Category: Lab life

March 24th was world TB day

TB stands for tuberculosis. It’s an infectious bacterial disease caused by Mycobacterium tuberculosis, which most commonly affects the lungs. It is transmitted from person to person via droplets from the throat and lungs of people with the active respiratory disease.

Like all other World Days regarding infectious diseases, it is meant to raise awareness about its global epidemiological aspects and the efforts to eliminate it. For tuberculosis, March 24th was chosen because Robert Koch first described Mycobacterium tuberculosis on March 24th, 1882. He then received the Nobel Prize in Physiology or Medicine for this in 1905.

On the WHO website, there is a huge amount of data that can be easily parsed (here too).

I was first interested in the estimated TB incidence per 100 000 population in 2009 (per 100,000 population) in the BRIC countries (see table below). Clearly, there is Brazil with a low incidence (compared to others, it’s still around 10 times values found for “occidental” countries) then Russia and China around 100 cases/y and finally 168 cases/y for India. I added their respective Gross Domestic Product (GDP) in the table as it’s often considered as an indicator of a country’s standard of living (in 2009, numbers from Wikipedia/IMF). I also added the annual growth rate of GDP per capita (in 2006, numbers from EarthTrends/World Resources Institute). The only interesting thing I see is that if your annual growth of GDP per capita is low, your estimated TB incidence per 10,000 is also low.

Country Est. incidence GDP per capita Annual growth rate …
Brazil 45 11,289 2.4
China 96 7,518 10.1
India 168 3,290 7.7
Russian Federation 106 15,807 7.2

Now if we look at some occidental countries (table below, same sources), this seems right.

Country Est. incidence GDP per capita Annual growth rate …
Belgium 8.6 36,274 2.6
France 6.1 34,092 1.4
Germany 4.9 35,930 2.9
Japan 21 33,828 2.2
UK 12 35,053 2.2
USA 4.1 47,123 1.9

The treatment involves medications for long period and is usually accompanied by antibiotics. Regarding prevention, Bacille Calmette Guerin (BCG) is the only current vaccine for tuberculosis and contains a live attenuated (weakened) strain of Mycobacterium bovis. TB eradication is part of the UN Millenium Development Goals (Target 6c: Have halted by 2015 and begun to reverse the incidence of malaria and other major diseases). It is also part of the WHO Global Plan to Stop Tuberculosis.

Recently (because of this World TB Day?), two interesting research papers were recently published in the litterature:

Today is *not* World Epilepsy Day

I continue in the serie of “World x Day” and for a reason still unknown even to myself, I thought today was the World Epilepsy Day (it’s in fact on March 26th, called Purple Day). But, anyway, epilepsy is “a common chronic neurological disorder characterized by seizures. […] Epilepsy is usually controlled, but cannot be cured with medication, although surgery may be considered in difficult cases.” (Wikipedia).

Out of curiosity, I was looking for mathematical models for the description of the epidemiology of epilepsy. But unfortunately, I couldn’t find anything. Probably because epilepsy is not an infectious disease for which tentative mathematical models have more predictive power (in terms of the population scale and time scale). The epidemiology of noninfectious diseases is primarily a study of risk factors associated with the chance of developing the disease. Nothing very fancy for a mathemarical model! 😉 (But if you find something, feel free to share! Thanks in advance!)

According to Wikipedia, the next World [Infectious Disease] Day is on APril 25th (malaria).

So today is just Valentine’s Day 🙂

World Cancer Day

It doesn’t seem jolly but last Friday, it was the World Cancer Day. About this, the WHO set up a nice website about cancer control.

Following my previous post on Jamie Oliver and the top 15 causes of death in the USA, I started to collect similar data from other countries. Linking this to cancers, the annual statistics on cancers in Belgium can be found on the Belgian Cancer Registry. The latest numbers are however from 2006. Here are the top 15 cancers in Belgium in 2006 (all sexes and regions mixed):

Rank Classification Cancer type Cases Remark
1. C50 Breast 9556  
2. C61 Prostate 9254 male only
3. C34 Bronchus and lung 6956  
4. C18 Colon 5233  
5. C44 Malignant neoplasms of skin 3110  
6. C20 Rectum 2264  
7. C67 Bladder 1986  
8. C82-85 Non-Hodgkin-lymphom 1925  
9. C43 Malignant melanoma of skin 1572  
10. C64 Kidney 1377  
11. C16 Stomach 1356  
12. C54 Corpus uteri 1320 female only
13. C25 Pancreas 1172  
14. C80 Unknown primary site 1168  
15. C15 Oesophagus 920  

It’s interesting to note a few things:

  • These figures represent cases of cancer and not deaths by cancer. Note also that prostate cancer is in third position but only concerns males.
  • The latests data is from 2006. The website doesn’t seem to be updated since 2008 (and 2008 seems to be the year when data from 2006 are available ; if we follow the 2-years-gap logic, I guess the data from 2009 are available somewhere but not on this website)
  • Data accessibility seems to be average. Data is there in Excel format (and PDF which is pretty useless if you want to reuse the data). On one side, these Excel files can be opened by almost every office suite. On the other side, some open format would have been preferred. And some direct interaction with the data on the website is now the norm (ok, I just wrote it doesn’t seem to be updated since 2008)
  • The classification is quite good since it uses the “Classification Internationale des Maladies” which is the “International Classification of Diseases” in English better known as ICD-10 (online).

A good issue of Nature, obviously!

The October 14th, 2010 issue of Nature is obviously a good one. It had to be a good one! I usually advocate Open Access but it is always nice to reading complimentary issues of Nature which is Closed Access but is also publishing very good articles about science at the same time.

