The Literature of Science and Medicine

1. The Literature of Science and Medicine Ilo-Katryn Maimets, Science Librarian Steacie Science and Engineering Library ilo@yorku.ca

2. How is information recorded in Science? • Publication cycle in science: • Formulating ideas • Testing ideas using the scientific method • Publishing ideas • Grey literature • Primary literature • Popular literature • Secondary literature • Tertiary literature • Accessing information • Controlled language and thesauri • Keywords

4. Flow of ideas in Science • Idea: first arises in the mind of a researcher or a group of researchers • In an academic context, this is often as a result of discussions between graduate students and their supervisors • Research: the idea is developed further over a time period • This is most often by conducting experiments based on the scientific method ***

5. ***Scientific Method: • Observe a phenomenon in the natural world. • Gelchoma plants growing in shade and poor nutrient environments have longer internodal segments than plants growing in well lit and high nutrient environments. • Form a hypothesis or a tentative description, that is consistent with the observation. • A plant forages for better conditions when it is growing in poor conditions • Make a prediction on the basis of the hypothesis. • When a plant is deprived of light and nutrients, it will “forage” for better conditions • Test the prediction by carrying out experiments • Grow plants in 4 different environments: • High light, high nutrients • High light, low nutrients • Low light , high nutrients • Low light, low nutrients • Modify the hypothesis in the light of those results and modify the experiments until there are no longer any discrepancies between theory and experiment and/or observation. • Hypothesis becomes a Theory which is used to explain a class of phenomena. • A plant indeed forages for better conditions when it is growing in poor conditions

6. Citation: • TI: THE EFFECTS OF LIGHT INTENSITY ON FORAGING IN THE CLONAL HERB GLECHOMA-HEDERACEA • AU: SLADE-A-J ; HUTCHINGS-M-J • SO: Journal-of-Ecology. 1987; 75(3): 639-650

7. Abstract: • AB: The growth form of 12-week old clones of Glechoma hederacea grown either under neutral shading (reducing light intensity by 75%), or in full daylight, was compared. All clones were genetically identical. (2) Clones grown under shading displayed a growth form characterised by a small number of slender, unbranched stolons with long internodes, and only a few small ramets. Dry weight per unit length of stolon was low. Proportional allocation of dry weight to roots was low, whereas allocation to petioles was high. Specific leaf areas was nearly three times higher in the shaded clones than in the unshaded clones. Mean ramet leaf area was the same for clones in both treatments. (3) The growth form of unshaded clones was characterised by short stolon internodes, frequent stolon branching and many large ramets. The dry weight per unit length of stolon was found time greater than in the shaded clones. Proportional allocation of dry weight to roots was high, whereas allocation to petioles was lower than in the shaded clones. (4) The results of this experiment are compared with published data analysing the response of G. hederacea to different levels of nutrient availability. G. hederacea displays qualitatively similar alterations in growth form in conditions of low light and low nutrient availability. Plasticity in growth form of G. hederacea enables clones to consolidate occupation of favourable sites, through intensive foraging, and to grow through less favourable sites, concentrating resources in extensive foraging which may result in establishment of ramets in more rewarding sites.

8. Invisible college • Invisible College: • Consists of colleagues and peers who are experts interested in a particular field of study. • They may meet to collaborate or discuss their research, both formally or informally in person or online through e-mail or listserves.

9. What is Grey Literature? • A more formal stage is reached when the ideas • are presented at conferences that do not have published proceedings • An even more formal stage is when the ideas are published through the author's department at an academic institution or in a governmental ministry as • preprints • technical reports • Librarians often refer to this sort of publication as grey literature. • It is not formally published in scholarly journals • It is difficult to collect in a systematic way • Therefore it is hard to find libraries who have this form of publication

10. Sources of grey literature: • Preprints • Internet • Agencies • Governmental Reports • Special interest groups • Consultants and other professionals

11. Primary Literature • Primary literature or Scholarly literature is the next stage in publication • It is Primary because it is thefirst write up of the actual experiments. • Two kinds of primary literature: • Conference proceedings • Not peer reviewed • Journal articles • Often peer reviewed***

12. What is Peer Review? A process by which articles are reviewed by researchers for scientific and technical merit. • Researchers submit their article to the journal they wish to be published in. • The publisher sends it to experts from outside the research team who assess the submitted article and report back to the publisher with their assessment. • This may include information about what applicants can do to improve the chances their article will receive a positive review. • Rerun some experiments • Provide more proof • Rewrite some parts – etc. • Once the article has been brought up to the standards imposed by the journal, it is accepted for publication, and it joins the ranks of other peer reviewed articles.

