Keywords, Boolean, and Diabetes: Finding a Journal Article

There are few serendipitous Google searches not resulting in tangential YouTube excursions. I mean, they put the videos right there on the first page. No, Google, I don’t want a video of cats jumping into an alley to the tune of “Sail”, but thanks for ruining my productivity. Or, for that matter, Wilford Brimley hilariously mispronouncing “diabetes”. For a search engine that has such a stronghold over the cutthroat world of internet traffic, you’d think searching for reliable, primary sources of information would be a piece of cake.

And it is, you just have to know how to work the system.

In my introduction to biological research course, we are required to make a poster fit for presenting. Before that, we need to have four primary research articles pertaining to our topic, and use the fourth article as the source for our poster.

I want to find articles on diabetes research, so I should start with a general search. Yeah, you could probably go straight to your favorite scientific or medical database, e.g., PubMed, SciFinder, or WorldCat, but that takes the fun out of everything. So, let’s start out with “diabetes in humans” as our search, and Google as our search engine.

A trainwreck of a search

A train wreck of a search

Holy shit, 18 megahits. At a click a second, I could open those links in almost 30 weeks. I can’t use that for anything. So what’s wrong with my search?

Well, there are several culprits here. First off, Google just indexes stuff and doesn’t discern quality. Clever webmasters can load up there webpages and send their links toward the top — or just buy adspace. Look at all of those spam links, I would get less adverts on AdultFriendFinder. So, Google is compromised here.

Secondly, I have got the blandest search you could make after “diabetes”, concerning my topic. In fact, I really don’t have a topic. Just some general terms, keywords. “Diabetes” and “humans” are obviously important words, so maybe I need to solidify their relationship. Google doesn’t search with English syntax, it speaks the language of Boolean operators. So let’s figure out what we can do with Boolean operators.

Million and million of hits

Million and million of hits

Woohoo, 17 million! Right? Wait. I want human diabetes. So, the culprit here is how general my searches are. I can move those numbers around, but they’re not getting any manageable. I need a better topic.

Right now, I’m working with this really cool transcription factor called Pdx1. It has been linked to diabetes, and happens to interact with a promoter sequence upstream of the insulin gene. I have an interest in diabetes, and an interest in Pdx1. Let’s see how the two are related.

best google

Snap, crackle, pop. Less than 5 million. That’s more manageable, right?

Well, not really. I need a better vehicle for finding information. And, for me, that vehicle is PubMed. The Wiki calls PubMed a “database accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics”, and I agree, so there’s a quote.

pubmed one

Well, I tried to get fancy with some parentheses, but that didn’t help. “AND” is an exclusive operator, so it only finds the stuff together in the same article. “OR”, on the other hand, is inclusive and doesn’t help with downsizing. However, it has its uses. Let’s introduce another term and see what happens.

pubmed two

And, there we have it. In a total of maybe a minute, I have gone from millions to hundreds. Not bad, right? Let’s look through a couple abstracts before I move on here.

Pancreatic Duodenal Homeobox-1 (PDX-1) is a homeobox protein which acts as a key regulator in the development of b cells in the Islets of Langerhans. […] There is strong evidence that PDX-1 plays a role in activating the insulin promoter and increasing insulin levels in response to glucose. (Blyth NJ)

Here, we report a procedure for induction of insulin-producing cells (IPCs) from bone marrow murine mesenchymal stem cells (BM-mMSCs). These BM-mMSCs have the potential to differentiate into insulin-producing cells when a combination of PDX-1 (pancreatic and duodenal homeobox-1), NeuroD1 (neurogenic differentiation-1), and MafA (V-maf musculoaponeurotic fibrosarcoma oncogene homolog A) genes are transfected into them and expressed in these cells. (Guo QS, Zhu MY, Wang L, Fan XJ, Lu YH, Wang ZW, Zhu SJ, Wang Y, Huang Y)

[The] level of Pdx-1 expression is closely correlated with level of insulin mRNA and insulin secretion level in differentiated MSC stable cell lines. These findings suggest that the level of Pdx-1 expression plays a key role in induction of MSCs to insulin secreting cells. (Yuan H, Liu H, Tian R, Li J, Zhao Z)

Did you get all of that? This stuff is all important, but there are some keywords that keep popping up. “Mesenchymal stem cells” (abbrev. MSC), “insulin”, “differentiated”, and “induction”. We may just be getting somewhere. So let’s experiment.

final image

ONE. One article to rule them all, one article to find them. But there’s a problem. While containing all of our terms with the specificity desired, this is a review, and is, by definition, secondary information. We want to cover the bases, but we don’t want to eliminate all of the primary information out there. Plus, I need four articles. So what do we do?

If you find yourself in this situation, read what you find and start new search parameters. Ultimately, you’ll come to the end of the road, with an awesome article on whatever you’re trying to find. Just pay attention to what you are reading — abstracts, introductions, methods, conclusions.

I am still finding articles now from the review article. So, hopefully, I’ll be able to narrow it down. In the meantime, if you have read this whole article, try to find something that interests you and let me know how quickly you can get there.

Citations and sources:

Blyth NJ. Mechanisms and techniques of reprogramming: using PDX-1 homeobox protein as a novel treatment of insulin dependent diabetes mellitus. Diabetes Metab Syndr. 2012 Apr-Jun;6(2):113-9. doi: 10.1016/j.dsx.2012.05.018. Epub 2012 Jul 8. PubMed PMID: 23153982.

Guo QS, Zhu MY, Wang L, Fan XJ, Lu YH, Wang ZW, Zhu SJ, Wang Y, Huang Y. Combined transfection of the three transcriptional factors, PDX-1, NeuroD1, and MafA, causes differentiation of bone marrow mesenchymal stem cells into insulin-producing cells. Exp Diabetes Res. 2012;2012:672013. doi: 10.1155/2012/672013. Epub 2012 Jun 19. PubMed PMID: 22761608; PubMed Central PMCID: PMC3385644.

Yuan H, Liu H, Tian R, Li J, Zhao Z. Regulation of mesenchymal stem cell differentiation and insulin secretion by differential expression of Pdx-1. Mol Biol Rep. 2012 Jul;39(7):7777-83. doi: 10.1007/s11033-012-1619-7. Epub 2012 Apr 10. PubMed PMID: 22488273.

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