Tag Archives: tips

articles, Library, Notes from the library, September 2017

Notes from the Library…Introducing JumboSearch

In June, Tufts Libraries launched a new iteration of our search platform, JumboSearch.  This means that the way you search for resources (books, journals, databases, articles, etc.) available through our libraries has changed.  This new search platform is part of our transition to a new integrated library system, which will improve how we manage our resources.

Here is a brief primer on how to use JumboSearch to find the resources you need.

How do I access JumboSearch?

The search box at the center of the Hirsh Health Sciences Library homepage (https://hirshlibrary.tufts.edu/) is for JumboSearch.

How do I find a book in JumboSearch?

Enter a title, author or keyword in the search box at the center of the Hirsh Health Sciences Library homepage.  Use the filters on the left side of the results page to limit your search to books.  Once you find the book that you need, click the title to view additional information, such as location and availability, and, if it is available electronically, access the full text.

What if the book I want is located at another Tufts library?

If the book is located at another Tufts library, then click the title of the book on the JumboSearch results page.  Select the ‘Log in’ link in the yellow bar at the center of the page.  Once you have signed in with your Tufts username and password, click the ‘Request item’ link to request delivery of the book to the Hirsh Health Sciences Library.  You will receive email notification when the book is ready for you to pick up at our Library Service Desk.

How do I find a journal? 

Enter the title of a journal in the JumboSearch box at the center of the Hirsh Health Sciences Library homepage.  If the journal is available through our libraries, then the title should appear at the top of the results.  Click the title of the journal to view print and electronic availability.

Another (and I find more efficient) method of finding a journal is to click the ‘Journals’ tab at the top of any JumboSearch page, which brings you to a page where you can search or browse our Journal list (versus all of our resources).

Can I use JumboSearch to find the full text of an article?

Yes!  If you have the title of a journal article and want to know whether or not the full text is available through Tufts, then copy and paste the title into JumboSearch.  If necessary, use the filters on the left side of the results page to narrow your results.  Once you find your article, click the ‘Full text available’ link.

How do I access my library account?

Use the ‘Log in’ link in the upper right-hand corner of any JumboSearch page, or in the yellow bar at the center of an item details page.  In your library account, you can see the items that you currently have checked out (including interlibrary loan books), requests, fines and blocks, as well as renew Tufts Libraries’ books.

February 2017, Library, Notes from the library

Notes from the Library…Approaching the Literature Review

Whether you are preparing a literature review for your thesis, a journal article, or grant application here are a few tips to help you get started and stay organized:

  1. Determine what information you need.

Why are you searching the literature?  Are you developing a research project and want to know what has been published about your topic?  Are you interested in literature on a particular method?  Are you preparing a grant application or manuscript to submit to a journal?  The answers to these questions will help you decide where to search, and whether or not the information that you find is what you need.

  1. Develop a focused question.

If you enter a few words, or a phrase, into a database, then you are likely to retrieve either a very large or very small number of results.  Developing a focused research question helps you construct a search strategy that will retrieve a precise set of results.  If you have a complex topic, then you may have multiple questions (and searches).

  1. Choose your resources.

Once you have determined what information you need and developed a focused question, then you are ready to choose your resources.  Choosing which resources to search can be overwhelming.  While PubMed is often a good place to start, think about where, and by whom, information about your topic is likely to be published, and what type of information you need (e.g. journal articles, conference proceedings, patents).  What disciplines might have a perspective on your topic?  What organizations, associations, institutes, companies or agencies investigate issues related to your topic?

Bibliographic databases, such as PubMed and Web of Science Core Collection, are organized collections of references to published literature (e.g. journal articles, conference abstracts, books).  When you are deciding which database(s) to search, consider the subjects, dates, and types of literature the database covers, as well as the search platform.  For example, MEDLINE, the database that is the principal component of PubMed, is also available through the Ovid search platform.  While PubMed and Ovid MEDLINE are similar, small differences in the content and search features of these two databases means that you will retrieve different results.  See the Sackler School Biomedical Sciences Research Guide for a list of biomedical database, or ask me!

  1. Create personal accounts.

You may think that you are finally ready to start searching.  Not quite.  Create a personal account with the databases, or platforms (e.g. Ovid, Web of Science), that you plan to search.  A personal account allows you to save searches and sets of results, and receive email notifications when new results matching your search criteria become available.  Unfortunately, you have to create a separate accounts for each database or platform, but it is a good idea to do so for the resources that you use frequently.  At the very least, I suggest that you create a My NCBI account, which is the personal account associated with PubMed and other National Center for Biotechnology Information (NCBI) databases, such as Gene and Protein.  See the March 2016, May 2016, summer 2016 and December 2016 PubMed Tip of the Month posts for more information on creating and using a My NCBI account.

