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Am. J. Respir. Crit. Care Med., Volume 164, Number 8, October 2001, 1333-1335

Taxonomy of AJRCCM, a New Series, and a Medley of Metaphors

Martin J. Tobin, Editor


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Before the first scientific journal appeared in 1665, scientists waited until they amassed enough material for a book to communicate new findings to fellow scientists. By enabling researchers to publish little units of information, the invention of journals may have been the decisive step in advancing the scientific method (1). But when a researcher starts to build on the work of other scientists, the scattering of papers in different issues of a journal and in different journals makes it difficult to find relevant preceding work. To help turn these centrifugal forces in a centripetal direction, AJRCCM is introducing a new series of articles, Year in Review.

Physician-scientists need to know everything about very little when working in a lab but a little about everything when rounding-their narrow peak of expertise is set in a broad plain of ignorance. In his recent biography, Michael Bliss tells of an undercurrent of critical talk among colleagues that William Osler was no longer keeping up after his fiftieth birthday (2). And that was before the advent of the first subspecialty journal, and said of a man who covered all of internal medicine in a single-author text. The new series in AJRCCM is aimed at helping readers keep up. The key findings of every article published in the Journal in 2000 are communicated in précis form and categorized by subject matter. The hypertext link in each summary allows the reader to return to the original article within seconds. In writing these summaries, I tried to select relevant conceptual material, unscramble the jargon, and present the key findings in words that can be rapidly assimilated. I may have misunderstood many points, missed others, and misrepresented some. But the summaries are not ends in themselves, but rather a trailer to the main feature. I hope the summaries cause you to read articles you might otherwise have missed, because the goal of good journalism is to fascinate people with topics they didn't think would interest them till brought to their attention. And like news, you want to hear about it as soon as it happens. New information has a short shelf life, and unlike brandy, cheapens with age.

Arranging the articles for Year in Review into a taxonomy is arbitrary because the categorical schemes are not fixed; I glossed over nuances and complexities to make generalizations. Describing and classifying natural objects forms the foundation of much scientific knowledge (3). Yet researchers in the hard sciences view this taxonomic exercise condescendingly. Science is "either physics or stamp collecting" quipped Ernest Rutherford. But he would never have split the atom nor won his Nobel Prize if generations of scientists had not classified the elements he tested. And the quantum leap of Darwin arose directly from taxonomic research. Whereas the Linnaean taxonomy classifies plants along a branching hierarchy, libraries catalogue books and journals along a single dimension. The tag on a spine works well for staff returning books to a shelf, but is far from satisfactory when you are trying to retrieve books. Unlike the linearity of a library shelf, scientific disciplines speciate, interpenetrate, overlap, and merge- the boundaries are convoluted and fractal. Fortunately, the Internet provides an unprecedented resource for cartographers faced with mapping this bibliographical terrain.

With the Internet, it is possible to take the variegated threads of information published in AJRCCM and spin and weave them into a sturdy cloth of knowledge. Employing the taxonomy of categories, you can scan the spectrum of subjects covered in AJRCCM and find an article relevant to your immediate need. The summaries in Year in Review would have little value without the hypertext links to the original article. The links and the taxonomy allow you to organize your reading material into a virtual filing cabinet. Researchers spend inordinate amounts of time trying to retrieve a needed reference (4). Which folder did I put it in? Am I in the wrong drawer? Or is it in the pile I have yet to sort? Stacks of articles are no help to a researcher unless organized into a system that allows easy retrieval. Year in Review replicates the old system of cutting out abstracts and sticking them on index cards. But there was never a good method for linking those cards. Nor did the cards give you immediate access to the original article-you still had to root in a drawer. Year in Review not only organizes your reading material by subject category, but it also gives you immediate access to the original articles. And unlike papers on paper, clicking on the hypertext of citations allows you to explore and exploit other bibliographical sources-the worth of the article you are reading increases dramatically. By interweaving journals and libraries into an interconnected archive of information, the Internet gives new meaning to E.M. Forster's precept: "Only connect!". AJRCCM is fortunately part of the HighWire Press stable of electronic journals, meaning that our readers have instant access to the world's largest free repository of biomedical publications: over 324,000 articles and increasing daily.

