Pediatrics: PubMed Tutorials and Exercises in Patient Safety Resources

Please view each of the tutorials below and enter answers or SNIP/screenshots as requested into your Assignment Document. The tutorials are drawn from YouTube, including an excellent series by Roy E Brown of the VCU Libraries and the National Library of Medicine's tutorials.

1. Searching by Breaking Question into Concepts (Roy E Brown, VCU Libraries- approx 4.5 minutes) https://www.youtube.com/watch?v=7dSCYHSgyv4

• Is it a good idea to put as many possible terms as you can into a search string? Why or why not? (Assignment document)

• Why does Brown suggest separate concepts searches which are joined later? (Assignment document)

2. Coming Up with Alternative Terms (Roy E Brown, VCU Libraries-approx 4.5 minutes) https://www.youtube.com/watch?v=NaXK6rA01TE

• Can you name 4 places you might search to find alternative terms for a search? (Assignment Document)

• What does R Brown say is a key factor in the kinds of terms a specific searcher first considers? (Assignment Document)

3. Search with Controlled Vocabulary (Roy E Brown, VCU Libraries- approx. 9 minutes) https://www.youtube.com/watch?v=Q4w6T6aovIQ

• Name 4 benefits of using controlled vocabulary that R Brown mentions. (Assignment Document)    

• What does R Brown tell us about the retrieval of citations when we use terms from the top of a hierarchical subject  tree? (Assignment Document)

• Where is controlled vocabulary found in the citation record in PubMed? (Assignment Document)

Go to PubMed. Enter this number in the search box and search: 26591098. Next, go to the pulldown menu labeled Abstract (upper left part of the page). Select MEDLINE from the pulldown – when the MEDLINE display appears, cut and paste the MH field tags (left margin/column) into your Assignment Document – the first one is

MH  - Cross Infection/*prevention & control 

When you perform a MeSH only search this is only part of the citation record that is looked at to retrieve a citation. Copy and paste the title field TI into your Assignment Document. When you search for title only, then only this field is searched. If no search field is indicated, then the default is to have all the fields searched in the citation record. A good practice can be to search with a MeSH field indicated or several if appropriate – together with keywords which have may or may not have an attached search field indicated. Sometimes searches will use the MeSH fields and the title fields if the searcher feels confident that a subject will appear in a title in the event that it was never indexed with the MeSH (there are a number of citations which are in PubMed but never indexed although this is not the rule).

4. Starting Search Broad and Then Narrow (Roy E Brown, VCU Libraries- 4.4 minutes) https://www.youtube.com/watch?v=y2WJ-HKfqLo

• Name 3 ways you can narrow your search in a database like PubMed? (Assignment Document)

5. Boolean Operators (Roy E Brown, VCU Libraries- approx. 4.3 minutes) https://www.youtube.com/watch?v=qLw8dAoLxqI

• Which Boolean Operator (AND vs OR) does not require a relationship between concepts in a search? (Assignment Document)

  In the tutorial, R Brown presents a grid showing the concepts linked by OR which are intersected by AND (ORing of concepts occurs row by row, while ANDing of concepts occurs across columns). The headings of the columns are “Hand Washing” (column 1) and “Hospital Acquired Infection” (column 2).Please recreate this grid in your Assignment Document (don’t do a screen print – go through the process of recreating his grid by hand so you have time to think through the process and patterning). Include the bracketed content too as it indicates subject headings and keywords. Learning how to create this kind of a grid for all your research topics is a most important behavior to become an organized, accurate, and comprehensive searcher.

Note, R Brown’s grid is theoretical to cover diverse databases. The current PubMed subject headings are actually different in a few instances. The grids you actually use in constructing searches across multiple databases should be precise with respect to the specific database being searched. The point of this exercise is to start learning this organizational pattern and use of Boolean Operators so that you can apply it to diverse databases, which will always vary by subject headings.

