Scientific journal: Difference between revisions

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*'''Research notes''' are short descriptions of current research findings which are considered less urgent or important than ''Letters''.
*'''Research notes''' are short descriptions of current research findings which are considered less urgent or important than ''Letters''.


==Formats of journal articles==
The formats of journal articles vary, but almost always follow the following general scheme.  They begin with an ''[[Abstract (summary)|abstract]]'', which is a one-to-four-paragraph summary of the paper.  The ''introduction'' describes the background for the research including a discussion of similar research.  The ''materials and methods'' or ''experimental'' section provides specific details of how the research was conducted. The ''results and discussion'' section describes the outcome and implications of the research, and the ''conclusion'' section places the research in context and describes avenues for further exploration.  Many journals make supplementary information about an article (e.g., detailed methodologies or calculations) available online.
The formats of journal articles vary, but almost always follow the following general scheme.  They begin with an ''[[Abstract (summary)|abstract]]'', which is a one-to-four-paragraph summary of the paper.  The ''introduction'' describes the background for the research including a discussion of similar research.  The ''materials and methods'' or ''experimental'' section provides specific details of how the research was conducted. The ''results and discussion'' section describes the outcome and implications of the research, and the ''conclusion'' section places the research in context and describes avenues for further exploration.  Many journals make supplementary information about an article (e.g., detailed methodologies or calculations) available online.


In addition to the above, some scientific journals such as ''Science'' will include a news section where scientific developments (often involving political issues) are described.  These articles are often written by science journalists and not by scientists.  In addition some journals will include an editorial section and a section for letters to the editor.  While these are articles published within a journal, they are not generally regarded as scientific journal articles because they have not been [[Research peer review|peer-reviewed]].
In addition to the above, some scientific journals such as ''Science'' will include a news section where scientific developments (often involving political issues) are described.  These articles are often written by science journalists and not by scientists.  In addition some journals will include an editorial section and a section for letters to the editor.  While these are articles published within a journal, they are not generally regarded as scientific journal articles because they have not been [[Research peer review|peer-reviewed]].
===Abstracts===
Efforts have been made to improve common formatting of abstracts.<ref name="pmid3826959">{{cite journal| author=| title=A proposal for more informative abstracts of clinical articles. Ad Hoc Working Group for Critical Appraisal of the Medical Literature. | journal=Ann Intern Med | year= 1987 | volume= 106 | issue= 4 | pages= 598-604 | pmid=3826959 | doi= | pmc= | url=http://www.annals.org/content/106/4/598.abstract }} </ref><ref name="pmid10188667">{{cite journal| author=Winker MA| title=The need for concrete improvement in abstract quality. | journal=JAMA | year= 1999 | volume= 281 | issue= 12 | pages= 1129-30 | pmid=10188667 | doi= | pmc= | url=http://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&tool=sumsearch.org/cite&retmode=ref&cmd=prlinks&id=10188667  }} </ref>


==Electronic publishing==
==Electronic publishing==

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Among academic journals, a scientific journal is a periodical publication intended to further the progress of science, usually by reporting new research findings, but also by publishing state-of-the-art reviews, commentaries, news of the activities of scientific societies, and by publishing feedback on articles by readers. Most journals are highly specialized, although some of the oldest journals such as Nature and Science publish articles and scientific papers across a wide range of scientific fields. Scientific journals contain articles that have been peer-reviewed, in an attempt to ensure that articles meet the journal's standards of quality, and have scientific validity in the view of the reviewers and editors. Issues of a scientific journal are rarely read casually, as one would read a magazine. The articles are written as part of the scientific method; they generally must supply enough details of an experiment that an independent researcher could potentially repeat the experiment to verify the results. Such journal articles are considered part of the permanent scientific record.

The standards that a journal uses to determine publication can vary widely. Some journals, such as Nature, Science, The Proceedings of the National Academy of Science (PNAS) or Physical Review Letters, will not publish an article unless they believe that it marks a fundamental breakthrough in its field, and hence will reject papers which contain good work that does not meet this criterion. In many fields, an informal hierarchy of scientific journals exists; the most prestigious journal in a field tends to be the most selective in terms of the articles it will select for publication. It is also common for journals to have a regional focus, specializing in publishing papers from a particular geographic region.

Articles tend to be highly technical, representing the latest theoretical research and experimental results in the field of science covered by the journal. They are often incomprehensible to anyone except for researchers in the field. Scientific journals are a crucial part of the scientific literature. Some scientific journals, like Nature and Science, provide summary reports of key articles in an issue written less technically and putting the discoveries in broader perspective.

