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NROD98: Thesis in Neuroscience

A guide for advanced research projects and supervised studies for neuroscience students.

Workshop FAQs

Fall 2022 Workshop Questions


Q: How do we identify a primary article?
A: The main thing to keep in mind here is that empirical/primary articles report on original research findings; based on that, you can look for clues in the text that point towards it being primary. Sample things to look for include:

  • A research question and hypothesis
  • A methodology section outlining how the study was conducted
  • results section reporting on key findings of the study

Use caution for studies like systematic reviews or meta-analyses! Even though these have methods for conducting research and report on 'new' findings, they build on existing primary literature and are classified as secondary/review articles.

If you struggle with finding primary literature, many databases have "primary" or "empirical" article filters that can help weed out other literature types from your search. Let me know if you need any help with this piece!


Q: How can I find articles/papers which critique primary research?
A: Most databases allow you to filter your search results by article type, which will usually include options for review-type articles (e.g. literature reviews, systematic reviews, meta-analyses, etc.). While these articles won't necessarily critique per se, they do give a summary analysis on the topic at hand based on existing primary research. This makes them a  great way to quickly get up-to-speed on a topic and see what the general state of a field is!


Q: How do I know if my search is too specific?
A: The biggest tell is generally lack of results when you do a literature search (though this can also be due to other factors, such as what kind of literature is indexed in a specific resource such as a database, or even lack of published literature at all, especially for a developing research area!). My general recommendations would be to:

  1. Try increasing your number of search results (see the "How do I broaden my topic/what do I do if I get too few results?" topic further down the page for specific tips on this)
  2. Search for your topic across multiple databases to check for any unique literature not indexed elsewhere

If you get to the end of these steps and find you still don't have what you need, talk to your supervisor and consider whether you need to make any changes to the scope of your research topic.


Q: Are operators case-sensitive? For example, is "AND" and same as "and"?
A: It depends on the tool that you're searching in! Some have case sensitivity, and others don't. Based on this, I recommend defaulting to capitalized AND/OR/NOT when searching just to be safe, especially if it's not clear whether the tool requires it or not.


Q: I'd like to know more about the legitimacy of open-access journal publishers.
A: I recommend starting with U of T Libraries' Deceptive Publishing guide, which provides an overview of predatory journals and some of its key resources such as the Identifying Deceptive Publishers Checklist. If you have additional questions around this, I'm happy to chat!


Q: Is there a way to manage citations or articles of interest? Do you have any recommendations for citation managers?
A: I highly recommend checking out our guide on citation management for an overview of popular tools available. There are a variety of citation managers (i.e. software) that allow you to collect, organize, and create citations/bibliographies for your references, which is super handy when you're working with a large volume of information. I'm particularly fond of Zotero, which is completely free and can be integrated with most browsers to quickly select citation information directly from a web page.


Q: How can you set up alerts for keywords in various journals of interest?
A: Some journal websites will allow you to make alerts at the keyword search level, while others may only have alerts for the entire journal (i.e. you'd get a full list of all articles released with every new issue). Once you do a search, check to see if the journal of interest has an alert option (see example below from the Journal of Neuroscience); you will usually need to create an account with the journal platform first.

screenshot of a search alert icon from the Journal of Neuroscience website

In cases where a journal doesn't offer a keyword-level search alert option, you could try using databases such as PubMed or MEDLINE to first create a search for your topic of interest, and then couple that with a journal search. From there, you can create an alert that will update you any time new literature is added that meets these criteria (similar to journal websites, you will first need to create an account with the database platform).

