Research Communication (writing, submitting, and analyzing research papers)

What is active vs. Passive voice?

- active voice is powerful and concrete while passive voice is ponderous and dull +passive "one hour was spent by the raters to observe patient's movement patterns so that the number of changes in static posture could be documented" +active " the raters spent one hour observing the patient's movement patterns to document the number of changes in static posture" -use active voice when possible, unless subject of sentence is unimportant or object or action should be emphasized +Ex. "Patients were randomly assigned" instead of "we assigned patients randomly"

What about first person?

-"I performed..." "We analyzed" -In the past, never used to see first person active voice in articles because of the notion that it detracts from the "scientific" or "objective" nature of research -First person is acceptable in selected instances +when emphasizing own actions, experiences, assumptions, or opinions ++"we think the logical interpretation of this finding is" ++" we found that this technique is" + Don't use "I" unless you are the only author + Presentation of results, procedures, methods requires attention to what and how, not who, so don't overdo the first person

What should be in the body of the paper in a review?

-Has subtitles/sections that are specific to the topic -include important results from researchers -mention types of experiments but dont hash out details of methods -explain importance of studies -point out controversies or discrepancies in field -may synthesize data from multiple studies into a table, graph, or figure -NOTE: you cannot use the figures, tables, etc from those research papers without explicit permission from the publisher of that article! just citing those figures is not enough-copyright violation

What about writing reviews?

-Purpose is to concisely review congruent progress in the field. In review is not a book report or term paper -A review is not a book report or term paper +Not just a summary -A review paper synthesizes the data from multiple research studies and provides an argument or interpretation of the "state of the field" -Format may vary depending on journal +Read review from journal of choice before formatting

What about the discussion?

-So, what does it all mean? -Here, you can express opinions +importance, limitations, future research, clinical implications -dont rehash results -discuss further questions/hypotheses -suggest future research -conclusions are typically included in discussion section +"the results of this study indicate" +"this study demonstrates"

Do you believe it?

-although the majority of scientists are honest, there are some bad seeds -more often, errors in research are not intentional, but simply mistakes or gaps in interpretation or knowledge of the subject -sometimes the results are valid, but he interpretation may be flawed or inappropriate -some authors may make conclusions that are not supported by the results or use wrong methods to answer a particular question

What about the abstract?

-concise! usually 150-300 words -You have to say a lot in a short space, don't get too flowery -cover the main ideas, most people skim abstract to decide whether to read article or not (some stop at the title!)

What about methods?

-describe various techniques used +Ex. section for cell culture, real-time PCR, western blot analysis, sequencing -If procedure is well known or standardized, a brief explanation can be given (with any deviations from standard) with references to original sources

What are the instructions to Authors?

-every journal has its own rules -read carefully! you don't want your paper rejected simply because of improper formatting -browse through previous articles to get idea of type of research highlighted in journal -make sure your desired audience is reached by journal +field specific journals +or do you want a broader audience? -Instructions usually explain +length +organization +Format of tables and figures (may specify file types .gif instead of .jpeg for example) +method of reference citations

What about tables and graphs?

-follow journal's guidelines for format -Tables will have a title and possible footnotes -figures (including graphs) will have legends -Legends include +title of figure +brief description of experiment +describe what is shown ++Ex A) gel electrophoresis, B) Western blot, C) Flow cytometry

What is the general format of a review include?

-introduction and background -body of the paper -conclusion (brief summarize main points) -Acknowledgements if applicable -References (usually alot, >20)

What about the references?

-journal should offer guidelines for reference style +APA, AMA, etc -although you read hundreds of articles to get you to this point, only reference those which are explicitly mentioned in the text -Programs such as Endnote are very valuable for organizing and constructing reference sections

What about the results?

-just the facts, ma'am -explain what was done and what was determined, do not interpret in this section -Tables and figures should complement but be independent of the text + refer reader to figures should for details and summarize details in the text + some results may only be in the text, or just a mention ++"Data not shown" can be used sparingly to mention negative or redundant results

What are some other forms of communicaiton?

-poster presentations +displayed on a large board to be read in casual atmosphere +typically used in conferences ++open poster session where people mill around and presenter is available to answer questions or engage in discussion

What is salami science?

