Archive for Medical Science

First Aid Viral Classification Algorithm for the USMLE Step 1

// August 4th, 2014 // 1 Comment » // Medical Science

The Missing Viral Algorithm

I love the Microbiology section in First Aid for the USMLE Step 1: 2014 Edition. I particularly love the bacterial algorithm for Gram(+) and Gram (-) bacteria. I was wondering why the same did not exist for the Viruses. Instead the Viral section is presented as a system of rules for DNA viruses and then a very large table to memorize for RNA viruses. While voraciously studying for the Step 1, I did some searching only to discover that generally in medicine Virology is not very well-represented and in some cases not well-understood at the moment. If you Wikipedia-search viruses you’ll find a lot of red links (indicating that the sub-pages for related information are not written and information is incomplete). It’s also lower-yield for the Step 1 — most of the questions are supposedly on Bacteria — you still have to know virology for all the viral matters involved in other organ systems, however. This is how I organized the DNA and RNA viruses to be able to end up with the information presented in First Aid that we have to know for the Step 1. It’s based mostly off of 2-3 viral classification trees from MicroCards and the Virology section of First Aid.

This may differ in areas from traditional Viral classification systems and perhaps a few virologist lecturers would be offended, but it allows one to derive the necessary level of details tested on the USMLE Step 1 (rather than the entire virus “kingdom”). It’s just an algorithm to remember the details the same way that the bacterial algorithm is used. Diseases are included for the RNA viruses and left out for the DNA viruses. There are 2 RNA viruses trees though the top of the second tree is somewhat obscured by the first. My apologies for my handwriting. This correlates all of the classification details for each virus relevant to the First Aid section. The highlighting is intuitive.

USMLE Step 1 Viral Classification Tree -- Based off of First Aid 2014 and MicroCards, 3edHow does one use this table?

First, use this table to tie together all of the mnemonics that are in First Aid. For example, remember that “PAPP smears and CPR for Naked Hepey (Hippy)” mnemonic? Well the ‘CPR for Hepe’ is under SS-Nonsegmented(+). Use the mnemonic to tie together the Family names in yellow and then remember the similarly-sounding genus and viral names underneath (and for example using the “PERCH” mnemonic for the Picornaviridae family). Second, start with all of the classification branch-heads in Pink and just remember which category those fit under — Enveloped/Non-enveloped or Icosahedral/Helical/Complex. Then, memorize those Family names with the viruses underneath using the mnemonics. I used something like ‘CPR to a Naked Hepe in Reo’ for Non-enveloped, then ‘The Flooded River Delta’ for the Enveloped under Icosahedral. Then for Helical I used a little mnemonic ‘C ARBOr PaRFait,” (as in “Sea Arbor Parfait“) 3 separate words for Cornoaviridae, Arena-Bunya-Orthoviridae, and Paramyxo-Rhabdo-Filoviridae and remember their classification. Do the same for the DNA viruses. Use First Aid’s mnemonics or what mnemonics you find helpful to visualize. After doing this I could more easily rattle off the viral classification for any given virus in First Aid, fast-recall that I need for test-taking.

Third, the table is pretty complete and includes all of the relevant details from First Aid (Note that wherever a virus is not circular it is linear). So start at one “leaf” of the tree and work yourself up to the root of the tree.

For example:
(1) “Eastern Equine Encephalitis is an Alpha Virus of the Togaviridate family, which is a single-stranded non-segmented positive-sense [linear] enveloped icosahedral RNA virus.”

Here’s another example:
“Norovirus is a Calicivirus of the Caliciviridae family which is a single-stranded non-segmented positive-sense [linear] nonenveloped icosahedral RNA virus.”

Do this for every virus until it becomes very natural. Then, correlate the remaining viral information in First Aid with this classification. I did the RNA viral classification trees in Red. Still memorize the rules in First Aid (which are great).

Conclusion I hope it helps. You can also memorize the messy RNA viral table in First Aid, but this algorithmic tree just makes it a lot easier to derive the classifications and cuts down on the heavy memorization, and it serves as a useful visual to have in mind when answering question-bank questions. Again, this is based off of First Aid and so all of what is high-yield for the Step 1 is included in this system.

Find an error? Have a suggestion? Please comment below. There’s already enough Wite-Out® Correction Tape but I don’t mind adding more. I hope this helps someone get this straight or at least give a basis for being able to think about viruses.

Sources Cited:
1. First Aid for all of the relevant and high-yield information (which has been around for 25 years and is a product of Yale)
2. MicroCards (also originally a product of Yale — why didn’t they communicate this structure to the First Aid Team?) for the classification scheme, slightly modified

Strange find: Physiologic Necrosis

// August 3rd, 2013 // No Comments » // Blog, Medical Science

“…under specific conditions such as caspase intervention, necrosis has been proposed to be regulated in a well-orchestrated way as a backup mechanism of apoptosis. The term programmed necrosis has been coined to describe such an alternative cell death.”

