Diarrhoea in Bangladesh: displaying results from fixed effects models

I ran into this 2008 paper doing hurricane work with Jesse. The results are not extremely surprising, but I really liked how they displayed their result.  Many of us use high-dimensional data and multiple regression models to try and account for the many different processes that occur in social data, but it is often difficult to clearly display the effect of just one process while also being clear about all the other controls in the model. I like the approach of this team: they show predictions form the complex model (eg. with week and month fixed effects, socioeconomic controls, etc.) overlaid with the real data.


Factors determining vulnerability to diarrhoea during and after severe floods in Bangladesh
Masahiro Hashizume, Yukiko Wagatsuma, Abu S. G. Faruque, Taiichi Hayashi, Paul R. Hunter, Ben Armstrong and David A. Sack

Abstract: This paper identifies groups vulnerable to the effect of flooding on hospital visits due to diarrhoea during and after a flood event in 1998 in Dhaka, Bangladesh. The number of observed cases of cholera and non-cholera diarrhoea per week was compared to expected normal numbers during the flood and post-flood periods, obtained as the season-specific average over the two preceding and subsequent years using Poisson generalised linear models. The expected number of diarrhoea cases was estimated in separate models for each category of potential modifying factors: sex, age, socio-economic status and hygiene and sanitation practices. During the flood, the number of cholera and non-cholera diarrhoea cases was almost six and two times higher than expected, respectively. In the post-flood period, the risk of non-cholera diarrhoea was significantly higher for those with lower educational level, living in a household with a non- concrete roof, drinking tube-well water (vs. tap water), using a distant water source and unsanitary toilets. The risk for cholera was significantly higher for those drinking tube-well water and those using unsanitary toilets. This study confirms that low socio-economic groups and poor hygiene and sanitation groups were most vulnerable to flood-related diarrhoea.

Why you should care about aerobiology

Last week's Eos had an interesting article on aerobiology (pdf here).  The authors summarize some of the science behing the dispersal of single celled organisms via the air, then talk about the social implications of air-dispersal (eg. the spread of infectious diseases over large distances) and current advances in monitoring and modeling the process (this last bit is left out below, see the article if you're interested).

[Other recent Eos articles are here and here]

The High Life: Transport of Microbes in the AtmosphereBy David J. Smith, Dale W. Griffin & Daniel A. Jaffe 

Microbes (bacteria, fungi, algae, and viruses) are the most successful types of life on Earth because of their ability to adapt to new environments, reproduce quickly, and disperse globally. Dispersal occurs through a number of vectors, such as migrating ani- mals or the hydrological cycle, but trans- port by wind may be the most common way microbes spread. 

General awareness of airborne microbes predates the science of microbiology. Peo- ple took advantage of wild airborne yeasts to cultivate lighter, more desirable bread as far back as ancient Egypt by simply leaving a mixture of grain and liquids near an open window. In 1862, Louis Pasteur’s quest to dis- prove spontaneous generation resulted in the discovery that microbes were actually single-celled, living creatures, prevalent in the environment and easily killed with heat (pasteurization). His rudimentary experi- ments determined that any nutrient medium left open to the air would eventually teem with microbial life because of free-floating, colonizing cells. The same can happen in a kitchen: Opportunistic fungal and bacterial cells cause food items exposed to the air to eventually spoil. 

Unknowingly, Pasteur founded the field today referred to as aerobiology, the science that studies the diversity, influence, and survival of airborne microorganisms. Sci- entists now have the ability to monitor the movement of atmospheric microorganisms on a global scale. But long-term molecular- based measurements of microbe concen- trations are still missing—such information is needed to improve understanding of microbial ecology, the spread of disease, weather patterns, and atmospheric circulation models.

Infectious cancers, genotyping, and indirect extinction pressure

The cover story of last week's PNAS covers attempts by scientists to analyze the Tasmanian devil genome. The hope is that by doing so they might better understand the devils' vulnerability to the infectious cancer that's currently wiping them out at an alarming pace:

The Tasmanian devil (Sarcophilus harrisii) is threatened with extinction because of a contagious cancer known as Devil Facial Tumor Disease. The inability to mount an immune response and to reject these tumors might be caused by a lack of genetic diversity within a dwindling population. Here we report a whole-genome analysis of two animals originating from extreme northwest and southeast Tasmania, the maximal geographic spread, together with the genome from a tumor taken from one of them. A 3.3-Gb de novo assembly of the sequence data from two complementary next-generation sequencing platforms was used to identify 1 million polymorphic genomic positions, roughly one-quarter of the number observed between two genetically distant human genomes. Analysis of 14 complete mitochondrial genomes from current and museum specimens, as well as mitochondrial and nuclear SNP markers in 175 animals, suggests that the observed low genetic diversity in today's population preceded the Devil Facial Tumor Disease disease outbreak by at least 100 y. Using a genetically characterized breeding stock based on the genome sequence will enable preservation of the extant genetic diversity in future Tasmanian devil populations.

Devil facial tumor disease manifests itself in a fashion as horrific as one might guess, and is considered a major threat to the species' existence. Infectious cancers are more common outside of humans, though DFTD is still particularly odd: it isn't viral but rather consists of parasitic cells which spread from host to host via blood-to-blood contact. It's very similar to canine cancers with similar behavior and is believed to originate in a subtype of neural cell called Schwann cells (want to scare a friend? show them the title to the Schwann cell Science paper and underline "clonally transmissible cancer").

DFTD is interesting to think about above and beyond its clinical oddness for the fact that it seems to be largely our fault: humans likely introduced the cancer in the first place via dogs (an invasive species in Tasmania), and are doubly at fault for having reduced the devil population (the 100 year old dip in genetic diversity mentioned above) thereby reducing genetic variation and the potential for resistance. Short of a human intervention soon (researchers are apparently trying to figure out why a very small number of females are partly immune), the species will likely go extinct.