6. Keyword Searching (Roy E Brown, VCU Libraries– approx. 10 min) https://www.youtube.com/watch?v=iK8LZRgc0s4

• Name 5 circumstances (according to R Brown’s tutorial) where your search is enabled by searching with keywords. (Assignment Document)

•  Name 5 circumstances (according to R Brown’s tutorial) where is it helpful to do more than a keyword search. (Assignment Document)

•  What is the benefit of searching for a phrase or grouping with quotation marks? (Assignment Document)

7. Searching PubMed with Keywords (Roy E Brown, VCU Libraries- 7 minutes). NOTE: Where R Brown talks about Get it @VCU, you can substitute Find it @ UIC.  https://www.youtube.com/watch?v=eEY1r_GDzcg

• Search for Patient Safety and show the details box for this search  (Assignment Document)

• Search for (Patient Safety) and show the details box for this search  (Assignment Document)

• Search for "Patient Safety" and show the details box for this search  (Assignment Document)

• Show Patient Safety AND A-TOPIC-OF-YOUR-CHOOSING  (Assignment Document)

The point of this exercise is to experience the ways in which PubMed translates a query - don't rely on a "rule" but always look at the query box to see what it actually did with your search. Note, PubMed looked for "Patient Safety"  (in quotes to indicate a phrase) in its internal translation table of known phrases and it did not break the quoted phrase apart. If it did not find a quoted phrase in the table, it would return with a message close to the top telling you the phrase is not found and it would break the phrase in quotes apart to search each individual word and the phrase as a whole. Always look at the translation. 

8. Doing a Medical Subject Heading (MeSH) Search in PubMed (Roy E Brown, VCU Libraries- 6 minutes). https://www.youtube.com/watch?v=1HMvR6kLBDY

• Show a SNIP/Screenshot of the MeSH term record for Obesity. Only the word Obesity appears on this page. Now, use the PubMed Search Builder box by pressing the Add to Search Builder button, which automatically pops the term Obesity in the box. Show the PubMed Search Builder box with the term added to it. Then, perform the PubMed search and show the results page. (Assignment Document)

• Show a SNIP/screenshot of the entry terms for Carbonated Beverages from the MeSH database (Assignment Document)

• Show a SNIP/Screenshot of the MeSH page and entry terms for Patient Safety. Note in your Assignment Document, the date the term entered the MeSH database. Now, search for Patient Safety in the MeSH databases and use the PubMed Search Builder box on the MeSH page and the Add to Search Builder button to perform a PubMed search of the MeSH term. If you do a MeSH search for Patient Safety, how many citations do you find? Now, put this phrase in quotes in the search box for PubMed (not the MeSH page) - "Patient Safety". How many citations do you find? Finally, if you search for the phrase - “Patient Safety”[mesh] OR “Patient Safety” – how many citations do you retrieve? Note, since Patient Safety is a MeSH term, entering the keyword phrase - "Patient Safety" - will cause the keywords to be searched as a phrase as well as the MeSH term (see the automatic query translation in the details box). (Assignment Document)

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  NLM tutorials

9. PubMed: Searching with the MeSH Database (NLM, approx. 2.3 minutes) https://www.youtube.com/watch?v=nF_oQNtnbuQ

• What is a major heading in PubMed? (Assignment Document)

10. PubMed: Applying Subheadings and Other Features Using the MeSH Database (NLM, approx 4 minutes) https://www.youtube.com/watch?v=LTtrvUQLsWo

• Show a search using the MeSH for Measles as a major topic and a subtopic of your choosing. (Assignment Document)

11. PubMed: Search by Author (NLM, approx 2 min) https://www.youtube.com/watch?v=kKAp5jc8g5s

In addition to the method of author searching shown above, there is another helpful tool provided by PubMed in the Single Citation Matcher search.

Here is a video from the University of Maryland medical library on this citation finding tool:  https://www.youtube.com/watch?v=ydJWxRwjxjE

• You are looking for an article with patient safety in the title that was authored by Klamen as first author. Can you find it using PubMed's Single Citation Matcher? Show the citation in your Assignment Document.

KEEP GOING ON ASSIGNMENTS ALL THE WAY TO THE BOTTOM OF THE WEB PAGE- THERE ARE 20 EXERCISES!

