Blogs

Please come visit us in the Library, which is all dressed up for the holidays! In particular, marvel at our iconic Book Tree, nestled by the fireplace in the Medical Historical Library. Library staff lovingly built the 3rd edition of our Book Tree, using almost 500 volumes from the National Union Catalog. We wish you a very happy holiday season!

Last night, while preparing an RNAseq dataset for functional analysis. I found this problem again. When opening high-throughput data results into Excel be aware that this software will convert (by default) some gene symbols into a date format- see examples in the table below. These conversions are not reversible so the original name cannot be recovered. Zeeberg et al. reported this problem back in 2004. If you are not aware of this and proceed with the functional analysis, those genes (converted into dates) will not be recognized and will not be computed. If you think that this will never happen to you, this error have been found in a project as important as the Cancer Genome Atlas.  

One way to avoid this –from the end-user bioinformatics perspective- is to define the column containing the gene symbols as “Text” under the “Column data format” as shown in the figure below. It is always recommended –whenever possible- to use unique identifiers (Ensembl IDs, Gene IDs, Affymetrix IDs, etc.) other than gene symbols. If you are not sure, you can always go to the Gene database (NCBI, NIH) whenever looking for the official symbol of a gene.   

For questions, consultations, or help with you functional analysis, please do not hesitate to contact me.

Example of some human gene symbols that will be converted into dates by Excel.

Thursday, November 19 is the American Cancer Society's annual "Great American Smokeout," encouraging smokers to quit, even if it's only for one day.  What better time than to round up a few key information resources on tobacco cessation?

• Smokers may find the American Cancer Society's website helpful, in particular its "Stay Away from Tobacco" section. 
• Yale clinicians can refer to Treating Tobacco Use and Dependence: 2008 Update, a guideline from the US Agency for Healthcare Research and Quality.
• For point of care reference, DynaMed offers a chapter on "Treatment for tobacco use," last updated October 30, 2015.

The DynaMed chapter offers patient education materials, as does ClinicalKey.  Click the dropdown menu to the left of the search box to filter results in the "Patient Education" source type. 

For help finding more evidence on tobacco and smoking cessation, you can always contact your department's librarian. 

Come out this Friday, November 13th, noon to 2pm, for a special Finn Friday celebration in honor of Finn's birthday! 

Monica Green, a scholar of the history of medieval medicine, recently profiled the Bamberg Surgery, which is part of the Medical Historical Library's collection.  The Bamberg Surgery is a surgical text dating from the mid-12th century which was acquired by Dr. Harvey Cushing and subsequently formed part of the original Medical Historical collection at Yale. 

Green writes:

The Bamberg Surgery doesn’t get a lot of love in histories of surgery, because of its patchwork character. As Corner himself said, “it is a notebook, a partially organized collection of notes, memoranda, prescriptions, and excerpts from other books.” But the Bamberg Surgery merits a closer look to contemplate the question with which we began: how do you begin to build up a body of written surgical knowledge when previously you had none?

The Bamberg Surgery draws selectively from the (now complete) translation of (Persian physician​‘Ali ibn al-‘Abbas) al-Majusi’s text, which it fuses with an early medieval text on phlebotomy that circulated under Hippocrates’ name. It then expands on these elements with new pharmaceuticals, new techniques, and elements of anatomical and physiological learning drawn from other texts. For example, al-Majusi’s text had never mentioned marciaton, a compound medicine for a wax-based unguent passed on through the early medieval Latin pharmaceutical tradition. The Chirurgia salernitana had recommended its use, and we find it in the Bamberg Surgery likewise, being recommended for nerve damage from a wound, broken bones, and dislocations.

Similarly, the author cites Galen’s Tegni several times, a translation of the foundational handbook of medicine composed by the 2nd-century Greek polymath, used widely in the Islamic world and, increasingly, in Europe as a basic introduction to medical theory and practice.

Click here to read Green's full post, which discusses a number of other medieval surgical texts.