“Wer einmal aus dem Blechnapf frißt” (Fallada) – following my linux box post yesterday here is my lunch box for today. I think it is as good as the Japanese BentÅ box, isn´t it?
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My linux box
When starting again analysis of pooled DNA samples – this time on the Affymetrix platform – I discovered not only the much improved “Genotyping Console” but also that my earlier Genepool binaries do not work anymore under VMWARE/Ubuntu. I therefore tried Continue reading My linux box
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New DNA sequencing technologies
New DNA sequencing technologies & human genome variation, San Diego, HGVS Meeting (ASHG satellite). From the program
On the road to the € 1,000 human genome sequence, DNA sequencing technology is currently developing at an incredible speed. Although we are still far from the ultimate goal, DNA sequencing cost has already dropped close to the range of € 1,000 per 1 million nucleotides. These developments have tremendous consequences for the number of DNA variants that we will discover, both pathogenic and harmless. To get an up-to-date overview of the technologies behind this revolution, the HGVS has selected DNA sequencing technologies as this year’s special topic for its annual meeting. Speakers from the major players in the field have been invited to explain in detail the different technologies, their strong and weak points and to show some first innovative applications and results using the new sequencing power.
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I do not wish to donate organs after death
True or not, there are reports about sale of human organs from prisoners in China (link1, link2) and India (link3). I do not want to be involved in a business where life is being prolonged until multi organ explanation and death being defined by ever changing arbitrary criteria.
I have also a deeply rooted belief about the integrity of the human body – there is natural barrier against organ transplantation both from an immunological and psychological side (cannibalism is a taboo in every human culture). So, I would like to ask doctors in the emergency room to work hard to save my life (as I did also for many years rescuing other lifes).
In case, you want to read more on that topic, please go to an excellent essay in the TAZ. Many other physicians will share my belief, that donation of organs should remain an individual decision.
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News about vitamin D’ficiency
“Normal vitamin D status despite of abundant sun exposure” would have been my title for a study in the JCEM this month. The authors, however, have choosen a different title: Continue reading News about vitamin D’ficiency
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QQ plot
Do you wonder what QQ means? These are quantile – quantile plots that rank observed test statistics against expected test statistics. They allow a visual inspection of overdispersion due to population substructure or other sources of biases.
QQ plots have been recommended earlier, are now frequently used and available in the snpMatrix R package. Yea, yea.
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Protected: ORMDL3 – what?
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Can we meet on next Tuesday at 2 pm?
Answering this question always takes me 30 seconds – looking for my mobile and doing some pen strokes OR starting Outlook on the laptop and clicking to the desired week (BTW Sunbird is still in version 0.5). Finally I found a solution that gives me a chance for a response within 3 seconds. Continue reading Can we meet on next Tuesday at 2 pm?
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Allergy – everything from fullerenes to cannabis
Allergy research continues to be one of the most active research fields. New studies show that that fullerenes may inhibit the allergic response
Human MC and peripheral blood basophils exhibited a significant inhibition of IgE dependent mediator release when preincubated with C60 fullerenes.
Continue reading Allergy – everything from fullerenes to cannabis
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Wer heilt hat recht
This is a German quote – frequently used in the context of alternative medicine – “who heals is right”.
The history of the qutotation is unclear; maybe it is a modification of the Latin “extra ecclesiam salus non est” .
In todays English “the doctor’s always right” (or “might is right”?)
Anyway it is utter nonsense as (1) a healer wants to be successful and not rightful (2) healing (at least on a few occasions) is no proof for the right treatment only fo the good outcome.
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Reset temporary system date
To evaluate software that is depends on an expired system date, you may want to use this batch that wraps around calling a program.
rundate.cmd.
|wj_rundate.cmd|
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When controls are no controls
So far in epidemiology case – control studies are defined by an approach where
… the past histories of patients (the cases) suffering from the condition of interest are compared to the past histories of persons (the controls) who do not have the condition of interest, but who otherwise resemble the cases in such particulars as age and sex ….
I usually explain controls as non-cases in the same overall environment Continue reading When controls are no controls
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Believe me, it ‘s not hygiene
I have written earlier about the hygiene hypothesis and my doubts that more or less “hygiene” influences the development of allergy (blog | paper). As we are further swamped with regular statements like Continue reading Believe me, it ‘s not hygiene
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Click chains
That seems a usual phenomenon now: I am reading an interesting article (at Edge), want to know more about an author (Fitch) and end at a storming website at University of Tübingen (recording new German words). German linguistics seem to merge day after day with English linguistics.
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1% decoded
Nature web focus today reports an overview of the four year project Encode (ENCyclopedia Of DNA Elements) that tried to identify all functional elements in 1% of the human genome. In addition, there are 28 companion papers in the June 2007 issue of Genome Research. The Nature issue includes a pull-out poster featuring a screenshot of the UCSC Genome Browser.
I am still in the process of reading all the GWA studies, so don´t expect any intelligent remarks. The main point seems to be that the majority of the human genome is being transcribed which is in sharp contrast to the textbooks (Strachan/Read IInd ed, p142 says that only ~3% of the nuclear genome is being transcribed). Using gene centric SNP panels in some of the GWAs therefore have not been such a good idea, yea, yea.
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