12. The  5 Tips for Searching PubMed tutorial by Duke University Medical Center Library demonstrates a patient safety topic search in PubMed - https://www.youtube.com/watch?v=6wWeeCBBlk4

This tutorial explores the patient safety search using 3 key concepts –

1) Health care workers   2) Influenza vaccine   3) Patient infection

Sign in to your MYNCBI account. Return to the PubMed homepage.  Please duplicate the Duke search in PubMed by following all of the steps in the tutorial exactly as shown - this is a challenge. Show your work via snip/screenshots in your Assignment Document.

Begin by finding the PubMed home screen through the LHS Library website http://researchguides.uic.edu/c.php?g=252191  - scroll down under Research Databases until you find PubMed. Consider bookmarking the LHS Medicine homepage.

After completing the 3 separate searches for Health care workers, Influenza vaccine, and Infection (you will need to copy the Duke modification of the Health care worker term from the tutorial), go to the Advanced page using the Advanced link under the PubMed search box. Create a search that intersects all 3 concepts (use AND to join the concepts together in an intersecting relationship). Show a snip/screenshot of your work from the Advanced page with the combined 3-concept search.

Currently, the search recreation should bring you about 202 search results. Write the librarian if you are struggling with this. Also, an easy way to get it right is to make a snip of the screen that shows you Duke's Advanced search page - then you can see exactly how they did it.  

13, View this tutorial for directions on using Filters and the Advanced page to complete the additional exercises: PubMed Advanced Search by the University of Michigan Library https://www.youtube.com/watch?v=vtjrN752Occ

On the search results page for the combined search above, use the following filters to modify the search – English language, last 10 years, randomized controlled trials. You will have to use the “Customize” and “Show additional filters” links to see some of these filters before you can select and apply them. Remember that the filter is not applied until you see the blue checkmark. The search results are finally reduced to about 3 citations once all the filters have been added. Show your work with a snip/screenshot.

Please follow the steps exactly in this exercise. You will be able to judge the correctness of your follow up by the results answers given at each step. Your aim is to duplicate these results exactly. 

Remember that when you use the left-column filters in PubMed, sometimes a two-step process is required. For example, when choosing an Article Types filter, first you request to see the filters by pressing More under the Article Types section heading, then you select whatever article type you do want to see. Once the article type appears on the filter list, you have the option to select it. A check mark should then appear to indicate that this filter is set.

a. Enter PubMed via the LHS gateway and sign into your MYNCBI account.

b. In the search box, enter the following search string into the PubMed search box:  ("2010/01/01"[Date - Completion] : "2014/05/19"[Date - Completion]) AND (patient safety and communication)  Your results should be about 2,417 results.

c. Go to the Ages filter section. and select More. When the filters menu appears, select 80 and over: 80+ years

Your results should now be 89

d. Return to the Article Types filters and press More. Select the Comparative Study box and Show. When the Comparative Study option appears, select it.

Your results should now be 9

e. At the bottom of the column, select the Show Additional Filters link. Select Journal Categories and press Show. Select the Nursing Journals filter in the Journal Categories section.

Your results should now be 2. The PMIDs of the remaining articles are   22271215  and  19773144

f. Go to the Clear All link and select it.

Your results should now be 2,417 as before!

g. Under the PubMed search box, select the Advanced link. This link will show you the recent search history. Note, this history from the Advanced page is temporary. It follows the IP address of the physical computer and browser - it lasts 8 hours only.

Find the search with 89 results and select the number link itself. You should land back on the results page. Note, the age filter 80+ is applied to this set.  Now, select Core Clinical Journals from the appropriate filter section.

Your results should now be 6.

h. Select Evaluation Studies from the Article Types Filters. (Remember select the More link and select the Evaluation Studies box, then press Show. Next, select this link and verify it by the check next to the study type).

Your results should now be 1.

i. Remember to Clear All your filters again!

Once you have completed steps a-i above - Using the Advanced page link (beneath the search box), go to recent search history and show a snip/screenshot of the searches above into your Assignment Document. If you have extra searches in the box, you can delete them by selecting the Search # (see the search column on the Advanced page) and choosing the Delete from History link. This is useful for cleaning up your record.

