail: [email protected]. © 2003 by The International Union of Biochemistry and Molecular Biology BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION Printed in U.S.A. Vol. 31, No. 4, pp. 237–241, 2003 This paper is available on line at http://www.bambed.org 237

Guidelines for writing research papers

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Articles

Guidelines for Writing Research Papers

Received for publication, April 24, 2003

Perry A. Frey‡

From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53726

The preparation of reports is as important a part of doingresearch as the actual execution of the research itself.Until the work is written up in an informative paper, theresearch is not complete. Among the reasons for this arethat research has little intrinsic value before it is dissemi-nated to the scientific community, and researchers, atleast good researchers, often subject their findings to themost critical analysis at the time they are writing them upin research papers. Unfortunately perfectly capable re-searchers frequently find it difficult to write up their work.This is often all too obvious to their readers, and when aresearcher’s problem with writing leads to a poorly writtenpaper that is difficult to read or understand, the effect is todiminish the impact of the research itself.

It is not possible in guidelines such as these to solve allwriting problems that may be encountered. Skill in suchthings as writing style, grammar, punctuation, sentenceand paragraph structure, and so forth can be acquired onlythrough extensive practice and attentive reading. One pur-pose of these guidelines is to help smooth the way to suchpractice by discussing and perhaps eliminating the firsthurdle that confronts anyone who undertakes to write aresearch report, the problem of organization. What infor-mation goes where? This question always arises. Anotherpurpose is to give some guidance on the writing process.

ORGANIZING THE PAPER

Technical and scientific papers are organized in sectionssuch as Theory, Introduction (or Introductory Statement),Results, etc. They also include data in the form of figuresand tables, and they include detailed descriptions of theexperimentation as well as an overall discussion of thesignificance of the experimental findings. Most journalsspecify the required sections while giving some leeway forincluding additional sections such as Theory or Appendi-ces. The traditional sections may be eliminated in shortcommunications. Consult the Instructions for Authors pub-lished annually by the journal you choose before starting towrite the paper.

A full research paper should consist of a Title, an AB-STRACT (or SUMMARY), an INTRODUCTION (or INTRO-DUCTORY STATEMENT), and sections entitled EXPERI-MENTAL PROCEDURE (or MATERIALS AND METHODS),

RESULTS, and DISCUSSION. Many journals allow somelatitude in permitting additional sections as well as permit-ting RESULTS and DISCUSSION to be combined whenconvenient and appropriate. The section headings shouldnot be numbered or carry subtitles. Each section may besubdivided into subsections, which are identified by de-scriptive titles that are underlined or italicized but notnumbered. For example, subsections of MATERIALS ANDMETHODS might be Chemicals, Enzymes, Substrates, En-zymes and Coenzymes, Chromatography, Assays, etc.Subsections of RESULTS arise from the descriptions ofseveral different experiments on the same system and soforth.

Each major section has a specific function that is impliedby its title. Readers have come to know what to expect ineach section, such as RESULTS, and are confused whenthe information they are seeking is not where they expectto find it.

The TITLE—The title creates a first impression thatshould be positive and by all means accurate. Never prom-ise anything in the title that you do not deliver in the paper.The title should be informative but not too long. It shouldconvey a general idea of what the paper is about and, ifpossible, something but not too much about the mainconclusion. Excessively detailed titles are clumsy and maynot entice readers with peripheral interests. Many titlesfound in journals today are more detailed and longer thanthey need to be because authors often wish to convey asmuch as possible about their papers to attract readers.This sometimes works, it must be admitted, but such titlesare nonetheless clumsy. And many readers may not botherto read a paper that has told them all they want to know inthe title.

It is often best to wait until a paper has been writtenbefore deciding on a title. This is because the content andsignificance of papers continue to evolve during the writingprocess, and so an author’s concept of the most funda-mental meaning of the work may continue to develop whilethe writing is in progress.

The INTRODUCTION—The introductory statement in apaper has the limited purpose of informing the readerabout the background for the work, including basic ques-tions being addressed in the research and why it would beimportant to obtain answers. The principal aims of thework should be straightforwardly stated as well as someindication of the experimental approach. The actual find-ings should be presented in later sections, although some

‡ To whom correspondence should be addressed: Dept. ofBiochemistry, University of Wisconsin-Madison, 1710 UniversityAve., Madison, WI 53726. E-mail: [email protected].

