Besides traditional and expensive epidemiological studies to compare disease prevalence over time, the net offers also some nice research tools – click on the thumbnail to see Google asthma trend results by today. The query counts are largely consistent with most recent scientific papers seeing the asthma epidemic now at a (high) plateau. Did the environmental risk now saturate all individuals at risk?
genetic-future has an excellent article why the recent genome scans failed (i) alleles with small effects? (ii) population differences? (iii) epistatic interactions? (iv) cnvs more relevant than snps? (v) epigenetic inheritance? (vi) disease heterogeneity? It is a thorough review better than everything Continue reading The many problems of GWAs
A study published earlier this year in the Lancet found a 18% reduction in mortality when women obtained supplements during pregnancy until 90 days post partum including additional 800 ug retinol, 200 IU vitamin D, 10 mg vitamin E, 70 mg ascorbic acid, 1.4 mg vitamin B1, 18 mg niacin, 1.9 mg vitamin B6, 2.6 ug vitamin B12, 15 mg zinc, 2 mg copper, 65 ug selenium and 150 ug iodine. Much of the effect will be due to the vitamin D supplementation Continue reading Vitamin D: A 18%! reduction in early infant mortality
A new abstract at the recent ATS congress now clears the 2007 controversy between the Camargo and Gale studies on the effect of vitamin D: Wheezing is not asthma (as the atopy component is missing?). Continue reading Not all that wheezes is asthma
For a clinical research project I need a fast webserver that understands both COLD FUSION (for the existing database stuff) and PHP (for dokuwiki). As this is a non-commercial project, I decided for the RAILO 2.0 community version that works right out of the box as it includes the Resin webserver and the H2 database as well. Following some recommendations found on the net, php is running now with with the fastcgi option showing good acceptable performance with eAccelerator.
php.cmd
|wj_php.cmd|
Just for curiosity I am collecting a list of allergy genes that are vitamin D dependent. The list is already rather long but now there is a prominent addition: CD14. Known as asthma gene for many years the vitamin D dependency isn’t such clear. A clever analysis, however, now shows that there is an intermediate step involved Continue reading CD 14 now also on the vitamin+allergy list
Despite the known allergy promoting effect of vitamin D in early childhood, there is mounting evidence that it may have beneficial effects during specific immunotherapy. A paper on “IL-10-inducing adjuvants enhance sublingual immunotherapy efficacy in a murine asthma model” by researchers from a French allergen company Continue reading Vitamin D as an adjuvans to specific immunotherapy
Just reveived an email from the creators of the Genetic Association Database (GAD)
… Your published genetic association study has been included in the recent update of the NIH based, Genetic Association Database (GAD), the database of human genetic association studies. Continue reading Genome Browser now with GADview track
Occasionally I see high R^2 values even between linkage disequilibrium blocks. The following plot was obtained from the German asthma family study; basically a haploview screenshot rescaled and inverted before using the Photoshop polar filter. Continue reading Trans-border LD?
Following the protestantic view of science here are some thoughts that I found in the new book by Benedetto XVI aka Joseph Ratzinger “Jesus von Nazareth”. Rationality as divine gift? Yes, Benedict follows the Historical Critical Method but wants to reconcile it with revelation that is not accessible to logical arguments. While it is not a book on science Continue reading A catholic view of science
Here is the announcement of an allergy meeting in London (where I will be too :-). Continue reading Allergy School
Over the years I have collected a lot of curious hypotheses how allergy develops. Only recently I ended this list as it became rather long – and to be polite – rather useless. Sorry, less polite – but nonsense at its best Continue reading Rough and tumble science
During my recent trip to London, I could get a brief glimpse into the 1932 book “Vitamin D” by Reed, Struck and Steck. As this volume is not available in a German library and as it was not allowed by the British library to travel, I took now the lengthy procedures of registering, waiting in the queue, before searching this book for any allergy related items.
It seemed to be worthwile, although with some unexpected results: Continue reading More retro vitamin D
Tip 1: Avoid loops.
They are generally slow – use a function instead. Even with the need of variable and fixed columns in a loop, a function may be constructed like
apply(data,2,function(col2){table(col1,col2)
Tip 2: Always show current state.
Include options(warn=1) and show current state with cat(“message\n”);flush.console();
Tip 3: Avoid merging steps.
Use instead datasets in same order and with the same subset of the larger table before updating anew column with data from the second table.
Laborjournal 4/2008 reports a new software tool for DNA addicted people: the Personal Genome Explorer which is based on SNP annotation by SNPedia. So, what I tried to institutionalize on a sound level as “Genome Explained” possibly within the framework of HGVS is now being done by a street initiative fueled by early adopters like Cross, Arlington, Halamka and Smolenyak. It looks very much like an unholy alliance of profit interests and technical curiosity than good science and responsible counseling, yea, yea.
Addendum: If you believe in support vector machines, you can even let your laptop screen the medical literature for genetic associations with GAPscreener. <irony> No more lengthy training in genetics, statistics, epidemiology and bioinformatics, no more years of collecting all relevant papers & abstracts, just let your laptop score your DNA variants </irony>