A challenge for readers of AJRCCM is the diversity of the subject matter, ranging from apoptosis caused by lung preservation solutions (5) to quality of life in sufferers of allergic rhinitis (6), from molecular biology of the glucocorticoid receptor (7) to exhaled nitric oxide for predicting bronchiolitis obliterans (8), from atelectasis caused by a heavy heart in the acute respiratory distress syndrome (9) to the effects of German reunification on clean air and childhood wheeze (10), from use of lipoarabinomannan for diagnosing tuberculosis (11) to the influence of the N-methyl-D-aspartate glutamate receptor on the hypoxic ventilatory response of the newborn (12), and from genetic polymorphisms in sarcoidosis (13) to a decrease in ventilator-associated pneumonia by rotating antibiotics (16). This broad diversity carries a risk of fragmenting pulmonary and critical care medicine into a myriad of mutually incomprehensible and noncommunicating sects. The insularity of domains slows the percolation of new ideas through a population, and too much indoctrination within a subfield inhibits imaginative powers. Original ideas rarely arise out of the blue, and usually consist of novel combinations of existing ideas. Cross-fertilization between disciplines becomes a major source of mental creativity, as illustrated by the collaboration between physicist Crick and zoologist Watson in arriving at the structure of DNA. A journal acts as a unifying force for members of a discipline, because it gives them interests in common (17). The summaries in Year in Review are presented in words that make it possible for sleep researchers to get ideas from studies of airway inflammation in asthma (18), for asthma investigators to get stimulated by recent advances in the molecular biology of sepsis (25), and for critical care researchers to catch hints in reports on the regulation of the vasculature in sleep apnea (33). And so on. Unlike newspapers, journals have a more intimate relationship with their readers, because readers are also the authors supplying the published articles. At AJRCCM, we recognize that we exist to serve authors and readers-not the other way around. And our success depends on how well we meet your needs.

The cornerstone of editorial policy at AJRCCM is the anonymous work carried out by our reviewers. At a time of wanton commercialism, reviewers donate untold hours with no monetary reward. The idealism is not surprising because reviewers are one of the principal owners of a journal. Without authors participating in peer-review, self-regulation-the hallmark of a profession-goes out the window. Reviewers are our primary instrument for ensuring quality control at AJRCCM. And the constructive criticism of reviewers, which transform manuscripts between the time of submission and publication, is the hidden treasure of the Journal. The more reputable a journal, the more it is regarded as authoritative, the stronger are its refereeing procedures and editorial norms (37). Like people, the reputation of an article is based on the company it is seen with. The increase of almost 300 submissions to AJRCCM in 2000-equal to the total annual submissions of many pulmonary journals-has necessarily resulted in a tightening of standards. The editors have a duty to maintain standards, but we also recognize that it is wounding for authors to get work rejected. Original papers are selected for publication in AJRCCM on the basis of significance, validity, novelty, and comprehensibility. A large number of papers are declined for publication, not out of problems with design or methodology, but because they fare poorly when a reviewer asks, "Does the manuscript contain information that is really new?" Or "Is it just a slight advance over previously published work?" Reviewers will have easy access to Year in Review to judge the novelty of a manuscript. But authors will also be able to contrast their manuscript with other recently published work and emphasize its novelty at the time of submission.

Reviewers get upset when an author gives insufficient credit to the work of other investigators in an area. To paraphrase Congreve, hell hath no fury like the reviewer uncited. This view is hardly surprising because like Newton's reference to giants, every scientist owes a debt to fellow researchers, competitors and collaborators alike. Recognition of this truth gives the scientific community its distinctive character. Although the etiquette of citation is not precisely formalized, it is a trademark of scholarship. We cite authorities not only out of humble deference to past achievements, but to enlist support for our own claims and to buttress our case (3). A published paper is of little significance unless other scientists cite it and build on it. Subsequent citations are as much a part the life of a paper, as the germ of the idea from which it sprouted. Citations embed a publication in the pre-existing consensus, authenticating it by linking it back to an archival source. And with hypertext tagging, it is possible to link publications backwards and forwards in time, making it easier to identify a seminal paper and the succession of reports of incremental knowledge culminating in a substantial new discovery, and then the ripple effect of that discovery on subsequent research. By organizing articles by subject category, Year in Review will help authors find relevant previous work. Citations demonstrate not only the accreditation but also the accretion process of science, whereby every paper builds on the preceding work that it cites.