-publication related results in "slices" aka "Least Publishable Unit" or LPU +data sets are split and published separately instead of being presented in a unified way - motivations for salami science +"publish or perish" +impression of increased productivity - why is it a poor practice? +fragmented data makes it difficult to evaluate +misleading, give inappropriate emphasis to one piece of work +unjustified multiple publications put strain on already over-worked peer review process -Quality is better than quantity +exceptions are if related data are presented for different purpose or audiences ++ex. one paper to describe a new, innovative method, another paper to present actual research utilizing the method +many journals have polices regarding Least Publishable Units and duplicate publications

How do you understand a paper?

-read the title + is paper relevant to your topic? + the big picture - reading a paper doesn't always happen in order -you may be looking for something specific +methods used +values from an experiment +particular interpretation of author -some people read beginning to end, looking at each table and graph as it comes up -others read, then evaluate results from figures -some skip right to the discussion/conclusion +warning-if you skip the results you are not critically examining the manuscript -there may be flaws or omissions in the methods or results section that would affect the validity of the interpretations in the study

What about reading reviews?

-reviews are great sources of general information -can aid in understanding topic -but be aware that a review presents a particular perspective, and may not be a comprehensive evaluation of relevant literature -when citing specific procedures or results that you came to know from a review, go to the original source -don't assume that the review author's interpretation of that study is the same as yours-see it yourself +plus you should give credit directly to the author of the original research unless you are citing the general overview of the review article itself ++EX"A comprehensive review is available that details the molecular basis for breast cancer (reference review)

What about writing style?

-simplicity of language +"in light of the fact that" =because + "in spite of the fact" = although +"with the exception of" = except -Dont be boring, but be concise -avoid "lab jargon" +ex. we ran a gel-you may know this is agarose gel electrophoresis to separate DNA fragments, but the reader needs to be able to distinguish between this and polyacrylamide gel electrophoresis of proteins or capillary separation, etc. +ex. 3T3 cells were analyzed for MHC using GFP and YFP 2' antibody by FACS after fixation with PFA +Be sure to define abbreviations upon first use and don't abbreviate every little thing!

Is the scientific paper a fraud?

-some critics of scientific communication believe that the format of scientific papers misrepresent the thought processes that led to the work reported -david goodstein writes, "every scientific paper is written as if that particular investigation were a triumphant procession from one truth to another. All scientist who perform research, however, know that every scientific experiment is chaotic-like war" -the "X factor" aka mRNA discovered by jacob and brenner

What about article format?

-what do you want to say? -Is this an original research article? A review? Hard science? educational? -Length and format depends on journal submitted to -consider which journal you plan to submit paper to before writing final paper

What about the introduction?

-what's the problem? -why should anyone care about it? -what's the background on the subject? +don't give exhaustive literature review here, just enough to make reader understand -State your purpose and hypothesis

What happens in the submission of manuscript?

-you generally can't submit your article to multiple journals at a time! +may cause conflicts in copyright -start high and work down +submit first to most desired journal +If rejected, move to second choice, and so on -Be prepared to revise +sometimes, a journal will accept with revisions +or will reject and provide comments +read comments carefully and try not to take personally ++comments may help in revision to allow next submission to be successful

What is involved in an evaluation of research reports?

-you have to evaulate research reports in order to do research -may have to serve as a peer reviewer for grants or papers -evaluate + importance of research + originality + appropriate research design +adequacy of methods +soundness of conclusions and interpretation +relevance of discussion +clarity in writing

What is the structure of a journal article?

ABSTRACT -overview and purpose -general description of methods -highlight of results -significance of results -general conclusions INTRODUCTION -statement of the problem -clinical relevance -Review of literature -rationale and theoretical framework -specific purpose and hypothesis METHODS -Study design -Criteria for and methods of subject selection -Description and number of subjects -Reagents and concentrations (primers, probe sequences) -Measurement methods and data collection techniques -Data analysis procedures (stats) RESULTS -narrative description of statistical outcomes -tables and figures that summarize findings -statements to support or reject hypotheses DISCUSSION (& CONCLUSION) -Interpretations of statistical outcomes -discussion of clinical significance -importance of the work -Comparison of results with work of others -How results support or conflict with theory -Critique study limitations and strengths -suggestions for further study ACKNOWLEDGMENTS -technical assistance -resources provided -funding source REFERENCES -list of all references cited in the article

What should you do first?

First do the research -as you are completing your research, start thinking about how you want your data to be presented -make figures publication quality as you go -be sure to carefully document all of your methods +write down reagents used, manufacturer, concentrations +Don't assume you'll remember! It is surprising how quickly you forget details after a few months