In this second example, I conducted a MeSH search for Parkinson Disease, then AND'ed that together with a journal search for Nature Neuroscience.

screenshot of how to create a search alert in the PubMed database


Q: How do we access various databases (without paywalls) beyond graduation?
A: This is unfortunately tricky, since access to most research databases is going to be tied to your university affiliation (via UTORid, in U of T's case) and thus becomes unavailable after graduation. Here are some options to consider:

  • While we can't grant remote access to databases, some U of T Libraries (including UTSC) offer guest accounts for local use; so if you're in the area after graduation, you can visit the library and use designated computers + guest accounts for browsing.
  • Beyond that, open access journals and platforms are your best bet. Some starting ideas here:
    • PubMed has a publicly-searchable web interface with a "Free full text" filter once you get to the results page of a search
    • The Directory of Open Access Journals (DOAJ) is a consolidated list of open access (OA) publications that can be searched at the journal or article level
    • Elsevier maintains a list of internal Neuroscience open access journals
    • If you come across an article that you're interested in that does have a paywall, see if it's possible to reach out to the author(s) and ask whether they can give you access! Many publishers grant researchers a certain number of final publisher version/PDF copies that they can distribute to other people; the author(s) may also have earlier copies of the manuscript that they can openly share. 


Questions from previous years can be found below:

Literature Searching

Q: How do we actually search a database? Any tips on using AND/OR, advanced searches, etc.?
A: Please see the database-specific tutorials under the "Databases" tab in the left menu for an overview of each platform. If you have questions about any other databases or building searching strategies in general, I'm also happy to touch base!


Q: How do I broaden my topic/what do I do if I get too few results?
A: There's a few things you can try to increase your number of results:

  • Remove AND'ed concepts from your search
  • OR in additional keywords or subject headings for your related concepts/synonyms
  • Check for broader and related terms in your subject heading's hierarchy list
  • Remove or loosen up some of your limits (e.g. published in the last 10 years vs. 5 years)
  • If none of the above work, revisit your research topic and consider broadening or altering it

Q: How do I narrow down a topic/what do I do if I get too many results?
A: There's a few things you can try to decrease your number of results:

  • Remove OR'ed concepts from your search
  • AND in additional keywords or subject headings
  • Check for more specific narrower terms in your subject heading's hierarchy list
  • Apply or strengthen some of your limits (e.g. peer-reviewed, empirical journal articles published in the last 5 years)
  • If none of the above work, revisit your research topic and consider narrowing or altering it


Q: What is the optimal amount of searching that should be done / is there a certain number of results I should aim for?
A: This entirely depends on the nature of your topic and the type of literature search you're doing. As a general rule, about 100-200 results is a good number to aim for per database (i.e. when searching in places like MEDLINE or PubMed). Keep in mind there may be more or less depending on your topic, however (for example, newer research areas might not have much published literature out yet, while more established ones will have stronger representation in the literature). Your main task is to cover due diligence as a researcher (e.g. making sure you look in the appropriate collection of research databases, that you are comprehensive in selecting your key words and building a search strategy, etc.) and then to critically evaluate the resources you find from there.

Q: How many sources should a literature review include?
A:  As with above, there is no perfect answer to this - it will entirely depend on your research topic and how much literature is available. If you find there is too much literature, you will want to think about ways to focus your research topic; likewise, if there is not enough literature, you might consider ways to broaden the scope of your topic. My encouragement would be to think less about numbers and more about the relevance of literature retrieved, i.e. Does this directly relate to my topic? if so, why is it significant?


Q: How would you go about searching literature for a case study?
A: Both PubMed and MEDLINE offer "Case Reports" as a filter when searching within their database. For PubMed, you will first need to customize the "Article types" menu to display Case Reports before you can select it; in MEDLINE, it can be found in the "Publication Types" menu.

PubMed "Case Reports" filter:

Case Reports limit in the PubMed database


MEDLINE "Case Reports" filter:

Case Reports limit in the MEDLINE database


Q: Is there a way to determine which papers talk about any "hot topics?"
A: Hmm, this one's a little tricky! It's common practice to set up email alerts for either a search strategy within a database, or even for a specific journal if it's in a subject area you're interested in, so that you can stay up-to-date with the latest papers for a certain topic or subject area. Utilizing email listservs and social media (e.g. Twitter, blogs, etc.) can also be a great way to network and stay up-to-speed with what researchers in a discipline are talking about/publishing on -- it's just a matter of tracking them down first!