Some scientific journals have primarily an educational purpose, targeting science students and teachers. The Journal of Chemical Education[1] qualifies as a scientific journal because of its high quality technical articles designed to apply scientific research to further the progress of science by educating teachers and students.

Types of articles

There are several types of journal articles; the exact terminology and definitions vary by field and specific journal, but often include:

  • Letters (not to be confused with letters to the editor) are short descriptions of important current research findings which are usually fast-tracked for immediate publication because they are considered urgent.
  • Articles are usually between five and twenty pages and are a complete descriptions of current original research finding, but there are considerable variations between scientific fields and journals: 80-page articles are not rare in mathematics or theoretical computer science.
  • Supplemental articles contain a large volume of tabular data that is the result of current research and may be dozens or hundreds of pages with mostly numerical data. Some journals now only publish this data electronically on the internet.
  • Review articles do not cover original research but rather accumulate the results of many different articles on a particular topic into a coherent narrative about the state of the art in that field. Specific types of reviews include systematic reviews and meta-analyses. Other examples of reviews include the 'Nature Reviews' series of journals and the 'Trends in' series, which invite experts to write on their specialisation and then have the article peer-reviewed before accepting the article for publication. Other journals, such as the Current Opinion series, are less rigorous in peer-reviewing each article and instead rely on the author to present an accurate and unbiased view. Review articles provide information about the topic, and also provide journal references to the original research.
  • Book Review serves as a check on the reseach published by academics in book form.
  • Essays or Commentaries written by established scientists with valuable perspectives.
  • Research notes are short descriptions of current research findings which are considered less urgent or important than Letters.


Formats of journal articles

The formats of journal articles vary, but almost always follow the following general scheme. They begin with an abstract, which is a one-to-four-paragraph summary of the paper. The introduction describes the background for the research including a discussion of similar research. The materials and methods or experimental section provides specific details of how the research was conducted. The results and discussion section describes the outcome and implications of the research, and the conclusion section places the research in context and describes avenues for further exploration. Many journals make supplementary information about an article (e.g., detailed methodologies or calculations) available online.

In addition to the above, some scientific journals such as Science will include a news section where scientific developments (often involving political issues) are described. These articles are often written by science journalists and not by scientists. In addition some journals will include an editorial section and a section for letters to the editor. While these are articles published within a journal, they are not generally regarded as scientific journal articles because they have not been peer-reviewed.

Abstracts

Efforts have been made to improve common formatting of abstracts.[2][3]

Electronic publishing

With the advent on electronic publishing, scientists are reading more articles and reading them faster.[4]

It has been argued that peer-reviewed paper journals are in the process of being replaced by electronic publishing. There is usually a delay of several months after an article is written before it is published in a journal and this makes journals not an ideal format for disseminating the latest research. In some fields such as astronomy and physics, the role of the journal at disseminating the latest research has largely been replaced by preprint databases such as arXiv.org. Scientific journals, however, still provide an important role in quality control, archiving papers, and establishing scientific credit. In general, the electronic materials uploaded to preprint databases are still intended for eventual publication in a peer-reviewed journal. Moreover, scientific journals increasing print accepted articles online on their journal website in advance of the print publication.

A number of journals have, while retaining their peer-review process, established electronic versions or even moved entirely to electronic publication. The latter include the Public Library of Science (PLoS) journals[5] and the BioMed Central journals[6].

Controversies

In health care journals, problems have been noted in the accuracy of abstracts as compared to the main body of articles.[7][8]

In health care journals, authors may to continue to cite older results from observations studies are their refutation by randomized controlled trials.[9][10] Many new ideas are eventually refuted.[11]

In health care journals, contributions of authors is not always clear (ghostwriting).[12] A large example of this occurred with Wyeth, the manufacturers of Prempro.[13] A trial has explored ways to improve reporting of authors' contributions to manuscripts.[14]

In health care journals, specialty journals are less likely to encourage standards for publication[15][16] and publish papers that are more likely to persist in advocated claims that have been previously refuted.[9]

In health care publishing, it is claimed that the journal Australasian Journal of Bone and Joint Medicine, published by division of Elsevier, is a marketing journal for Merck and Co and was paid for by Merck.[17][18]

Presentation of results

In health care journals, quantitative results may be overstated either because p-values without statistical significance are interpreted as refuting the null hypothesis[19], results are often presented with relative risks rather than absolute risks[20].