13. When peer review works: • Peer review maintains checks on what is published, and controls the quality of what is published • Good work is published in the most prestigious journals • Best researchers get grants to carry on with research of high caliber • Second-rate, inaccurate, invalid and dishonest work is weeded out by peer-review

14. The Down-Side of Peer Review • Censors unpopular ideas or ideas that are controversial • Promotes conservativeness, cliquishness and established lines of thought • Weeds out the new and the original • People who publish in the system must have certain types of educational preparation – graduate degrees from established academic institutions – that predisposes them to have certain ways of thinking • Had peer review been common in past centuries, neither Galileo nor Darwin would never have been able to publish • The eccentric genius has no place in this system

15. What does a primary article in science look like? • Abstract – Informative rather than evaluative • Summarizes the article from an objective point of view • Contains the important results and conclusions • Introduction • Provides the background for the research (literature review) • States the thesis (usually toward the end of the intro) • Materials and methods • Subjects: experimental and control groups, tests run, etc. • Results • Tables and Figures • Conclusions • What the results mean in the framework of the research • Discussion • How does this research fit into the big picture? • Why is it important to the field? • Reference list • Provides support and evidencefor the research conducted and the statements made

16. Focus of Primary Science Literature • Audience: other researchers • Tone: scholarly, informative, objective • Language: jargon specific to the field of research • Purpose: • To convey information about the research i.e. materials and methods, conclusions and results • To provide enough detail to enable other scholars to repeat the experiments and obtain the same results • Emphasis: to convince other scholars of the importance of the research, and establish their position on the “leading edge” in the field • Examples of scholarly journals in science: • Nature • Science • New England Journal of Medicine • Canadian Nurse

17. Focus of Popular Science Literature • Audience: the general public • Ranges from well informed and highly educated to less informed and lower education levels, differing age groups and differing interest groups • Tone: popular - arousing curiosity • Language: tailored to a lay target audience • Purpose: • To translate and convey the highlights of the research to the general public in understandable language • Point out implications of the research and make connections to their lives • Ranges from informing to sensationalism depending on the target audience • Emphasis: to convince the lay reader of the importance of the work, and often the need for action • Examples of popular journals in science: • Scientific American and National Geographic • Discover Magazine • Science News • Health pages in the newspaper

18. What to read in a primary article • Abstract • To tell whether this article contains the information that you are looking for • Introduction • To inform yourself of the background material that the article is based on and find out why this research was done • Hint: look for the thesis statement in the introduction • Discussionand/or Conclusions (sometimes they are written as one section) • To see how this research fits into the big picture • Materials & Methodsand Results • If you are interested in how the experiments were conducted, and if you want to evaluate the procedures used. • These sections are often very technical and complex requiring a high level of expertise to understand them

19. Secondary Literature • The next stage is a description of the research in the secondary literature • Examples of secondary literature: • Abstracts • Indexes • Review articles • Summarize and point at the primary literature very soon after it has appeared • Main purpose of this secondary literature is to facilitate access to scientific information soon after it has been published

20. Review articles provide: • Historical overview of a topic • Summary of the work conducted in a lab over a period of time • Summary of research from several labs • They are usually less technical and more suited to a broader though still a specialized readership • Their purpose is to facilitate the movement of information from the leading edge to the stage where it becomes general knowledge and accepted theory

21. Focus of Review literature Much like popular science articles, review literature is written for a number of applications and audiences: • Abstracts: summarize the content of the article – help indexers and searchers to determine what the article is “about” • Review articles: written for researchers and professionals who want to gain a grasp of the developments in a field. • Reference lists contain further reading for those interested in going into more depth on the topic • Reviewing services: provide a “digested” overview of research in various fields e.g. MedScape organizes medical literature for doctors, nurses, health professionals depending on their field of interest • Consumer health sites: provide a similar service for public consumption

22. Tertiary Literature • Final stage: description of research in the tertiary literature • summarizes and points to the primary literature, only after it has become widely accepted and believed. • Examples of tertiary literature: • Handbooks • Encyclopaedias • Textbooks • Monographs (books) straddle the last two stages. • some monographs or books point only to well accepted scientific research • other monographs point also to scientific research that is still being evaluated.

