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>
It was difficult to find but I knew it should be there: a letter of Herrmann von Helmholtz about his private attempt to cure hay fever. Published in the increasingly important Nature magazine on May 14, 1874 von Helmholtz describes the vibrio like bodies in his own nasal fluid and the successful local treatment with quinine.
Unfortunately there is a consecutive letter that did not confirm this effect. I also do not know how this treatment would have worked. Fiction, placebo or true antiparasitic side-effect? We even know of quinine induced allergy, making even reverse causation possible.
G. Kanny, J. Flabbée, M. Morisset M, D. Moneret Vautrin. Allergy to quinine and tonic water. Eur J Intern Med 14 (2003), p. 395-396.
R. Cundall, Idiosyncrasy to quinine in bitter lemon. Br Med J 20 (1964), p. 1638.
Do you still have some doubts on a recent experiment in mice that were sensitized under vitamin D co-exposure?
Here is another nice paper from Nature, Jan, 21, 1967 where rabbits are fed allergen & vitamin in a germ-free environment Continue reading Vitamin, germs and allergy – 41 years ago
A new paper – the second bioinfomatics approach following the groundbreaking work by Perez-Iratxeta – is now coming up with some interesting remarks beyond IL-13 and TGF-ß1 Continue reading Where is the asthma gene?
It turned out to be a tricky job to move from pixel maps to a Garmin vector map; I first thought that is impossible but here is a way to do that:
1. Find the area of interest with Geocoder
2. Get digital elevation data from de Ferranti
3. Import them in 3DEM, export as GEO-TIFF, import in DEM2TOPO and export in Polish map format.
4. Finalize with Mapedit. Mapedit will read Polish format, import your already available GPS tracks or positions saved in Oziexplorer. The best Mapedit feature is certainly the Google Earth overlay. Nevertheless map editing remains a time consuming enterprise but may be the only way if there is no other map available. I wish there would be more of these maps like for Iceland or Garda Lessinia.
As always, a longer literature search prevents from new discoveries… Here comes a nice piece from 1952 on the antagonistic effect of LPS on vitamin D (Is that really LPS or did I interpret it wrong?). Although not included in my recent review on vitamin D and allergy – I attributed the effect to Lyakh et al. – here is the first description of this effect. Continue reading A factor in hay prevents vitamin D action
Although there are numerous reports and even whole schools of thought building on a prenatal origin of allergy, a new study now clearly states that sensitization does not develop in utero. IgE traditionally measured in cord blood IgE is a contamination of maternal IgE. The authors show that there is a correlation with IgA and the “spurious specific IgE” at birth “vanishes” during the following 6 months. If you ever had a cord in hand, you will understand how easily contamination occurs.
The “prenatal origin” party doesn’t give up basically with the arguments:
The authors explain the maternal/fetal association “by maternal inheritance of atopic IgE responsiveness on chromosome 11q and other gene loci” BUT unfortunately there is neither atopic IgE responsiveness on chromosome 11q nor is there any evidence of imprinting. So – according to our best evidence allergy starts only after birth. To convince me it would not need 922 neonates but 1 B cell of proven fetal origin that makes IgE – making the whole story at least a good example how insufficient methods produce doubtful conclusions, yea, yea.
As filaggrin – one of our best atopy genes – is vitamin D dependent, I tried to find out more about epidermal differentiation. The plot here summarizes an earlier review:
There seems to be a clear calcium gradient with the expression of differentiation specific marker in the single strata. So there is some good chance that filaggrin effects may be modified by external vitamin D supply.