`Complex String Construction Assignment:  You must read all of these instructions please!

Your task is to construct several complex search strings that include 3 terms that are subordinate to the MeSH term “Health Services” in the MeSH tree – together with terms related to the concepts of “Patient Safety” and “Quality Improvement”.

I will model the first string for you and ask that your recreate it by typing the string manually into your Assignment Document – please do NOT use the screenshot/SNIP tools because I want you to think about what you are doing.

Look up “Health Services”[MeSH] in the MeSH database. You will see over 150 subordinate child and grandchild terms, beginning with “Adolescent Health Services”, “Child Care”, “Infant Care”, etc.

Pick your 3 child terms and create the MeSH string for each term using the MeSH builder. For each term, look at the MeSH record and put the Entry Date for the term in your Assignment Document. For each of the 3 terms, also construct a keyword phrase the way I did. In the case that you pick a term where the MeSH does not translate to a natural English phrase, write it as a natural language phrase.

We will also use both the terms “Patient Safety” and “Quality Improvement” as MeSH terms and keyword phrases in a unified concept set.  Note, I use keyword phrases for terms like Patient Safety, which had a very recent entry date of 2012. A MeSH-only search for Patient Safety would exclude decades of research prior to 2012.  

My Example – (Watch the use of parentheses!):

• First, I construct the CONCEPT SET for the children of “Health Services” – notice I keep the keywords phrase in quotes. So, this to be part of this unified first set, an article only has to contain one of these 6 terms.  

("Adolescent Health Services"[Mesh] OR “adolescent health services” OR "Community Health Services"[Mesh] OR “community health services” OR "Emergency Medical Services"[Mesh] OR “emergency medical services”)

• Secondly, I construct the CONCEPT SET for patient safety and medical errors (you can just copy this). So, to be part of this unified second set, an article only has to contain one of these 4 terms. I am using OR in this example to treat these concepts as relatives comprising a larger family, but I could also treat them as intersecting concepts if I put AND between them. They are not identical concepts but often show up in the same fields and research areas.  

("Patient Safety"[Mesh] OR “patient safety” OR "Quality Improvement"[Mesh] OR “quality improvement”)

• Third, I combine the first and second concept sets together using AND to create an intersection of these first 2  concept sets. So, to be part of this combined set, an article must satisfy the inclusion condition of the first set plus the inclusion condition of the second set. An article about "patient safety" and "emergency medical services" will satisfy both conditions and be in the result set.

(("Adolescent Health Services"[Mesh] OR “adolescent health services” OR "Community Health Services"[Mesh] OR “community health services” OR "Emergency Medical Services"[Mesh] OR “emergency medical services”))  AND  (("Patient Safety"[Mesh] OR “patient safety” OR "Quality Improvement"[Mesh] OR “quality improvement”))

Now, you do a string for your Assignment Document! 

Use at least 3 child terms from the parent “Health Services” in the string. Use the MeSH term and also use a phrase between quotes as a keyword term. Sometimes this is as simple as translating the MeSH term - "Patient Safety"[MeSH] -  to "Patient Safety"

Note, the keyword phrase will bring you many more search results than a search that uses only the MeSH term.

Use the "Patient Safety" OR "Quality Improvement" string from above to intersect  your 3-concept string. Follow the format I laid out.

Please highlight the Boolean Operators the same way that I did so you are clear about what you are doing the first few times – do not hesitate to write me at mdclark@uic.edu if you have any trouble. 

EXERCISE: Take a look at Appendix I in Neville's guide book on plagiarism.

How many of the 10 instances addressed in the answer grid do not require a reference?

Please summarize the answers for no. 9 and no. 10 in your assignment document.  

The content in SAGE Research Methods offers you a comprehensive introduction to the basics of research. SAGE’s content will help you design and conduct your own projects.  SAGE Research Methods can help you  support others as a project supervisor or methods instructor.

