Genetics

Euchronos

I am fascinated by circadian clocks that enable organisms to cope with daily environmental changes by adjusting biological processes. This certainly impacts health and quality of life in regulating sleep; particular interesting is entrainment, the synchronisation to the external day.

Here is a link to an EU project that I recently came across during a poster session – euclock. Another study funded by the “Gottlieb Daimler- und Karl Benz-Stiftung” can be found at the clock work site.

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Allergy, Vitamins

Higher metabolic rate or better signalling

In a forthcoming paper in Allergy (scienceblog:doi:10.1111/j.1398-9995.2007.01437.x:) we will show an association of vitamin D (25-OH-D3) serum levels and allergic rhinitis (AR) mainly in white Caucasians. Here is a supplemental figure that shows the seasonal variation in AR+ and AR- individuals.

Except of the singular peak in white children, I can´t see so much difference – so probably the vitamin D signalling pathway is different in AR.

Figure: Month of examination in allergic rhinitis patients of NHANES III by age age and ethnic background – no clear effects by higher metabolism.

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CC-BY-NC Science Surf accessed 29.11.2025
Software

Print book preview

It seems that the online book giant as well as the internet search giant have disabled the print function from their preview pages – maybe somebody can explain to me what is the difference between free viewing and prohibited printing?

Looking at the page code, it seems that there is no encryption at all but some low grade user camouflage as shown in the Web Developer Extension. Is this “encryption” just an alibi function?

If you are interested in a more in depth analysis of the new library of Alexandria that Google is planning, German Tagesspiegel “Google hupf!” discusses three interesting points:

  • human knowledge is monopolized – is democratized
  • author sucks – is the winner
  • culture needs recollection – needs to forget

 

CC-BY-NC Science Surf accessed 29.11.2025
Genetics, Joke

Falling asleep

A new study in Science now finds that facts and experiences were better recalled from memory when subjects were cued with a scent during the memorization process and again during slow wave sleep.

Re-exposure to the odor during slow-wave sleep (SWS) improved the retention of hippocampus-dependent declarative memories but not of hippocampus-independent procedural memories. Odor re-exposure was ineffective during rapid eye movement sleep or wakefulness or when the odor had been omitted during prior learning. Concurring with these findings, functional magnetic resonance imaging revealed significant hippocampal activation in response to odor re-exposure during SWS.

I wonder how this could be used for preparing presentations, situations where a persons typically fall asleep during or after the session ;-)

 

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Philosophy

It’ s a small world

Sometimes erroneously described as global village phenomenon the notion of a small world goes back to an experiment by Stanley Milgram (who became famous with the “obedience to authority” experiment – I did not know until last weeks that the punishing experiments had been repeated here in Munich where 85 percent of the subjects continued until to the end!).

The small world theory says that everyone in the world can be reached through a short chain of social acquaintances. The concept gave rise to the famous phrase of phrase six degrees of separation – I believe that a scientist may even reach another scientist in 4-5 steps.

My first PubNet example here is to reach F. Sanger by joint co-authors. This doesn’t work – my estimate would be 3 intermediary steps.

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My second PubNet example is to reach N. Morton (the foreword of his anniversary book says that a qualification of a genetic epidemiologist can be counted as “Newton”-points – the number of joint publications with Professor Morton).

smallw2.png

Addendum 8/7/08

Arxive.org has the largest study so far: 6,6 steps in 30 billion messenger conversations among 240 million people.

 

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Allergy

Climate change

There is no need for another diagnosis here. There is also no need about the impact of the automobile industry – I have published in 1993 the first large epidemiological study about traffic and respiratory health here in Munich.
What could we do? People need to move but need alternatives to public transport or 1000kg cars.

One such alternative is being the Swiss made twike Twike that I could get for a ride – excellent driving experience (quite fast too!) while needing only 0.5 l equivalent per 100 km. Although I am also attracted by recumbents and gyrocopters, this seems to be the best alternative ;-)

img001160.jpg.

 

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Software

An alternative to ISI’s impact empire

In my experience Google Scholar already shows more counts than ISI Web of Science. A new paper in first monday highlights another search engine that allows even truncation of search terms*: Exalead is a European (Paris) based search engine which does allow truncation and has a nice interface too.

exalead.png

Addendum

A new series of papers in the BMJ discusses some alarming consequences of “impact” measurements

The impact factor now has a worrying influence not just on publication of papers but on the science behind them too … One consequence has been to make universities prioritise laboratory based life sciences that produce research published in the highest impact factor journals, causing substantial damage to the clinical research base.

that goes beyond the previous view of Seglen.