© 2003 by The International Union of Biochemistry and Molecular Biology BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATIONPrinted in U.S.A. Vol. 31, No. 4, pp. 237–241, 2003

This paper is available on line at http://www.bambed.org 237

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authors like to give an indication of the main conclusions inthe introduction. Exhaustive reviews of the literature are tobe avoided, but literature that pertains directly to the in-troduction itself should be cited.

The MATERIALS AND METHODS/EXPERIMENTALPROCEDURE—A decision must be made early in the writ-ing whether to have a section on MATERIALS AND METH-ODS or whether there should be a more extensive sectionentitled EXPERIMENTAL PROCEDURE or EXPERIMEN-TAL SECTION, which should include Materials and Meth-ods as subsections. In general, if detailed newly developedexperimental protocols are to be described, one writes asection entitled EXPERIMENTAL PROCEDURE, EXPERI-MENTAL SECTION, or simply, EXPERIMENTAL. The sub-sections will include new procedures such as syntheticprotocols, purifications, new analytical procedures, etc. aswell as materials and methods. The protocols should bedescribed in complete detail exactly as they are actuallyperformed. This is so they can be repeated by other work-ers. This is as important a part of the paper as the RE-SULTS section.

If no new experimental protocols involving preparativeor analytical procedures are to be described, the sectioncan be brief and entitled simply MATERIALS and METH-ODS. In this case, the origins of the materials used arecited as briefly as possible, e.g. the names of commercialsuppliers and whether and by what means commerciallyobtained materials were further purified. Materials pre-pared by published procedures should be identified assuch, and the appropriate literature should be cited. Sim-ilarly all general methods, e.g. analytical or chromato-graphic methods, should be described briefly, and theappropriate literature should be cited.

In an EXPERIMENTAL PROCEDURE, it is occasionallyconvenient to include a figure to illustrate specialized ap-paratus or some experimental data that relate exclusivelyto the protocol being described. When the inclusion ofsuch a figure under RESULTS is inappropriate, it is some-times reasonable to include it in the EXPERIMENTALPROCEDURE.

The synthetic protocols for new compounds must beaccompanied by spectroscopic data (NMR and IR) andelemental analyses or mass spectral data as well as anyother information supporting the assigned structures.Structural characterization of new compounds is a criti-cally important part of the research. Such characterizationshould be as complete as possible and described in detail.

The labeled subsections for a section entitled MATERI-ALS and METHODS could include such things as Chemi-cals, Enzymes and Coenzymes, Chromatographic Materi-als, Rate Measurements, Assays, Chromatography, etc.The labeled subsections for a section entitled EXPERI-MENTAL PROCEDURE should include those listed aboveand such additional subsections as Synthesis of (namedcompound), Reaction of (briefly described reactants), andother newly developed or special protocols especiallywhen they are used repeatedly in experiments describedunder RESULTS or when the detailed protocols are toolong to be given in footnotes to tables or in figure legends.

The RESULTS—The RESULTS section describes thescientific findings as they relate to the basic questions set

forth in the INTRODUCTION. The experimental strategiesand rationales are explained, and the data are presentedwithout going into experimental details such as composi-tions of reaction mixtures or detailed protocols, whichhave been described in the experimental section or infootnotes to tables and in figure legends. The text of thissection should read smoothly as a direct exposition ofwhat strategies were adopted, what experiments wereperformed, what data were obtained, and what could beconcluded from the data. Data should be presented intables and figures except in cases where they can bestated simply in a few words, perhaps as two or threenumerical parameters with associated error limits. Judg-ment must be exercised, but in general when more thanthree numerical entries are involved a table is appropriate,and where quality of data is best displayed in a figure, thisshould be done. It is sometimes appropriate to useschemes such as reaction schemes or flow charts to assistin explaining experimental strategies in the text of theRESULTS.

The tables with associated footnotes and the figureswith associated legends should be interpretable withoutreference to the text. The footnotes and legends shouldcontain enough information to transmit a clear picture ofwhat was done in the experiment so that the data givencan be interpreted without referring to the text. This en-ables readers to make their own interpretations beforereading yours. It also simplifies your references to tablesand figures in the text because the entries can be cited andtheir meaning discussed without the need to go into detailsabout exactly how the experiments were carried out. Therule is that experimental details belong in the experimentalsection or in footnotes to tables and legends to figures, notin the text.

