Wednesday, June 22, 2016

How is your favourite research area doing?





Just out of curiosity I wanted to check out some of the publication trends on some of my favourite research topics. I used an online tool that outputs data the number of query publications for each year (available here). Below I plotted the results of a few. The queries with multiple words were put in quotations. Importantly the results for cancer in the plot were divided by 100 as to fit on the scale of the graph. So not only is cancer a much larger topic, with about 14 000 / 100 000 papers on pubmed, but it is also growing at over 100 / 100 000 papers every year. This is much faster than the other topics presented. Data up to to and including 2013 is included because the tool itself suggests that more recent data may not be very accurate.
I was fairly surprised to see the growth in papers on cancer stem cells especially when compared to oncolytic viruses. There are obviously lots of problems with evaluating a research area with this data. First is that the growth of a smaller topic may not be apparent when using data that is / 100 000 papers. Second is the issue of the query. It may not encompass the field well and a more popular term may be gradually replacing an older query. Third is that while there may be fewer papers, the papers that are published may be of higher impact factor. It is possible for example that oncolytic viruses are moving more into the clinic and that kind of research takes longer and the rate of publication may be reduced but the importance of the research may be greater than ever. A tool to evaluate the trends in impact factor of a query would be very interesting also.






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Tuesday, May 03, 2016

CRISPR/Cas9

Never have I missed being in a lab as much as I have since I started hearing about CRISPR/Cas9 a couple years ago. This is a genome editing technology that was developed by adapting an antiviral mechanism found in bacteria. If anyone has some first hand experience I would love to hear about it.
Here is a good introduction to CRISPR/Cas9, where it came from, and how it works.
I was also interested in what kind of commercial products are available to make this even easier, and here is a video of the CRISPR/Cas9 offerings from ThermoFisher (long 41:49). I don't think I've really grasped the implications of this technology however it seems it is facilitating the beginning of the genetic engineering of our species.


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Tuesday, February 02, 2016

Response to the current Zika virus epidemic

Scientific American has an article that briefly summarizes the link between Zika virus infection during pregnancy and fetal microcephaly. While the circumstantial evidence is strong for a causal link, the article discusses the fact that conclusive evidence will likely only come from retrospective analysis of the current epidemic. Wired magazine has a more speculative article that has some additional interesting facts about the outbreak and the response to it."Most of Brazil's microcephaly cases are in the northeast, and it's unclear why Zika would cause more birth defects there than in other places." Multiple Zika strains or perhaps lagging microcephaly diagnosis may account for this observation. Unfortunately, these types of issues complicate efficient analysis of the current situation. Recent responses to the epidemic reflect serious concern. El Salvador has recommended that pregnancy should entirely be avoided until 2018, and the WHO has declared Zika a public health emergency of international concern allowing it to make decisions that are international law. Do these responses and the responses to the 2014 Ebola outbreak inspire any confidence in our ability to contain these and future frightening viral epidemics? The fact that the vaccine development is already underway, without many confirmed numbers and a lack of conclusive causal evidence, is amazing to me.


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