  1. Use a citation manager.

Choose a citation manager before you embark on a literature review.  Citation managers allow you to organize and store your own collection of references, and insert formatted citations and bibliographies into documents.  Contact me (laura.pavlech@tufts.edu) if you need assistance selecting or using a citation manager.

  1. Document your search methods.

Get into the habit of documenting the parameters of your search, including: the databases that you searched; the platform on which you searched (e.g. Ovid, Web of Science, etc.); years covered by the database; complete search strategies; any limits applied, such as year, age, language; and the date on which you ran the searches.  While this information is not typically required for a manuscript (unless, of course, you are doing a systematic review, meta-analysis or scoping review), or grant application, a literature search is part of your research and should be recorded as you would any other experiment.  Doing so saves you considerable time and effort if you need to replicate the search in the future.

February 2017, Library, PubMed Tip of the Month

PubMed Tip of the Month: Single Citation Matcher

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If you have limited information about a journal article (e.g. author name and year of publication), then PubMed’s Single Citation Matcher may help you locate the article.  Accessible from the PubMed homepage, this tool does exactly what its name implies: it matches citation information to PubMed records.  Single Citation Matcher can quickly narrow your search to records that match the information you have.

Single Citation Matcher in PubMed
Single Citation Matcher in PubMed

 

October 2016, Techniques

Top Techniques: The Basics

Western Blot

PCR

IHC

Immunoprecipitation

February 2016, Library, PubMed Tip of the Month

PubMed Tip of the Month: Searching for Methods

There are several techniques that can help you find methodology articles in PubMed:

  • MeSH Headings for Methodology: “Methods” and “Research Design” are MeSH headings. You can try combining these terms with MeSH headings or keywords for your topic.
  • MeSH Headings for Particular Technique(s): Depending on your area of research, there may be a specific MeSH term for the category of techniques in which you are interested, e.g. “Cell Culture Techniques”.
  • Subheadings: Subheadings are used in conjunction with MeSH terms to further describe a particular aspect of that term. Subheadings follow a MeSH term, e.g. “Polymerase Chain Reaction/methods”[MeSH].  Subheadings can also be free-floated in a search, e.g. “DNA Replication”[MeSH] AND “Methods”[Subheading]. Two useful subheadings for methodology searches are “Isolation and Purification” and “Methods” (yes, Methods is both a heading and subheading).
  • Search Particular Journal(s): You may wish to narrow your search to one or more journals devoted to methodology. To do so, open the Advanced Search Builder by clicking the Advanced link below the PubMed search box. Select Journal from the dropdown menu and start typing the title of the journal in the adjacent search box. Choose the journal from the list of titles that appear. Enter a search term in the next search box to search the journal for articles on a specific topic, e.g. “Methods in molecular biology”[Journal] AND CRISPR.

PubMed Journal Search

articles, November 2015, Techniques

Techniques – Wild, Wild West(erns)

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Need some help to tame that wild western blot? Here are some tips and tricks to help you along the way –

  • Always check ladder migration pattern based on specific gel and electrophoresis conditions, as these factors can shift the apparent molecular weights from the supposed “standard” ladder image given out by the company.
  • When testing a new antibody, leave the blot intact, opting to strip it and perform a control protein blot after probing for your target protein. Cutting the blot and using different pieces for your target and control protein on a first try may obscure alternative target protein isoforms or off-target background staining.
  • High background? Try a more stringent blocking condition than just BSA or milk by adding goat serum or fish gelatin to your solution. Blocking overnight also can help clean up your blots.
  • Is you gel “smiling” or “frowning”? This usually happens when your sample buffer has too much salt.
  • Make sure your PVDF membrane is pre-activated with methanol for 20 minutes before making gel sandwich. It’s also a good idea to mark which side of the membrane is facing the gel with a sharpie, on a top corner.
  • It’s always a good idea to do a Ponceau stain on your membrane after transfer to make sure your transfer went all right. Alternatively, you can also stain your gel with Coomassie blue.
  • It is possible to over-transfer, especially for low MW proteins (<10 kDa) – optimize transfer time or reduce voltage. On the other hand, high MW proteins will take longer time to transfer.
  • Have a dirty secondary? Consider adding a wee-bit of Tween-20 to your washes (0.01-0.5%).
  • When loading your samples, press on the pipet just enough to get any possible air bubbles out and run the tip through the running buffer in the tank before putting it in the well. And make sure your sample was denatured prior to running.
  • If power supply reading shows 0 when switched on, make sure your power cables are properly connected to the power supply. If that doesn’t work, check for broken electrodes or blown fuses. Lastly, try with a higher limit power supply.
  • As always, make sure you write down the protocol before-hand and check through every step when performing. This will help you track your steps back to see at which step things could have gone wrong.

 

Source - http://prooffreaderplus.blogspot.com/2014/05/one-of-my-favourite-memories-good-bad.html
Source – http://prooffreaderplus.blogspot.com/2014/05/one-of-my-favourite-memories-good-bad.html