 

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Genetics, Joke, Software

Face recognition, face value

With a new child, people are always asking if the baby looks like the father or the mother – probably a prehistoric social reflex to confirm that this is your offspring that you are caring about.
Face recognition clearly is a science of its own – a lot of heuristics and Bayesian computing – more at face-rec.org – and even a big business if you think of automatic passport control or age determination for goods that are only allowed for adults.
Face recognition works quite robust as I found in the advanced online demo at betaface.com. A new browser plugin from polar rose will even allows to annotate web pictures – Orwell meets Flickr.

img000843.jpg

 

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Philosophy

Search engines are about algorithms w/o structure, while databases are about structure w/o algorithms

NYT today has an interesting article about freebase (no, nothing about cocaine here) a forthcoming sematic web approach.

On the Web, there are few rules governing how information should be organized. But in the Metaweb database, to be named Freebase, information will be structured to make it possible for software programs to discern relationships and even meaning.
For example, an entry for California’s governor, Arnold Schwarzenegger, would be entered as a topic that would include a variety of attributes or “views” describing him as an actor, athlete and politician — listing them in a highly structured way in the database.
That would make it possible for programmers and Web developers to write programs allowing Internet users to pose queries that might produce a simple, useful answer rather than a long list of documents.

Valleywag – the famous tech gossip – also has something about semantic webs.

 

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Genetics, Software

Many, many maps

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Ever since I created a linkage map of the human genome with old-fashinoned crimap, we are talking about “mapping” diseases and genes. GIS mapping also ever increases – see the interesting first monday article Many, many maps: Empowerment and online participatory mapping, that has a lot of details about grassroots initiatives building on Keyhole/Google technology. I learned also about Common Census – looks like grassroot epidemiology.

 

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Genetics

Barker to the power of 2

It is certainly hard to understand how early life events are leading to later disease. Here is an incredible nutrigenomics story done in agouti mice:

We find that the somatic epigenetic state of Avy is affected by in utero methyl donor supplementation only when the allele is paternally contributed. Exposure to methyl donor supplementation during midgestation shifts Avy phenotypes not only in the mice exposed as fetuses, but in their offspring. This finding indicates that methyl donors can change the epigenetic state of the Avy allele in the germ line, and that the altered state is retained through the epigenetic resetting that takes place in gametogenesis and embryogenesis. Thus a mother’s diet may have an enduring influence on succeeding generations.

agouti.png

 

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Allergy, Vitamins

Lymphopoetin and allergy

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This is to convince me that the thymic stromal lymphopoietin (TSLP) is a master switch in allergy

15 Aug 2004

Skin-specific overexpression of TSLP resulted in an AD-like phenotype, with the development of eczematous lesions containing inflammatory dermal cellular infiltrates, a dramatic increase in Th2 CD4+ T cells expressing cutaneous homing receptors, and elevated serum levels of IgE.

5 Jun 2006

Topical application of the physiologically active ligand [1{alpha},25-(OH)2D3; calcitriol] of the vitamin D receptor, or of its low-calcemic analog MC903 (calcipotriol; Dovonex), induces TSLP expression in epidermal keratinocytes, which results in an atopic dermatitis-like syndrome.

22 Jan 2007

TSLP, synergistically with interleukin 1 and tumor necrosis factor, stimulates the production of high levels of Th2 cytokines by human mast cells (MCs) … TSLP is released by primary epithelial cells in response to certain microbial products, physical injury, or inflammatory cytokines.

23 Jan 2007

Proinflammatory TNFalpha or IL-1alpha and Th2 (IL-4 or IL-13) cytokines synergized to induce the production of TSLP in human skin explants … Our data provide the first evidence of TSLP induction and subsequent DC activation in human skin.

25 Feb 2007

Mice with an IEC[intestinal epithelial cell]-specific deletion of IKKbeta show a reduced expression of the epithelial-cell-restricted cytokine thymic stromal lymphopoietin in the intestine and, after infection with the gut-dwelling parasite Trichuris, fail to develop a pathogen-specific CD4+ T helper type 2 (TH2) response and are unable to eradicate infection. Further, these animals show exacerbated production of dendritic-cell-derived interleukin-12/23p40.

June 2007

… (TSLP) and interleukin-7 share a common receptor chain, IL-7Rα … The gene encoding the IL-7Rα chain is polymorphic, and investigation of inhalation allergic patients compared with controls showed significant association with two alleles at position +1237 and +2087.

Aug 2007

… TSLP represents a master switch of allergic inflammation at the epithelial cell and dendritic cell interface.

 

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