Citation inaccuracies

In health care journals, problems in the accuracy of quotations and references by authors have been noted[21] In addition, although articles are more accessible due to the Internet, authors are citing less articles in in their writings.[22] More specifically, academic papers have been found to contain inaccurate citations[23]that have been cataloged into the following types:[23]

  • citation bias (preferentially citing positive articles over negative articles)
  • citation diversion ("citing of content but the altering of its meaning in a manner that diverts its implications")
  • citation amplification (citing of published review articles that make a relevant claim but "lack data addressing the claim"). The authors propose this can be avoided by citing only primary data when making claims which may result in "amplification minimal networks"
  • citation invention (through "mechanisms either deliberate or through scholarly negligence" cite articles that make no relevant statement).

Publication bias

In health care journals, publication bias threatens the interpretation of a body of literature leading to overly positive conclusions.[24]

Conflict of interest

Case studies of industry conflict of interest affecting scientific publication
Drug or device Manufacturer Comment
Second-generation antidepressants Multiple Selective publication of clinical trials with positive results[24]
Duloxetine Lilly "Salami slicing" - redundant publication of systematic reviews for marketing purposes[25]
Gabapentin Parke-Davis "stimulating off-label prescribing despite the lack of FDA approval"[26]
Quetiapine AstraZeneca "Cherry picking" - selective publication of positive results[27]
Rofecoxib Merck •  "Seeding trial" - conducting and publishing a randomized controlled trial for the purpose of promotion[26]
•  Guest authorship and ghostwriting[12]
Rosiglitazone GlaxoSmithKline •  Possible interference with steering committee of a trial[28]
•  Suppressing negative research results[29]
Estrogen replacement therapy Wyeth •  Ghost writing: “You can't just put another name on the article, but you can plagiarize the way we did when we wrote papers in college. What you need to do is give your potential authors Karen's version of the article before the author modified it. Then have your authors modify it for publication under their name. Wyeth owns Karen's draft, not the final publication”.[30]

Authors with conflict of interests are increasing.[31] However, in health care journals conflicts of interests among authors may not be requested by journals[32] and are frequently omitted from publication.[33] Lower impact journals and journals not endorsing International Committee of Medical Journal Editors guidelines are less likely to full report. Recommendations to reduce the impact of conflicts have been proposed.[34]

Authors with conflict of interests are more likely to report positive results[35] and less likely to share knolwedge.[36]

Industry sponsored research may be higher quality than other research in studies of obesity.[37]

Insufficient attention to limitations of research findings

Journal articles may not adequately describe limitations of their findings.[38]

Plagiarism

Plagiarism has been demonstrated among authors of articles in scientific journals.[39]

Open access

For more information, see: Open access.

Often the authors of an article are required to transfer the copyright to the journal publisher. Publishers claim this is necessary in order to protect author's rights, and to coordinate permissions for reprints or other use. Many authors, especially those active in the open access movement, find this unsatisfactory, and would prefer a situation in which they give the publisher an irrevocable license to publish, but retain the other rights themselves.

Cost

Another controversy is the cost of scientific journals. Many scientists and librarians have protested against the cost of journals, especially as they see these fees going to large for-profit publishing houses. To allow their researchers online access to journals, universities generally purchase site licenses, permitting access from anywhere in the university--and, with appropriate authorization, by university-affiliated users at home or elsewhere. These may be quite expensive, sometimes much more than the cost for a print subscription.