Inasmuch as several related experiments are generallydescribed under RESULTS, the section is divided intosubsections, each of which is given a descriptive titleabout one column line long on a typical journal page. Suchsubsections may be entitled Purification of (an enzyme ornatural product), Synthesis of (some compound, e.g. anenzyme inhibitor), Kinetics of the reaction of (named sub-stances), pH dependence of (some process), Inactivationof (etc.). Each subsection describes an experiment or se-ries of experiments with a common theme, generally meth-odological, and reference is made to the relevant tablesand figures in which the data are set forth. The conclusionsbased on the experimental results are, whenever possible,clearly stated at or near the end of each subsection.

The DISCUSSION—The DISCUSSION provides an over-all correlation of the significance of the findings presentedunder RESULTS. This correlation is generally bimodal. It isfirst an integration of the conclusions from the subsectionsof the RESULTS, leading to overall conclusions about thequestions and problems defined in the INTRODUCTION.This part of the discussion is narrowly limited to the con-text of the problems defined and experiments described.

The research is then further discussed with reference tothe field as a whole. When the conclusions have a signif-icant bearing on questions of current interest, this is in-cluded in the last part of the DISCUSSION. In this subsec-tion the related findings of other workers can be compared

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and correlated with those in the manuscript, and any ad-ditional conclusions or new questions that arise from thisprocess should be stated. Any new directions that may beindicated for the field may also be projected in this section.

The ABSTRACT or SUMMARY—The paper should besummarized in a short ABSTRACT or SUMMARY. This isusually the last section to be written but the first section tobe read. It may be the only section that is read by readerswho have only a passing interest. For this reason thissection is easily as important a section as any other.

The ABSTRACT or SUMMARY should describe con-cisely the experiments that were done, the results thatwere obtained, and the main conclusions that were drawnin the paper. As such, it is a brief statement of the RE-SULTS together with that part of the DISCUSSION that isconcerned with the main conclusions. Any broader or longrange impact of the work in the field should not be men-tioned in the abstract unless the impact is decisive andunusually important. Similarly experimental details shouldnot be included except when they are themselves highlyoriginal and broadly applicable in the field as a whole. Inthe latter case, such experimental procedures may beindependently publishable as the main focus of a separatepaper in a journal devoted to methods.

The ABSTRACT or SUMMARY should be no longer thanabout 200 words. The important thing is to transmit to thereader as efficiently as possible the essential facts uncov-ered in the work and the main conclusions drawn fromthose facts. For nearly all papers this can be done in about200 words.

WRITING THE PAPER

The actual writing process can be a significant hurdle formany people even once they have understood what kindsof information are to go into the various sections. The mostdifficult part of writing often is making a start, getting thefirst sentence on paper. Again organization can be veryhelpful. In the preceding sections the overall organizationof the paper was discussed, including major sections andsubsections. It is important in the writing process to rec-ognize, however, that there is, or should be, an underlyingorganization in each subsection and in each paragraph ofthe paper. Organization is also the key to composing use-ful, informative tables and graphic illustrations for figures.An organized approach facilitates the writing process byhelping the writer to get started and then to write effi-ciently. Once begun, the writing process can be self-sus-taining, especially when the writer maintains an organizedapproach.

A good way to get started on a section is to prepare awritten outline. This should be a detailed plan specifyingthe subsections (titles too) and their contents, what dataare to be included, and whether they will be presented infigures or tables, etc. The outline defines the section orchapter in terms of how its components, i.e. subsections,data, and text, interact and support one another. It simpli-fies the writing process by defining the conceptual frame-work for the section or chapter. One then completes thework essentially by “filling out” the outline with expositoryprose.

Outlines can even facilitate writing at the subsection and

paragraph levels. A well written paragraph has a structurethat can be outlined, beginning with a principal, thematicsentence, usually the first sentence, followed by sentencesthat further explain, support, and expand or limit thetheme.

The most efficient approach is to prepare a completeoutline of the entire paper before beginning to write anysection. Such an overall outline is just as important as asection outline because of the relationships and interac-tions among the various sections. One should at the veryleast define explicitly what will appear in each sectionbefore beginning to write.