In this issue, I was interested in various topics …

First, there is a serie of articles about the US midterm elections and what (US) scientists feel about two years of Obama administration. Obama promised total transparency in American science, a new era of integrity and more freedom for scientists. From what I read, this isn’t the case yet.

Then, there are two article about publishing computer code from scientific experiment. In a World View, Nick Barnes, director of the Climate Code Foundation takes some concerns about that to pieces. The main reasons to provide computer code is to improve programming skills (the software author’s and others’) and enable others to engage with your research. Don’t be ashamed of the quality of your code. Don’t be afraid of starting the trend if no one around you share their software. Don’t be afraid to refuse support when badly asked for. Don’t overestimate the intellectual property value of your code. Nick Barnes also wrote a blog post about it. And you can comment on the Nature article here.

In a News Feature, Zeeya Merali tells stories of scientists who found themselves in uneasy positions regarding to the software they wrote but, at the same time or later on, realised publishing their software was the best thing to do. Besides formalising one’s training in programming, Zeeya Merali advocates some simple steps to practise “safe software”: use a version-control system ; track sources, data and events ; write testable software ; test the software and encourage sharing of software.

I was also interested in these articles in two ways. First, I also realised the need of a formal training in programming during my Ph.D. and I eventually got a B.Sc. in computer science. In the team and field where I’m now working (Health Economics and modelling of infectious disease), I can clearly see the benefit of having such training. Don’t get me wrong: I meet wonderful colleagues every day who don’t have the training but have lots of skills and can solve lots of problems ; I just often see the ease to grasp algorithms as well as some better procedures and testing that comes with training. And, second, I would like to addd that free software licences are to be considered when publishing your software (for science or not).

In the same issue, there was also a small news about the Europe’s use of research animal. This reminded me of the good-old-days :-). Fundamental biology still account the largest proportion of animal experiments but what intrigued me is the 12.2% of “Other” usage.

There was also a comment on a book, The Professional Guinea Pig, about paid participants in phase I clinical trials. Interesting perspective from “the other side” of trials.

There is also an Outlook on the Lindau Nobel Laureate Meeting. It features interviews with 10 Nobel laureates (it’s always nice to readd their comments on science) and an article about science in the digital age (not yet read but it seems interesting).

Finally, an ad for my previous lab (GIGA ULg) caught my attention, as well as the small article about Science in Belgium. I must however write that this article is a bad summary of the research landscape in Belgium with, for example, mention of only two universities: the KUL and the UCL (we have many more). Souvenirs, souvenirs.

"Facts & data"

A colleague of mine is always hammering home the message of bringing facts and data to a discussion rather than rumors, hearsays and daily newspaper articles. Since a few days (because H1N1 is not a pandemic anymore?), newspapers are coming with another “Superbug” or “Germinator“, wrongly named “NDM-1“. So, before spreading fear, uncertainty and doubt, please read the scientific litterature or, at least, read quality newspapers (articles from The Guardian are quite fair and balanced).

NDM-1 (New Delhi metallo-beta-lactamase) is just the name of a gene in a plasmid that two bacteria at least, K. pneumoniae and E. coli, can carry. This gene makes bacteria resistant to almost all antibiotics. If you want to know more about this gene, Yong’s paper characterised it (access without subscription). Health care agencies know about this issue at least since last year.

Now, you can still go to India and Pakistan. New Delhi is still a safe city to visit. But yes, in general, the world will face a problem in the future because bacteria are becoming resistant to more and more antibiotics.

FluTE makefile for wxDev-C++ (Windows)

FluTE is an influenza epidemic simulation model written by Dennis L. Chao at CSQUID. It works out-of-the box on GNU/Linux (just type make and run it).

I wanted to see how it works. But since I’m temporarily stuck with a Windows laptop, I downloaded a free C++ compiler for Windows (wxDev-C++), imported all the files in a project and compiled. For those who want to try, here is the project file and the specific makefile in a zip file (2 kb). Just decompress the FluTE archive (I used version 1.15), copy the two files from the zip file above and launch the IDE. In the project options (Alt+P), specify the custom makefile (in the "Makefile" tab) as the one from the zip file above. Compile (Ctrl+F9). Done.

On my Intel Core2 Duo T5450 (2Gb RAM), it took 6 minutes to simulate the "two-dose" example.

Please note that I didn’t try to compile with OpenMPI. Maybe for next time.

Ph.D. thesis

As I promised before, you’ll find here the text and slides of my Ph.D. thesis (btw text and slides are in French). The oral presentation was on March 24th, 2010 and everything was fine 🙂 Slides can be watched below.

Effets du sommeil et de la privation de sommeil sur le protéome hippocampique de rat après apprentissage topographiquehttp://static.slidesharecdn.com/swf/ssplayer2.swf?doc=3557617&stripped_title=effets-du-sommeil-et-de-la-privation-de-sommeil-sur-le-protome-hippocampique-de-rat-aprs-apprentissage-topographique-3557617

Redesigned Pubmed

I often wrote about Pubmed here. Briefly, it’s a search engine for publications in the biomedical domain. They recently redesigned their user interface and, although there are a lot of new things to save time that came with the new design, there is still a problem with their interface: the new search box takes too much space …

Redesigned Pubmed homepage
Redesigned Pubmed homepage (bigger image)

Redesigned Pubmed result page
Redesigned Pubmed result page: search box is hiding the logo, the display settings and the first result (bigger image)

To be fair, I must say these screenshots were taken with Firefox 3.5.3 on Fedora Linux but I didn’t see this problem with other operating systems nor other browser (not even Firefox on MS-Windows). Seems they tested their design with everything except Linux 😦 (A search with Pubmed redesigned doesn’t work with text-only browsers although the previous one perfectly worked)