Reviewing Articles

Q: How do I go about combing through the literature over many days without losing my "place"?
A: This one depends on what sort of literature search/article review process works for you. If you like to work one database/resource at a time, you might want to save your search strategy within the tool (most databases platforms allow you to do this with a free account) and then keep track of how far you get through reviewing the results. You can then re-run the saved search and pick up where you left off next time. Others like to do all their searching across multiple databases first and then export citations to a citation manager, where they then review everything in one place. Citation management software usually has built-in note-taking and tagging tools that you can use to keep track of your progress. Regardless of what method works for you, I definitely recommend having some sort of research log to track things like what you searched, where you searched, your takeaways from reading the article's full-text, etc.


Q: How do you know (at a quick glance) if a long article is long due to a lot of content, or just "fluff" and lack of brevity?
A: This can be tricky! I would do a quick scan of each of the key sections of the article (e.g. Introduction, Methods, Results, Discussion, etc.) and check for "filler" content - e.g. redundant wording, excessive detail, etc. Look for sub-sections which help organize ideas and determine whether paragraphs have a clear focus and flow throughout the text. UTSC's Writing Support has a number of handouts on Academic Style which may also be helpful for identifying additional criteria to evaluate a piece of writing.


Q: Would it not be recommended to use an article if we're only taking a bit of information from it?
A: For me, this would depend on how critical that information is; for example, is this unique information that I cannot find anywhere else? Is it an important "puzzle piece" compared to other existing literature on my topic? The main thing I want to avoid is including "extra fluff" that doesn't add substance to my paper. So my recommendation here would be to include a source if its information is genuinely relevant, regardless of how small that piece of information may be within the scope of the larger paper. Otherwise, reconsider whether the source is truly needed.


Q: What's the best way to summarize all your research and articles for easy reference?
A: This will vary from person-to-person, so it's worth trying a number of strategies to see what works best for you. Some people like to create comparison charts that outline different facets of articles (e.g. methods, findings, discussion, etc.), some like to use index cards to summarize each study, some like to create concept maps to find connections and link related ideas, etc.


Q: How can we easily find a gap in the literature regarding a particular topic?
A: My first recommendation is: read read read! The better you know the field and the more acquainted you are with literature in a specific subject area, the more likely you'll be to catch any glaring omissions. It can be helpful to a) read broadly to see how other researchers address gaps/what sort of things they look for and b) read deeply so that you become a mini-expert in your subject area and know the ins-and-outs of your topic. It can also be helpful to look at the Discussion sections of relevant articles and look for explicit mentions of future research. Once you've identified gaps, you can then check whether newer studies have since attempted to fill these gaps.

Citations and Citation Management

Q: Is there a way to find papers connected to a specific papers? Do we just check the section called "cited by"?
A: You can use "citation chaining" to locate related papers on your topic. Backward citation chaining involves reviewing the sources at the end of a publication (i.e. the References, Bibliography, or Works Cited section) for older relevant literature. Forward citation chaining involves moving forward in time to find articles that cite a published work, usually using citation indexes; most databases will have a built-in "cited by" feature that you can use. You can also pop a work's title into Google Scholar to check their "Cited by" feature, though be mindful that you'll want to be extra careful about screening for peer-reviewed work for any sources gathered here.


Q: Would you recommend
A: Based on background research, it looks like this is a fairly new tool (launched June 2020) that is dependent on Semantic Scholar's open research corpus and to pull papers. I don't see any immediate red flags to using it, though I would say be aware of its limitations (see their About page for more details on how graphs are generated) and use it as a supplementary tool to database-specific literature searching.


Q: How to use Zotero or related citation sources?
A: Check out our comprehensive Zotero guide for tips on how to install and use the software for managing your citations/references. The University of Toronto Libraries also has a broader Citation Management guide if you'd like to see some other popular tools that are available. I'm happy to follow up if you have any specific questions not answered by either guide!


Q: Do all graduate students and researchers use citation management tools (e.g. Zotero) or is manual citation common?
A: Citation managers are pretty common at the graduate and researcher level due to the nature of their work and the number of references they typically work with. This is especially pertinent when working on research teams where access to a shared library of citations is needed. That being said, not everyone uses citation managers, which in my experience is usually either due to personal preference or lack of awareness for the tools.


Q: How do we properly write a meta-analysis paper?
A: I recommend reviewing the Gerstein Library's page on mete-analyses, which has information on key methods and study elements.