23. QUESTIONS ??

24. Indexes and Databases Vast amounts of research are published every day • Access: • difficult without a systematic approach to organizing it so that it can be found by the searcher • Indexing and abstracting services: • produce subject-specific databases that enable searching in general and interdisciplinary fields as well as specialized disciplines. • Indexing: • is time-consuming, costly (particularly in the sciences) and requires a high level of human input and subject-specific expertise. Academic libraries allocate significant portions of their budgets to databases and subscriptions to journals

25. Research Guides from the library homepage: www.library.yorku.ca • Under E-resources: Find articles by subject: Click on the field you are interested in e.g. Biology or Medicine and Nursing for: • Databases • Web Guides • Encyclopedias and Dictionaries • Government sources • E-books • etc

26. Which index to search? Indexes too, are geared to certain audiences, and serve specific needs • General indexes provide access to a broad spectrum of topics in a variety of formats e.g. • Web of Science: • Indexes 8,500 research journals across the Sciences, Social Sciences, and Arts & Humanities. • Has good coverage of interdiciplinary science and technology topics, particularly in fields such as ecology and engineering. • Allows you to search for articles by topic or author, title, journal, • and for articles that cite a known author or work (citation searching). • Coverage is from 1945 - present.

27. WoS search

28. Keyword Searching • Write out your research topic or question. • Note the core concepts (keywords) in your topic (nouns only) • Wetlands Water quantity • Identify synonyms or related terms for your keywords. • Wetland marsh bog swamp fen • Water quantity flooding • Type your search into the Search box, using • OR to group synonyms together inside round brackets (Wetland OR wetlands OR marsh OR bog OR swamp OR fen) (Water quantity OR flooding) • The truncation symbol $ in the library catalogue, and * in most other databases picks up words with variant endings such as plurals • (Wetland* OR marsh* OR bog* OR swamp* OR fen*) • AND finds the intersection of different concepts

29. Medical database - Pubmed • Pubmed is a service of the National Library of Medicine (US) that is provided free on the Web to anyone who has internet connection. • It includes over 15 million citations for biomedical articles back to the 1950's. • These citations are from MEDLINE journals and additional life science journals. • PubMed includes links to many sites providing full text articles and other related resources. • What makes it so powerful is the Thesaurus that indexers use when they assign subjects to each article that is entered into this database • Medical Subject Headings (MeSH) are specific terms (words) that group all records related to a concept under one common term. • articles about Cancer, Tumors and Neoplasms are all indexed under one Subject Heading: Neoplasms

30. What kind of search? • Subject Headings are specific terms that group all records related to a concept under one common term • If you do a MESh search in PubMed for ‘nosocomial’ it leads you to ‘cross infection’ as the preferred term • Subject searching gives you articles that are “about” that subject. • Keyword searching gives you articles that have that word somewhere in the text.

31. Subject Search searches articles that cover the same topic, regardless of which synonyms you use. all commonly used synonyms that you type in will point to one or more subject headings. don’t need to run searches on all of the synonyms. picks up all articles in which the subject heading is a significant topic. good to use when there is a lot written about a topic, and you want to narrow down your search to only relevant articles. Keyword Search searches articles that have the keyword anywhere in the title or the abstract WHETHER IT IS A SUBJECT IN THE ARTICLE OR NOT there is no single term that you use for searching. you need to run searches using all the synonyms you can think of. picks up all articles that include the keyword even if it is not a significant topic. good to use IN COMBINATION WITH A SUBJECT SEARCH when your topic is rare or new and not a lot has been written about it. Subjectsearch OR Keywordsearch ?

32. How to search Medline (Pubmed) • Select the MeSH database to construct your search • Type in one term e.g.SARS and select the best SH that describes your topic • Send it to the search box • Type in another term e.g. Canada and select the best SH • Send it to the search box using AND • Search Pubmed for articles that combine those two terms as subjects • Limit your search by clicking on Limit, and selecting the parameters, e.g. Review (if you want an overview of a topic) or Clinical Trials (if you want to review the actual research yourself)

33. Medical Subject Headings – MeSH search –

34. MeSH search

35. MeSH search

36. MeSH search results:

37. Biological Abstracts • Indexes over 5200 biological and medical research journals comprehensively. • Covers every modern life science discipline including: agriculture, agronomy, biochemistry, biotechnology, botany, ecology and the environment, genetics, medicine, microbiology, neurology, pharmacology and zoology. • Coverage is from 1969 to the present

38. BA search

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