The specially commissioned collection of social research case studies from SAGE Research Methods Cases can be searched or browsed. It is intended to help you understand the application of abstract methodological concepts in realistic research contexts.    

EXERCISE: Link into Sage's Research Methods resource below. On the Browse Methodologies pulldown, select  Methods Browse, then select Policy research (~64). Look for a video called "How do I design policy focused research?" by Naomi Jones. On the video page, look for the Related Content box. Name 3 titles in the box or include a screenshot/snip in your assignment document. Consider browsing these resources... 

Access this link to a poster on Bad Science - http://www.compoundchem.com/2014/04/02/a-rough-guide-to-spotting-bad-science/

 Summarize at least 5 identifying characteristics of a potential bad science article according to the poster in your assignment document.  (Hint: This should be a matter of just looking at the poster and reading the points of evaluation it summarizes. Noting the bold headline is enough - e.g. ) Sensationalised Headlines".)

Visit Vanderbilt's brief tutorial on scholarly publications - http://www.library.vanderbilt.edu/peabody/tutorial_files/scholarlyfree/index.html

What is a trade publication? (Answer in your assignment document).

Visit the University Library at Urbana-Champaign (UIUC) webpage "Using Refereed/Peer-Reviewed Research" at http://www.library.illinois.edu/learn/research/peer_review.html - read the page and particularly the essay portion, "What to Look for in a Refereed/Peer Reviewed Journal".

Visit the HIMSS.org website page for HIE White Papers - http://www.himss.org/resourcelibrary/TopicList.aspx?MetaDataID=1737

Select the link to the white paper, "Trends in HIE Organizational Staffing: A Deeper Look At Staffing Challenges". Download the paper.

Does this look like a Refereed/Peer-Reviewed Research article? Why? Why not? Answer in your assignment document.  (Hint: Just say what you think and your reasons - this is a question to help us understand whether the point about what is peer-reviewed and what is not is well enough understood to the students).

Go to PubMed and put this PMID in the search box -  24477917

You should find an article entitled, "Lessons learned from a health record bank start-up."

Now, we want to look at the NLM Catalog entry for the journal that published this article. From the top of the citation record for the article, copy the journal title -  Methods Inf Med. and paste it in the search box. Next to the search box, there is a pull-down menu that currently has PubMed in it (since you were just searching the PubMed database). Use the pull-down menu to select NLM Catalog (this is yet another database). Now search the NLM Catalog for the title  Methods Inf Med - the record that appears will have two entries for the title. Pick the second one that is "currently indexed in Medline" and use the link.  

On the NLM Catalog Entry for this journal, look for the electronic link: http://www.schattauer.de/en/magazine/subject-areas/journals-a-z/methods.html - and access the journal's home page.

Inspect the journal - sections, editors and board, about section, etc. Does this journal look like it publishes Refereed/Peer-Reviewed articles according to the criteria established on the UIUC website? (Assignment document).

Name 3 factors that match the UIUC standards. ? (Answer in your assignment document).

In the About section of the journal's website, select the Student Editorial Board link. What does the "Methods of Information in Medicine" intend to teach its junior partners? ? (Answer in your assignment document).

Visit the Ulrich'sWeb resource from the Databases A-Z link on the UIC-LHS website. http://library.uic.edu/lhs/chicago (find the "U" section and enter Methods of Information in Medicine" in the search box. Pass your cursor/pointer over the Star and the Black Shield icons. What do they tell you about the journal "Methods of Information in Medicine"? (Answer in your assignment document).

Go to the AHRQ PSNET website: https://psnet.ahrq.gov/

Select Topics from the upper pull-down menu. Choose "Safty Target" from the list. Choose "Fatigue and Deprivation".On the left sidebar, choose Setting of Care/"Patient Transport". This should produce about 3 articles.  Please take a screenshot/snip of this results page with the 3 or so articles and paste it into your Assignment document.

Now, have some fun on your own with exploring this wonderful resource! The best is sometime last ...and sometimes fast.

For the next exercises, go to the Patient Safety Guide (Expanded), which is linked to from the Home page of this guide. Select the Databases and Resources tab. Scroll down to the E-books box for the links referenced in this section.

