Library Resources for Cell/Molecular Contamination Seminar, PH292/293, Spring 2013

Instructor: Dr. Gertrude Buehring

Presented by Michael Sholinbeck

URL for this web page: www.lib.berkeley.edu/PUBL/SPH/CellLines_S13.html

Contents:

• The Public Health Library, Location, Reference, Off-Campus Access to Library Resources
• PubMed Tips
• Beyond PubMed: Other Resources for Finding Journal Articles and More
• Critically Evaluating What You Find
• A Closing Thought

The Public Health Library, Location, Reference, Off-Campus Access to Library Resources

Sheldon Margen Public Health Library home page
  Hours:
    Mon.-Thurs. 9-8
    Fri. 9-5
    Sat.-Sun. 1-5

Reference Services
  In-person: come to 1 University Hall (in the basement)
  Reference Desk hours: M-F 10-12, 2-4
  Other options include IM chat (24/7) and email reference.

How to set up off-campus access to library resources (databases, online journals, etc.)

PubMed Tips

PubMed: Citations to over 22 million journal articles and books, with links to full text via

First, let's talk about indexing!
  » Do you want articles on labor or articles on labor? Or is it labour?
  » Do you want articles on HIV (a virus) or articles on HIV diseases?
Index means a controlled vocabulary is used to assign subject terms to articles.
Subject terms may also be called thesaurus terms, descriptors, or (in PubMed) Medical Subject Headings (MeSH).

PubMed top tips for better searching:

1. Combine terms (as well as searches) with AND or OR
2. Use Filters (formerly called Limits) (eg, Age group, Publication type, language, etc.)
3. Search for your term as a word in the title or title or abstract (using Filters, Advanced Search, or Field Tags)
4. Use MeSH (Medical Subject Headings), with subheadings
5. Try PubMed's Clinical Queries or Topic-Specific Queries
6. Use the Related Articles link, once you find a set of relevant citations

» PubMed Quick Guide: Basic search help.

» PubMed exercise set:  PDF  |   DOCX   (from the Public Health Library)

» Combining search terms with Boolean operators (AND, OR, NOT - remember Venn diagrams?)

» Combining searches using History: Searches can be combined or used in subsequent searches using Advanced search History.

» Filters: Limit your search by language, age group, publication type, publication date, and more.
   Also use Filters to restrict your search to words in the article title, abstract, or Medical Subject Heading (MeSH).
   Note that Filters stay in effect until you clear them.

» Use Medical Subject Headings (MeSH):

• Searching by using the MeSH Database.
  Remember: think of your concept narrowly. Look at the MeSH definition. Remember there's a difference between a disease and a disease causing agent (eg, a virus).
• All MeSH Categories
  MeSH is hierarchical. This link will show you the top-level categories of MeSH. Click on any category, and you will see how MeSH narrows down. For any MeSH term, clicking on the full display will show you all the available subheadings for that term. As you select terms, send them to the search box to begin building your search.
• MeSH Qualifiers (Subheadings): Definitions
  Narrow your MeSH searches: Biomedical Research/standards looks for articles only on this aspect of biomedical research, not on other aspects of this disease (such as economics, education, history, etc.)
• Besides disease and anatomical terms, MeSH is robust in describing probability and statistical analyses, epidemiologic methods, behaviors and attitudes, and much more.
• MeSH terms of possible interest include: Research Design, Quality Control, Reproducibility of Results, Validation Studies as Topic, Cell Culture Techniques, and Cell Line.
  » Be sure to examine the hierarchies of these terms!
• Doing research on retraction?
  Be sure you understand the difference between:
  • a retracted publication (the article that was retracted);
  • retraction of publication (the published notice that an article was retracted);
  • a published erratum (acknowledgment of an error)
  • retraction of publication as topic (discussions of retraction).
  » Understand that not all retraction is evidence of scientific misconduct
• Check out the brief MeSH tutorials linked from the MeSH home page.
• Using MeSH is harder with some concepts, like life course or obesogenic environment.
  If you can not find a MeSH (or combination of MeSHs) that adequately describe your concept, search using words or phrases in the title or title/abstract. Then, see which MeSHs are used in the relevant citations you find.

» Federal grant numbers seen in PubMed citations may be used to search the NIH RePORTER for information on research funded by this grant: investigators, institutions, funding amounts, results (ie, publications), clinical studies, and more.

» Clinical Queries: Finding systematic reviews on your topic can help you find more research literature and give you a sense of the body of knowledge on a topic.

» Saving citations temporarily using the Clipboard

» My NCBI:

• Save search results (citations) in collections. Create as many collections as you wish
• Save searches and get automatic updates as new citations are added to PubMed that match your saved search
• Retain recent activity (searches, citations you viewed, etc.) for 6 months
• Create filters to group citations found from a search by selected criteria (age groups, subjects, methods, etc.)
• Customize the look and feel of PubMed to meet your needs

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Beyond PubMed: Other Resources for Finding Journal Articles and More      

Remember those PubMed "Top Tips"? Many are applicable to the databases below as well as several other databases.