Writing the MATERIALS and METHODS/EXPERIMEN-TAL PROCEDURE—Because getting started is a majorhurdle it makes sense to start with the easiest, moststraightforward part of the paper. In a scientific researchpaper this might often be the EXPERIMENTAL PROCE-DURE or MATERIALS and METHODS. This is a sectionthat almost writes itself in that once it is outlined the actualwriting is fairly straightforward. The MATERIALS andMETHODS is essentially a listing, in no special order, of thematerials and methods used, the sources of materials, andbrief mention of any additional purifications, etc. togetherwith appropriate literature references. General methodsthat have been described before are listed with literaturereferences. Specific variations or slight changes in pub-lished methods can be briefly described in one or twosentences.

A section entitled EXPERIMENTAL PROCEDURE is alittle less straightforward to write but still fairly obviousonce the specific procedures to be described have beendecided upon. The rule is that procedures should be de-scribed in sufficient detail to enable scientific peers toreconstruct the procedure in their laboratories. The mainreasons for the inclusion of experimental procedures are toenable critical readers to evaluate the validity of the resultsand to permit other scientists to repeat and extend theexperiments.

Preparing Figures and Tables—Obviously the MATERI-ALS and METHODS/EXPERIMENTAL PROCEDURE can-not be written until the contents of the paper have beendecided upon. These decisions, as well as how the paperwill contribute to its scientific context, are part of theintellectual process associated with the design, perform-ance, and evaluation of the research itself. As such, theyprecede in time the writing of the paper although notnecessarily its conceptualization. The research generatesdata, however; and these data must be presented in thepaper.

Data may be presented in figures, in tables, and in thetext of the paper. Once the experimental section has beenwritten, it is a fairly natural transition to turn to the data asa next step in the writing process. Decisions must be madeabout the most effective means of organizing and present-ing data, that is, what part should appear in figures, whatpart in tables, and what part in the text. Figures should beused when the point to be made is best communicatedgraphically. Data that must be presented in numerical formwill appear in tables or, if they consist of only one or a fewnumbers, in the text.

Presentations of data are often most clear and effective

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when first illustrated graphically and then in some wayrepresented in numerical form. Journals normally will notpublish the same data as both a figure and a table; how-ever, it is often helpful and even essential to present nu-merical parameters pertaining to figures in the text of thepaper. In many cases where numerous sets of data havebeen obtained, kinetic data for example, sample data maybe illustrated graphically in one or a few figures, whilenumerical parameters obtained from all the experimentsare set forth in one or two tables.

A figure is a graphical illustration that should establishone or a few specific points as clearly as possible. Anyscales such as graphical axes must be numbered andlabeled, and the labels must include any relevant units ofmeasurement. The figure should include whatever isneeded to be readily interpretable without appearing clut-tered, and excessive vacant space should be avoided.Graphs should be enclosed by axes on all four sides witheach scale marked with hash marks. It is often useful toplot two different quantities on vertical axes; when this isdone, the left ordinate is scaled and labeled for one quan-tity, and the right ordinate is scaled and labeled for theother. In selecting type sizes and line widths, keep in mindthat the figure must be legible when reduced to the sizethat will appear in the journal.

Each figure is accompanied by a legend consisting of acaption, or title, followed by any necessary explanatoryinformation. Such information as experimental conditions,including solvent, temperature, compositions of reactionmixtures, and any other information pertaining specificallyto the data in the figure, is given in the legend. When thisinformation has been included under EXPERIMENTALPROCEDURE, this fact is simply stated in the legend. Thelegend is concluded with definitions of any symbols usedin the figure such as, for example, the meanings of sym-bols such as E, ● , �, and f used for data points and themeanings of dashed, dotted, continuous, etc. lines in illus-trations of multiple overlaid graphs. Occasionally, whenthe figure is itself fully self-explanatory, the legend mayconsist simply of a caption.

The figures are numbered consecutively with arabic nu-merals, as Fig. 1, Fig. 2, etc. and are collected together inorder at the end. The legends are listed consecutively in asection labeled Figure Legends, which appears just beforethe figures.

