Current timelines for the book

Tuesday, January 27th, 2009 by hinrich

Draft cover for the book

After a lot of discussion the decision has been made: We will stick to our working title: "Gene Expression Studies Using Affymetrix Microarrays". By including the reference to the Affymetrix system in the title we are true about the content and our expertise. However, the book covers a lot of areas that are applicable to other gene expression microarray platforms as well. And looking at the data analysis part, a large number of pages provides the reader with background information that are also useful for other types of molecular profiling data.

The current time lines are: We will receive the copy edited pages around February 24th. The final manuscript is to be submitted by April 6th. The scheduled publication date is now June 1st, 2009.

We have just finished collecting all copyright permissions for figures that we have included in the manuscript. Also, a first draft of a potential cover has been designed by Kenneth Cools (as you can see on the left). However, the cover designers from Chapman and Hall are currently also working on a draft, so we can choose what we like best - or maybe merge elements from both.

Posted in Molecular Profiling

Home web server behind ADSL

Sunday, January 18th, 2009 by hinrich


As I had mentioned in an earlier post, my "web server" is a NSLU2 which uses two USB memory sticks (= no hard disks) and consumes very little power. The disadvantage of such a small server is that it is not very fast. I tried to make the web site as small as possible with respect to data transfers. The server essentially only serves text while all the images are hosted by ImageShack. That should enable "ok" response times from a low-traffic web site.

However, over the last couple of weeks traffic had increased and the response times went down. What could be done? I looked at my setup and realized that the server was not directly linked to my ADSL router, but upstairs connected via another rather old router. Therefore I moved my "slug" downstairs today and connected it directly to the ADSL router. And ... response times are much faster again! Hopefully this will be sufficient with my current ADSL speed.

Posted in Computer

Unprecedented activity of a once-weekly drug combination

Wednesday, January 07th, 2009 by hinrich

Article by Veziris et al.

Treating tuberculosis patients requires a monitoring of medicine intake to ensure that patients comply with the drug administration requirements. Given the long treatment against Mycobacterium tuberculosis (typically a once-daily for six months), it would be desirable to treat patients once-weekly.

Veziris et al. have now published an article where they describe an unprecedented activity of a once-weekly regimen in a mouse model: Eight once-per-week doses of a triple-drug combination of TMC207/R207910, rifapentine and pyrazinamide resulted in negative lung-cultures in 9 out of 10 mice (Combination therapy is administered to prevent the emergence of resistant bacteria). They also show that the bactericidal activity of TMC207/R207910 alone in the mouse model correlates with the total dose irrespective of the frequency of administration (TMC207/R207910 has a long half-life of approx. 7 days in humans and 2 days in mice).

While the disease shows some differences between the situation in human and in the mouse model, these findings are encouraging and could potentially indicate the possibility of a short-course treatment of tuberculosis.

You can read the paper here.

Posted in Tuberculosis

Learning a new instrument

Sunday, January 04th, 2009 by hinrich


In September of 2008 I started to play a new brass instrument (Harmonie TOG Engelen): Instead of playing trumpet (we had too many trumpets versus only two tenor-voiced brass instruments), I am now learning Euphonium. The name refers to a Greek word which means something like "good sounding". I would not dare describe my way of playing the instrument with such words, but that will hopefully get better soon...   :-)

Our year end concert ("Engelen bij kaarslicht" on 14 December) has now been the first time I have played Euphonium. While the concert could have been better (we had done the mistake of first playing outside in the cold), it was great fun. Let's hope that helping in getting a more balanced mix of instruments in our orchestra will benefit us in the long run!

Posted in Misc