Of metaphors applied to science, the most evocative is the building of an edifice of knowledge with every paper serving as a brick (38). Each modest contribution remains a permanent part of the edifice long after the researcher is forgotten. The library is the quarry of the researcher's materials, where the documents can be mined, sifted, sorted, and reordered. The storage, searchability, and speed of the Internet make it an important addition on the building site. Every mason knows that the durability of a building depends on selecting the right brick and placing it on a sound foundation. And every so often, a researcher needs to stand back, take a look at the edifice as a whole and ask where the next brick can have greatest effect. I hope Year in Review will serve as a blueprint, helping researchers decide what part of the edifice needs another brick and to find a sturdy predecessor for the addition. I also hope that the distilled and digestible delivery will help time-constrained clinicians stay abreast of advances over a broad range, making AJRCCM the journal you quote on rounds.


    References
TOP
ARTICLE
REFERENCES

1. Bynum WF, Lock S, Porter R. Medical Journals and Medical Knowledge. London: Routledge; 1992. p. 1.

2. Bliss M. William Osler: A Life in Medicine. New York: Oxford University Press; 1999. p. 260, 302.

3. Ziman J. Real Science: What it is, and What it Means. Cambridge: Cambridge University Press; 2000. p. 119, 260.

4. Bernal JD. The Social Function of Science. London: Routledge; 1939. p. 117-118.

5. Fischer S, Maclean AA, Liu M, Cardella JA, Slutsky AS, Suga M, Moreira JF, Keshavjee S. Dynamic changes in apoptotic and necrotic cell death correlate with severity of ischemia-reperfusion injury in lung transplantation. Am J Respir Crit Care Med 2000; 162: 1932-1939 [Abstract/Free Full Text].

6. Leynaert B, Neukirch C, Liard R, Bousquet J, Neukirch F. Quality of life in allergic rhinitis and asthma. A population-based study of young adults. Am J Respir Crit Care Med 2000; 162: 1391-1396 [Abstract/Free Full Text].

7. Gagliardo R, Chanez P, Vignola AM, Bousquet J, Vachier I, Godard P, Bonsignore G, Demoly P, Mathieu M. Glucocorticoid receptor alpha  and beta  in glucocorticoid dependent asthma. Am J Respir Crit Care Med 2000; 162: 7-13 [Abstract/Free Full Text].

8. Gabbay E, Walters EH, Orsida B, Whitford H, Ward C, Kotsimbos TC, Snell GI, Williams TJ. Post-lung transplant bronchiolitis obliterans syndrome (BOS) is characterized by increased exhaled nitric oxide levels and epithelial inducible nitric oxide synthase. Am J Respir Crit Care Med 2000; 162: 2182-2187 [Abstract/Free Full Text].

9. Malbouisson LM, Busch CJ, Puybasset L, Lu Q, Cluzel P, Rouby JJ. Role of the heart in the loss of aeration characterizing lower lobes in acute respiratory distress syndrome. CT Scan ARDS Study Group. Am J Respir Crit Care Med 2000; 161: 2005-2012 [Abstract/Free Full Text].

10. Heinrich J, Hoelscher B, Wichmann HE. Decline of ambient air pollution and respiratory symptoms in children. Am J Respir Crit Care Med 2000; 161: 1930-1936 [Abstract/Free Full Text].

11. Chan ED, Reves R, Belisle JT, Brennan PJ, Hahn WE. Diagnosis of tuberculosis by a visually detectable immunoassay for lipoarabinomannan. Am J Respir Crit Care Med 2000; 161: 1713-1719 [Abstract/Free Full Text].

12. Ohtake PJ, Simakajornboon N, Fehniger MD, Xue YD, Gozal D. N-Methyl-D-aspartate receptor expression in the nucleus tractus solitarii and maturation of hypoxic ventilatory response in the rat. Am J Respir Crit Care Med 2000; 162: 1140-1147 [Abstract/Free Full Text].

13. Petrek M, Drabek J, Kolek V, Zlamal J, Welsh KI, Bunce M, Weigl E, du Bois R. CC chemokine receptor gene polymorphisms in Czech patients with pulmonary sarcoidosis. Am J Respir Crit Care Med 2000; 162: 1000-1003 [Abstract/Free Full Text].

14. Schurmann M, Lympany PA, Reichel P, Muller-Myhsok B, Wurm K, Schlaak M, Muller-Quernheim J, du Bois RM, Schwinger E. Familial sarcoidosis is linked to the major histocompatibility complex region. Am J Respir Crit Care Med 2000; 162: 861-864 [Abstract/Free Full Text].

15. Grunewald J, Berlin M, Olerup O, Eklund A. Lung T-helper cells expressing T-cell receptor AV2S3 associate with clinical features of pulmonary sarcoidosis. Am J Respir Crit Care Med 2000; 161: 814-818 [Abstract/Free Full Text].