SpringerLink e-Books

• Exercise 20a for SpringerLink

Search for “patient safety” AND SBAR. On the left sidebar in the “Content Type” section, select “Article” to limit your results. Next, look at the results and identify the article with “IGBOs” in the title. Copy/Paste the title with IGBOs into your assignment document.  Release the filter for article content types by clicking the X  next to “Articles” and observing the other content types reappearance on the sidebar.

• Exercise 20b for SpringerLink

Books @ Ovid 

• Exercise 20c for Books@OVID

Select Search from the top banner (to the left of Journals, Books, Multimedia, etc.)  In the search box area, UIC Books@Ovid should be present. Next, select the Natural Language Search option. Do not use the keywords option.

Enter this in the search box: resident handoffs AND medical errors. Scroll down and notice the Search Terms used section. Copy/Paste the search terms used into your assignment document.

Be aware that some phrases are treated as whole phrases and others are not. When you enter a phrase, it is either recognized as a phrase made of related terms or it is not. If it is recognized, it is searched as a whole phrase. If it is not, it is searched as separate and unrelated terms.

• Exercise 20d for Books@OVID

Next, select the Natural Language Search option. Do not use the keywords option.

Credo Reference Collection – Medicine

These exercises are designed to support your investigation of the range of questions and topics the Credo Collection  engages.

• Exercise 20e for Credo Reference - Medicine

Credo-Reference Books in Medicine.  Use the pull-down menu to find the Select Subjects or Titles link. Next, select Health & Medicine link by pressing the + sign, and expand the list of resources in this area.  Notice Medicine and Nursing are both sub-collection areas. Select the “Dictionary of Medical Terms” and search for ADVERSE in the search box. Be aware that two search boxes are available. One will search all of Credo (the upper box in the green band) and the other (correct) box is below it and on the right side. This second box is not in a green band and will limit the search to the selected resource, Dictionary of Medical Terms.  List the first 3 ADVERSE terms found (these terms are linked to definitions). COPY/PASTE the 3 adverse definitions in your assignment document. Note, you have to open each of the results up to see the definitions as they are not visible from the top search results page. 

• Exercise 20f for Credo Reference - Medicine

Go to “The Cambridge Historical Dictionary of Disease” and look up EBOLA. Answer this question from the essay: What was the number of deaths and number of cases resulting from the June 1976 Ebola outbreak in the Sudan?  Enter the answer in your assignment document.

• Exercise 20g for Credo Reference - Medicine

Go to “The Encyclopedia of Elder Care” and search for PATIENT SAFETY. In the paragraph on page one under the section heading “Patient Safety Definitions” is a sentence constructed as such (my blanks added in): “The NPSF believes that unintended health care outcomes can be caused by errors of _____________, ______________ or ___________.”   Please list the 3 types of errors noted in your assignment document.

• Exercise 20h for Credo Reference - Medicine

Go to “Macmillan Dictionary of Toxicology” and COPY/PASTE into your assignment document the definition for the term: “LOWEST OBSERVED ADVERSE EFFECT LEVEL (LOAEL)”after completing your search.

• Exercise 20i for Credo Reference - Medicine

Go to “SAGE Key Concepts Series: Key Concepts in Health Studies” and look for “The Lived Experience of Health and Illness”. Scroll down to the bottom of the page to find the APA citation style for this essay. COPY/PASTE the APA citation for this essay in your assignment document.

IMPORTANT NOTE: If you have a problem logging into the MyNCBI account again or get a frame-within-a-frame problem, try these steps -

1 Logoff MYNCBI in every site and on every browser

2 Clear out all the bookmarks for all the browsers related to PubMed and MYNCBI links – Pubmed distinguishes browsers and treats them differently – you can be logged on in one browser and not another

3 Clear the caches in the browsers

4 Do not use the link from the MYNCBI sign up page to access MYNCBI again once you have registered

5 Use this link from the LHS Library page to access PubMed - http://www.ncbi.nlm.nih.gov/pubmed?otool=uiclib