SIRT4 a potential new important cancer drug target

// July 27th, 2013 // No Comments » // Medical Science

Marcia Haigis, HMS associate professor of cell biology, led a team that has uncovered SIRT4 as an important player in the DNA damage response pathway.  Here’s an article I haphazardly discovered today on an important sirtuin protein called SIRT4. Harvardianites have discovered that when SIRT4 is absent from mice, the cell cycle doesn’t function to arrest cell division and keep the cell from becoming malignant/cancerous. SIRT4 acts as a physiological weigh-station to prevent the cell from proceeding when there’s a stressed, cancer-producing environment (such as with excessive UV rays) that could lead to cancer. What does this mean? It means that drug discovery could have room for a new target that could lead to some important therapies. I’m interested in it. During undergrad I did undergraduate research in drug discovery and got a sense of what goes into figuring all of these systems out. I appreciate this research greatly.

Here’s the link to the article:

Tell them Isaac sent you.

Math Meets Medical Science – Additive Emetogenic Potential

// May 19th, 2012 // No Comments » // Medical Science

I was just playing around with some numbers one day after a lecture for school and came up with some formula for calculating the additive emetic level of more than one antineoplastic drug. I thought I’d share it here in case anyone thought it was interesting (and, well, there’s little else to share). Maybe someone’s doing a Google search and would think this is cool like I did… (I didn’t know what else to do with this since I never got a chance to use it for the exam :-/ Garrrr…)

Antineoplastics are categorized according to their emetogenic potential, Frequency of emesis
▫ Level 1 (<10%), Busulfan, Vincristine, Chlorambucil
▫ Level 2 (10-30%), Gemcitabine, Paclitaxel, Asparaginase
▫ Level 3 (30-60%), Cyclophosphamide, Methotrexate
▫ Level 4 (60-90%), Carmustine, Cisplatin, Irinotecan
▫ Level 5 (>90%), Mechlorethamine, Dacarbazine
Combining antineoplastics may increase emetogenic risk:
For example:
(1) 2 + 2 + 2 = 3
(2) 2 + 2 + 3 = 4
(3) 3 + 3 + 3 = 5
If you have 3 drugs that give about a Level 2 Emesis (10-30%), the aggregate that the patient would experience would be 30-60% (More Emetogenic)

If you’re given a list of drugs and need to find the additive emesis level for that list based on the level of each drug:
Let a = Minimum Range Number for a given drug’s Level number
Let b = Maximum Range Number for a given drug’s Level number
Let m = The percentage of emesis for a given drug (1 singular drug).
Let n = The number of drugs in the list given (if 1 drug, n=1; if 2 drugs, n=2, etc.)
Let p = The sum of the percentages for a number of drugs (many drugs)

Formula #1: m = (b/2)
— For a given drug “n” Formula #2: p = sum(m) + 1
— Letter j represents Then, answer = the level of p.

2 + 2 + 2 = 3 – There are three Level 2 drugs given.
Therefore, n=3.
– Level 2’s Range is 10-30%.
Therefore, a = 10, b = 30
– m1 = (30/2) = 15%
– m2 = (30/2) = 15%
– m3 = (30/2) = 15%
– p = sum(15% + 15% + 15%) + 1 = 46%
The answer is “3” since 46% is in the Level 3 range

2 + 2 + 3 = 4 – There are two Level 2 drugs and one Level 3 drug given.
Therefore, n = 3.
– Level 2’s Range is 10-30%.
– Level 3’s Range is 30-60%.
– m1 = (30/2) = 15%
– m2 = (30/2) = 15%
– m3 = (60/2) = 30%
– p = sum(15% + 15% + 30%) + 1 = 61%
The answer is “4” since 61% is in the Level 4 range.

3 + 3 + 3 = 5 – There are three Level 3 drugs and one Level 3 drug given.
Therefore, n = 3. – Level 3’s Range is 30-60%.
– m1 = (60/2) = 30%
– m2 = (60/2) = 30%
– m3 = (60/2) = 30%
– p = sum(30% + 30% + 30%) + 1 = 91%
The answer is “5” since 91% is in the Level 5 range.

Hope that amuses someone out there. -ID

Golgi Tendon

// January 26th, 2012 // 1 Comment » // Medical Science

I was looking around YouTube for a demonstration of muscle contractions for something that we’re studying in school and stumbled upon something interesting that we didn’t cover: The Golgi Tendon. Its job is to protect certain muscle tendons from an overexertion or greater force than can be tolerated by the muscle. If I’m living weights and I’m lifting way more than I can handle, I’d rather my body tell my arm to stop for me than to rip the tendon off of the bone — wouldn’t you? Well, that’s what it does. It sends signal to an inhibitory interneuron that shuts down the muscle to reduce the force. It’s called the GTO — Golgi Tendon Organ.

The first part of the video covers the monosynaptic stretch reflex. In school they taught us this differently from what the video demonstrates. We learned a 4-step process with certain steps that occur simultaneously. They sort of show a signal that’s delayed in its traveling — that’s more confusing for a demonstration of a reflex. But, after that, is the Golgi Tendon at about 1:44. Well worth seeing.