16. Gruson D, Hilbert G, Vargas F, Valentino R, Bebear C, Allery A, Bebear C, Gbikpi-Benissan G, Cardinaud JP. Rotation and restricted use of antibiotics in a medical intensive care unit. Impact on the incidence of ventilator-associated pneumonia caused by antibiotic-resistant gram-negative bacteria. Am J Respir Crit Care Med 2000; 162: 837-843 [Abstract/Free Full Text].

17. Fox T. Crisis in Communication. London: The Athlone Press; 1965, p14.

18. Inoue H, Aizawa H, Nakano H, Matsumoto K, Kuwano K, Nadel JA, Hara N. Nitric oxide synthase inhibitors attenuate ozone-induced airway inflamamtion in guinea pigs. Possible role of interleukin-8. Am J Respir Crit Care Med 2000; 161: 249-256 [Abstract/Free Full Text].

19. Schuster M, Tschernig T, Krug N, Pabst R. Lymphocytes migrate from the blood into the bronchoalveolar lavage and lung parenchyma in the asthma model of the brown Norway rat. Am J Respir Crit Care Med 2000; 161: 558-566 [Abstract/Free Full Text].

20. Krug N, Cruikshank WW, Tschernig T, Erpenbeck VJ, Balke K, Hohlfeld JM, Center DM, Fabel H. Interleukin 16 and T-cell chemoattractant activity in bronchoalveolar lavage 24 hours after allergen challenge in asthma. Am J Respir Crit Care Med 2000; 162: 105-111 [Abstract/Free Full Text].

21. Magnan AO, Mely LG, Camilla CA, Badier MM, Montero-Julian FA, Guillot CM, Casano BB, Prato SJ, Fert V, Bongrand P, Vervloet D. Assessment of the Th1/Th2 paradigm in whole blood in atopy and asthma. Increased IFN-gamma -producing CD8(+) T cells in asthma. Am J Respir Crit Care Med 2000; 161: 1790-1796 [Abstract/Free Full Text].

22. Van Den Heuvel MM, Poland DC, De Graaff CS, Hoefsmit EC, Postmus PE, Beelen RH, Van Dijk W. The degree of branching of the glycans of alpha 1-acid glycoprotein in asthma. A correlation with lung function and inflammatory parameters. Am J Respir Crit Care Med 2000; 161: 1972-1978 [Abstract/Free Full Text].

23. Hunt JF, Fang K, Malik R, Snyder A, Malhotra N, Platts-Mills TA, Gaston B. Endogenous airway acidification. Implications for asthma pathophysiology. Am J Respir Crit Care Med 2000; 161: 694-699 [Abstract/Free Full Text].

24. Bonazzi A, Bolla M, Buccellati C, Hernandez A, Zarini S, Vigano T, Fumagalli F, Viappiani S, Ravasi S, Zannini P, Chiesa G, Folco G, Sala A. Effect of endogenous and exogenous prostaglandin E2 on interleukin-1beta -induced cyclooxygenase-2 expression in human airway smooth-muscle cells. Am J Respir Crit Care Med 2000; 162: 2272-2277 [Abstract/Free Full Text].

25. Kuebler WM, Borges J, Sckell A, Kuhnle GE, Bergh K, Messmer K, Goetz AE. Role of L-selectin in leukocyte sequestration in lung capillaries in a rabbit model of endotoxemia. Am J Respir Crit Care Med 2000; 161: 36-43 [Abstract/Free Full Text].

26. Fujii Y, Magder S, Cernacek P, Goldberg P, Guo Y, Hussain SN. Endothelin receptor blockade attenuates lipopolysaccharide-induced pulmonary nitric oxide production. Am J Respir Crit Care Med 2000; 161: 982-989 [Abstract/Free Full Text].

27. Arsalane K, Broeckaert F, Knoops B, Wiedig M, Toubeau G, Bernard A. Clara cell specific protein (CC16) expression after acute lung inflammation induced by intratracheal lipopolysaccharide administration. Am J Respir Crit Care Med 2000; 161: 1624-1630 [Abstract/Free Full Text].

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30. Lanone S, Mebazaa A, Heymes C, Henin D, Poderoso JJ, Panis Y, Zedda C, Billiar T, Payen D, Aubier M, Boczkowski J. Muscular contractile failure in septic patients: role of the inducible nitric oxide synthase pathway. Am J Respir Crit Care Med 2000; 162: 2308-2315 [Abstract/Free Full Text].

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