Sunday, May 26, 2013


In preparation for the start of my MPH program (specialty: infectious disease), I've been brushing up on various subjects for which I lack formal academic training, in particular parasitology, virology, and immunology. The latter is probably my weakest subject, and so I'm studying intensely to make up for lost time. I'm quickly finding that immunology is incredibly fascinating, and had I known the subject possessed so much intrigue, I might have pursued it as an undergraduate. I'm astounded by the complexity with which our immune systems function, and the armchair military historian in me is impressed by the multiform stratagems our bodies have evolved to battle invaders.

To achieve a firm grasp on the fundamentals of immunology, I'm drawing from two textbooks:

- The University of South Carolina School of Medicine's online Microbiology and Immunology
(a thorough, excellent resource available at     
- How the Immune System Works (3rd Ed., Lauren Sompayrac). This slim text is brilliant. It reads like a collection of lectures, meant to be completed in the course of a few days. The author breaks the material down into easily-digestible chunks, replete with helpful illustrations, and yet still imparts enough solid information to build a sound foundational knowledge of immunology.

In addition to textual sources, I'm utilizing a wide array of freely-available animated content.
McGraw-Hill's online components for its Human Anatomy textbook include many useful explanatory animations, like this one on phagocytosis.   
YouTube also has an abundance of material, like this video detailing respiratory burst:

Animation is a wonderful tool for the immunology student, as it so easily and clearly conveys what are otherwise complex and recondite processes. It is simple to understand how C3b or IgG works when you see it modeled in action, when on paper the fundament can be lost in a sea of associations and interactions with endless other acronyms. 

Saturday, May 11, 2013


Kernel Density Estimation (KDE), also known as a "heatmap," is a wonderful way to graphically convey epidemiological data for outbreaks of infectious disease. At a glance, one can discern likely points of origin, routes of transmission, and density by area. KDE maps are attractive and fairly easy to render in QGIS, but it can be exceedingly difficult to obtain spatial point data, which is necessary for creating the nodes used by the software to model density. For this KDE, the underlying raster image is John Snow's original 1854 map, with vector overlays of spatial point data showing water pumps and cholera deaths. The proportional mortality is most densely concentrated around the Broad Street pump (the source of infection as deduced by John Snow). For proper viewing, click HERE to enlarge.

Density radius: 30m
Decay rate: 0
Cell size X,Y: ~1,1
Global transparency: 20%

Snow's original map is available in a high resolution format here:

Unfortunately I did not bookmark the site which offered the spatial point data for download, but if I can locate it again, I'll be sure to give appropriate credit here.


Wednesday, May 8, 2013


Here in Ohio, spring is in full swing. Trees are budding fervently, reptiles can be spotted basking in the midday sun, and the forest floors are beginning to grow a healthy layer of undergrowth to cover last autumn's leaf litter. Hiking is presently a joy, as the mosquitoes have not yet made their presence felt, and the days of high humidity and sweltering temperatures are still a few months away. I've been spending an abundance of time outside and, although it is only early May, have already noticed an unusual pervasiveness of a certain  arachnid: Dermacentor variabilis -- the wood tick. In the last week I've found them in my car, on my dog, and even in the house. I'm not particularly worried, as D. variabilis isn't regarded as a particularly competent vector for serious human disease (especially in Ohio), but the sightings do make me wonder if this will be a bad summer for another species of tick, Ixodes scapularis--the deer (or black-legged) tick. 

Ixodes scapularis is of serious concern to humans for a variety of reasons. First of all, it is much smaller than the wood tick, and is far more likely to feed unnoticed by the host. The black-legged tick is also a more efficient vector of human pathogens, including Lyme disease. While nearly everyone has heard of Lyme disease, and its notoriety has been enhanced by media and pop culture, the opposite is true of Babesia microti and babesiosis. Apart from parasitologists, Babesia is virtually unknown. Although mammalian infection with this parasite is ubiquitous, human infection is less common, and many cases are asymptomatic.

B. microti is a piroplasm, a protozoal parasite, that bears some similarity to malaria, causing hemolytic disease which results in generalized "flu-like" symptoms that are often difficult to accurately diagnose. These include headaches, body aches or pains, diarrhea, fatigue, lethargy, chills, and fever. In severe cases of infection where parasitic load is high, more serious symptoms/complications like jaundice, hemolytic anemia, respiratory failure, renal failure, and congestive heart failure can occur. The risks of Babesiosis are greatly increased for patients who have had the spleen removed or are otherwise immunocompromised.        

Life cycle of Babesia microti.

1. Despommier, Gwadz, Hotez, Knirsch. Parasitic Diseases (5th Ed.), Apple Trees Productions, LLC. New York: New York (2005).

2. Centers for Disease Control, Parasites - Babesia

Monday, May 6, 2013


After an extended hiatus, I've again taken to toying with QGIS. Below is a choropleth map that I made last week. It illustrates all reported cases of H7N9 in China, by province, as of 05/03/13. (Click to enlarge.)