Tables are simpler to prepare than figures. Data shouldbe arranged in columns that are labeled with appropriateheadings and units of measurement. The layout consists ofa table number at the top using Roman numerals, e.g.Table I, Table II, etc., a title just beneath the number, theTable itself beneath the title, and beneath the table thetable footnotes a,b,c, etc. are printed single spaced. Thetable footnotes give information required to understandthe data in the table, e.g. experimental conditions, whenthis information has not been provided under EXPERI-MENTAL PROCEDURE.

In papers submitted electronically, the journal mayspecify that figures and tables be inserted into appropriateplaces in the text. Consult the Instructions to Authors.

Writing RESULTS—Once the figures and tables are pre-pared, much of the data content of the results section is

defined. An outline of the section is prepared, specifyingsubsections, locations of figures and Tables in subsec-tions, and so forth. The text is then written, insofar aspossible, using simple declarative sentences and the ac-tive rather than passive voice. The story of the research istold in this section using clear language. Definitive conclu-sions and any reservations or qualifications are stated. Allinterpretations, discussions, and conclusions in this sec-tion must relate to the research appearing in the manu-script or report. Reference to other work is made when it isdirectly relevant to the research being described, but dis-cussion of the broader significance of the research isreserved for the DISCUSSION.

Writing the DISCUSSION and INTRODUCTION—Thesesections are usually written last. The INTRODUCTIONshould be brief, including only a straightforward statementof the research problem being addressed and the scientificcontext in which the problem is defined. This section maybe untitled and appears just after the ABSTRACT or SUM-MARY. The DISCUSSION may be longer because it relatesthe major findings and conclusions to the field as a whole.Any speculative discussion of results is reserved for thissection, and it must be presented as speculation. A mis-take frequently made by authors is to engage in wideranging discussions that gradually become increasinglyspeculative and lead finally to conclusions. This approachis guaranteed to gain the unfavorable attention of refereesand other critical readers. Conclusions must never followfrom speculation! But limited speculation is fair and ac-ceptable in the DISCUSSION when it is clearly identified.Speculation can inspire further experimentation.

References—Reference may be made to published lit-erature in all the sections of a manuscript. When this isdone in an abstract or summary, the reference is given inparentheses at the point of citation. Literature referencescited in the other sections are gathered together in asection entitled REFERENCES or BIBLIOGRAPHY, whichfollows the DISCUSSION, or, if acknowledgments aremade, the ACKNOWLEDGMENTS section. The two majorways for listing references are: (a) in alphabetical orderbased on the last name of the first author, or (b) in the orderin which the citations appear in the manuscript. In theformer case (a) the citations in the manuscript appearparenthetically as (Smith, 1978) or (Smith and Jones, 1981)or if there are more than two authors (Smith et al., 1980). Inthe latter case (b) the references are numbered in the orderin which they appear in the manuscript and are cited bynumber, either as 7 (a superscript) or in parentheses (7).The best way to prepare the list of references varies ac-cording to requirements of the journal or the taste of theauthor. There is much to say for citing references during thewriting process by first author and year of publication (Smithet al., 1980) and compiling the references as a running list inalphabetical order. This allows for convenient addition ofreferences during revision. Then when the manuscript isotherwise completed, the references can either be num-bered, cited by number and properly ordered, or orderedalphabetically and the citations left unchanged dependingupon the system being used. References can convenientlybe managed throughout the writing process by the use ofEndnote in your word processing program.

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Revision—It is rare for the first draft of a paper to besuitable for submission to a publisher. Skilled writers in-variably find many ways to improve their first efforts. Thereshould be no reluctance to revise manuscripts two andeven three or more times.

Revisions take the form of grammatical improvements,condensation of rambling prose, cutting excess words,eliminating redundancies, improving diction and writingstyle, and even removing or adding sections.

Modern word processing programs facilitate revision byallowing the writer to “cut and paste” segments of the

manuscript, reordering and rewriting sentences and para-graphs as well as inserting new material and deleting othermaterial to improve the presentation. The important thing isto get a first draft written as quickly and efficiently as pos-sible, read and evaluate it critically, and wherever improve-ments can be made, revise and polish the manuscript.

Once the paper is written and revised, it is good practiceto print it and set is aside for at least 1 week. Then read thepaper and mark additional revisions or corrections. Thesecan be entered in the final paper before submission to theeditor of the journal.

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