BIOSIS Previews
The most comprehensive database for life science research. Coverage includes traditional areas of biology, such as botany, zoology and microbiology, as well as related fields such as biomedicine, agriculture, pharmacology and ecology. Interdisciplinary fields such as medicine, biochemistry, biophysics, bioengineering and biotechnology are also included, as well as instrumentation and methods. Includes journal article citations, books and meeting abstracts, papers and posters.
» Use Concept Codes, Taxonomic Data, and more to focus your BIOSIS Previews search.
» What's not in PubMed?
    Better searching by taxonomic data, includes meeting abstracts ...
» Guide to BIOSIS previews:  html  |  pdf
» Use BIOSIS Citation Index to see how many time articles in BIOSIS have been cited. See also Web of Science, below.
» In BIOSIS Previews, retraction and errata are Literature Types. Use the drop-down menu by the search box to select one of these Literature Types.

Embase
Broad biomedical scope with strong coverage in pharmaceutical and toxicological research, including economic evaluations. Useful for clinical medicine, genetics, biochemistry, molecular biology, microbiology, infectious diseases, healthcare policy & management, biomedical engineering & medical devices, and more. Embase is a primary resource for conducting systematic reviews and researching evidence-based medicine. Includes abstracts of over 2,000 conferences.
» Embase does use a controlled vocabulary. Click Emtree above the search box to search or browse for terms.
» What's not in PubMed?
    Better coverage of drug/toxicology topics, more non-US literature, sophisticated indexing scheme ("Emtree"'), search by CAS RN ...
» In Embase, retraction and errata are both searched using the term Erratum as a Publication type. Use Advanced Search, enter erratum, and choose publication type from the field limits. Also, use Retracted Article or Erratum as Emtree terms.

Web of Science
Large, multidisciplinary database; links to cited articles and times cited are provided for retrieved articles.
» Web of Science does not use a controlled vocabulary; it uses author keywords and keywords assigned algorithmically.
» What's not in PubMed?
    Scope of database is broad; best resources for cited reference searching.
» Cited Reference Searching exercise (from the Public Health Library)   PDF   |   DOCX
» Search Tips for Web of Science
» Cited Reference Searching
» In Web of Science, use the terms retraction, retracted, errata, erratum, etc. in the topic field to find these types of articles. There are no indexed terms to use for these in WoS.

Federal Register
Use this query:
  (misconduct | fraud | contamination) & ("cell line" | "cell lines")
to see a number of cell line misconduct or contamination reports in the FR. (The Federal Register is the official daily publication for Rules, Proposed Rules, and Notices of Federal agencies and organizations, as well as Executive Orders and other Presidential Documents.)

Retraction Watch
"Tracking retractions as a window into the scientific process," the Retraction Watch blog has published reports of scientific article retraction since 2010. It details several hundred retractions, and you can browse by author, country, journal, institution, publisher, reason for retraction, subject, and more. You can also search by any keyword (eg, cell line).

What do the journals say?
A simple web search author instructions "cell line" will bear fruit on this. Add more terms as needed to refine, such as a journal publisher or title, eg PLoS.
Or, find the instructions for authors page on a journal's website to see if cell line validation is discussed. Examples: Journal of Biological Chemistry, American Association for Cancer Research journals, Journal of Immunology, etc.

News sources often report on high-profile cases of scientific retraction, fraud, and misconduct. A few to try: Factiva, LexisNexis Academic, or the New York Times.
YouTube and blogs often contain interviews, commentary, and more on scientific retraction. For blog searching, use LexisNexis Academic (select Blogs from the Source Type menu), or Google blog search.

Don't forget to ask a librarian for help if you are having trouble with your topic.

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Critically Evaluating What You Find

What is evidence? Things to keep in mind:

• All research is (potentially) "evidence" and there are no "perfect" studies.
• Is there an agenda (bias)?
  » It's doubtful that any study of humans is totally without some kind of bias, either in the study design, or in the author's pre-existing beliefs, not to mention the source of the research funds. How bias in methodology was controlled and the significance of bias in any particular study is what's relevant.

The Critical Appraisal Skills Programme (UK) has a nice set of brief PDF checklist documents on critically evaluating different types of studies (eg, cohort studies, case-control studies, qualitative studies, etc.).
  » This web page also includes a nice summary of "critical reading."

Literature Review Matrix (.doc):
This chart may help you organize what you find in your literature search.
This is a simplified version of the matrix presented in Health sciences literature review made easy: the matrix method (J. Garrard; Sudbury, MA: Jones and Bartlett Learning, 2011), available in the Public Health Library, call number R118.6 .G37 2011 (Reference Section)

EndNote, RefWorks, Zotero, Mendeley, and other such tools can help you keep track of citations you find. In addition, these software will let you link to PDF files, or store PDF files in your database, as well as working with Word to correctly cite citations. Information on a substantial student discount for EndNote is available from the Cal Student Store. Call 642-9000 ext. 697. RefWorks is licensed by the UCB Library and is free to use while you are here. Zotero and Mendeley are free.

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A Closing Thought

"History of science teaches us that scientific endeavor has often in the past wasted effort in fields with absolutely no yield of true scientific information."
    (Ioannidis, 2005; see handout (.doc))

"The first man I saw was of a meagre aspect, with sooty hands and face, his hair and beard long, ragged, and singed in several places. His clothes, shirt, and skin, were all of the same colour. He has been eight years upon a project for extracting sunbeams out of cucumbers, which were to be put in phials hermetically sealed, and let out to warm the air in raw inclement summers. He told me, he did not doubt, that, in eight years more, he should be able to supply the governor’s gardens with sunshine, at a reasonable rate."
    (Gulliver's Travels by Jonathan Swift, 1726-1727)

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