References

  1. ↑ Journal of Chemical Education Website
  2. ↑ (1987) "A proposal for more informative abstracts of clinical articles. Ad Hoc Working Group for Critical Appraisal of the Medical Literature.". Ann Intern Med 106 (4): 598-604. PMID 3826959. [e]
  3. ↑ Winker MA (1999). "The need for concrete improvement in abstract quality.". JAMA 281 (12): 1129-30. PMID 10188667. [e]
  4. ↑ Renear AH, Palmer CL. Strategic reading, ontologies, and the future of scientific publishing. Science. 2009 Aug 14;325(5942):828-32. DOI:10.1126/science.1157784 PMID 19679805
  5. ↑ PLoS Journals Website
  6. ↑ BioMed Central Journals Website
  7. ↑ Pitkin RM, Branagan MA, Burmeister LF (1999). "Accuracy of data in abstracts of published research articles". JAMA 281 (12): 1110–1. PMID 10188662. [e]
  8. ↑ Wong HL, Truong D, Mahamed A, Davidian C, Rana Z, Einarson TR (April 2005). "Quality of structured abstracts of original research articles in the British Medical Journal, the Canadian Medical Association Journal and the Journal of the American Medical Association: a 10-year follow-up study". Curr Med Res Opin 21 (4): 467–73. PMID 15902784. [e]
  9. ↑ 9.0 9.1 Tatsioni A, Bonitsis NG, Ioannidis JP (December 2007). "Persistence of contradicted claims in the literature". JAMA 298 (21): 2517–26. DOI:10.1001/jama.298.21.2517. PMID 18056905. Research Blogging.
  10. ↑ Antman EM, Lau J, Kupelnick B, Mosteller F, Chalmers TC (July 1992). "A comparison of results of meta-analyses of randomized control trials and recommendations of clinical experts. Treatments for myocardial infarction". JAMA 268 (2): 240–8. PMID 1535110. [e]
  11. ↑ Contopoulos-Ioannidis DG, Alexiou GA, Gouvias TC, Ioannidis JP. Medicine. Life cycle of translational research for medical interventions. Science. 2008 Sep 5;321(5894):1298-9. PMID 18772421
  12. ↑ 12.0 12.1 Ross JS, Hill KP, Egilman DS, Krumholz HM (April 2008). "Guest authorship and ghostwriting in publications related to rofecoxib: a case study of industry documents from rofecoxib litigation". JAMA 299 (15): 1800–12. DOI:10.1001/jama.299.15.1800. PMID 18413874. Research Blogging. Cite error: Invalid <ref> tag; name "pmid18413874" defined multiple times with different content
  13. ↑ The PLoS Medicine Editors (2009). "Ghostwriting: The Dirty Little Secret of Medical Publishing That Just Got Bigger". PLoS Med 6 (9): e1000156. DOI:10.1371/journal.pmed.1000156. Retrieved on 2009-09-10. Research Blogging.
  14. ↑ Ivanis A, Hren D, Sambunjak D, Marusić M, Marusić A (September 2008). "Quantification of authors' contributions and eligibility for authorship: randomized study in a general medical journal". J Gen Intern Med 23 (9): 1303–10. DOI:10.1007/s11606-008-0599-8. PMID 18521691. Research Blogging.
  15. ↑ Altman DG (May 2005). "Endorsement of the CONSORT statement by high impact medical journals: survey of instructions for authors". BMJ 330 (7499): 1056–7. DOI:10.1136/bmj.330.7499.1056. PMID 15879389. PMC 557224. Research Blogging.
  16. ↑ Smidt N, Overbeke J, de Vet H, Bossuyt P (November 2007). "Endorsement of the STARD Statement by biomedical journals: survey of instructions for authors". Clin. Chem. 53 (11): 1983–5. DOI:10.1373/clinchem.2007.090167. PMID 17954503. Research Blogging.
  17. ↑ Grant B. (2009) Merck published fake journal. The Scientist
  18. ↑ Elsevier Published Fake Journals « The Scholarly Kitchen.
  19. ↑ Boutron, Isabelle; Susan Dutton, Philippe Ravaud, Douglas G. Altman (2010-05-26). "Reporting and Interpretation of Randomized Controlled Trials With Statistically Nonsignificant Results for Primary Outcomes". JAMA 303 (20): 2058-2064. DOI:10.1001/jama.2010.651. Retrieved on 2010-05-26. Research Blogging.
  20. ↑ Schwartz LM, Woloshin S, Dvorin EL, Welch HG (December 2006). "Ratio measures in leading medical journals: structured review of accessibility of underlying absolute risks". BMJ 333 (7581): 1248. DOI:10.1136/bmj.38985.564317.7C. PMID 17060338. Research Blogging.
  21. ↑ de Lacey G, Record C, Wade J (1985). "How accurate are quotations and references in medical journals?". Br Med J (Clin Res Ed) 291 (6499): 884–6. PMID 3931753. [e]
  22. ↑ Evans, James A. (2008-07-18). "Electronic Publication and the Narrowing of Science and Scholarship". Science 321 (5887): 395-399. DOI:10.1126/science.1150473. Retrieved on 2008-07-18. Research Blogging.
  23. ↑ 23.0 23.1 Greenberg SA (2009). "How citation distortions create unfounded authority: analysis of a citation network.". BMJ 339: b2680. DOI:10.1136/bmj.b2680. PMID 19622839. PMC PMC2714656. Research Blogging.
  24. ↑ 24.0 24.1 Turner EH, Matthews AM, Linardatos E, Tell RA, Rosenthal R (2008). "Selective publication of antidepressant trials and its influence on apparent efficacy". N. Engl. J. Med. 358 (3): 252–60. DOI:10.1056/NEJMsa065779. PMID 18199864. Research Blogging. Cite error: Invalid <ref> tag; name "pmid18199864" defined multiple times with different content
  25. ↑ Spielmans GI, Biehn TL, Sawrey DL (2010). "A Case Study of Salami Slicing: Pooled Analyses of Duloxetine for Depression.". Psychother Psychosom 79 (2): 97-106. DOI:10.1159/000270917. PMID 20051707. Research Blogging.
  26. ↑ 26.0 26.1 Steinman MA, Bero LA, Chren MM, Landefeld CS (2006). "Narrative review: the promotion of gabapentin: an analysis of internal industry documents.". Ann Intern Med 145 (4): 284-93. PMID 16908919.
  27. ↑ Spielmans GI, Parry PI. From Evidence-based Medicine to Marketing-based Medicine: Evidence from Internal Industry Documents. J Bioeth Inq, 2010 DOI:10.1007/s11673-010-9208-8
  28. ↑ Nissen SE (2010). "Setting the RECORD Straight.". JAMA 303 (12): 1194-5. DOI:10.1001/jama.2010.333. PMID 20332408. Research Blogging.
  29. ↑ Harris G (7/12/2010). Diabetes Drug Maker Hid Test Data on Risks, Files Indicate (English). New York Times. Retrieved on 2010-07-13.
  30. ↑ Fugh-Berman AJ (2010) The Haunting of Medical Journals: How Ghostwriting Sold “HRT”. PLoS Med 7(9): e1000335. DOI:10.1371/journal.pmed.1000335
  31. ↑ Buchkowsky SS, Jewesson PJ (April 2004). "Industry sponsorship and authorship of clinical trials over 20 years". Ann Pharmacother 38 (4): 579–85. DOI:10.1345/aph.1D267. PMID 14982982. Research Blogging.
  32. ↑ Rowan-Legg A, Weijer C, Gao J, Fernandez C (January 2009). "A comparison of journal instructions regarding institutional review board approval and conflict-of-interest disclosure between 1995 and 2005". J Med Ethics 35 (1): 74–8. DOI:10.1136/jme.2008.024299. PMID 19103950. Research Blogging.
  33. ↑ Weinfurt KP, Seils DM, Tzeng JP, Lin L, Schulman KA, Califf RM (2008). "Consistency of financial interest disclosures in the biomedical literature: the case of coronary stents". PLoS ONE 3 (5): e2128. DOI:10.1371/journal.pone.0002128. PMID 18461146. Research Blogging.
  34. ↑ DeAngelis CD, Fontanarosa PB (April 2008). "Impugning the integrity of medical science: the adverse effects of industry influence". JAMA 299 (15): 1833–5. DOI:10.1001/jama.299.15.1833. PMID 18413880. Research Blogging.
  35. ↑ Als-Nielsen B, Chen W, Gluud C, Kjaergard LL (August 2003). "Association of funding and conclusions in randomized drug trials: a reflection of treatment effect or adverse events?". JAMA 290 (7): 921–8. DOI:10.1001/jama.290.7.921. PMID 12928469. Research Blogging.
  36. ↑ Evans JA. (2010) Industry collaboration, scientific sharing, and the dissemination of knowledge. Social Studies of Science October 2010 40: 757-791 DOI:10.1177/0306312710379931
  37. ↑ Thomas O, Thabane L, Douketis J, Chu R, Westfall AO, Allison DB (2008). "Industry funding and the reporting quality of large long-term weight loss trials.". Int J Obes (Lond) 32 (10): 1531-6. DOI:10.1038/ijo.2008.137. PMID 18711388. PMC PMC2753515. Research Blogging.
  38. ↑ Ioannidis JP (2007). "Limitations are not properly acknowledged in the scientific literature.". J Clin Epidemiol 60 (4): 324-9. DOI:10.1016/j.jclinepi.2006.09.011. PMID 17346604. Research Blogging.
  39. ↑ Long, Tara C.; Mounir Errami, Angela C. George, Zhaohui Sun, Harold R. Garner (2009-03-06). "SCIENTIFIC INTEGRITY: Responding to Possible Plagiarism". Science 323 (5919): 1293-1294. DOI:10.1126/science.1167408. Retrieved on 2009-03-09. Research Blogging.

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