I find it handy to have a quick link in appointments to the recent correspondence. Unfortunately there is no easy way to do that. Continue reading Mac OSX: Create a symbolic link to Thunderbird Emails in an Ical Appointment
A new feature article in Nature about sparse coding let me wonder if we could construct also some Waddington-like picture of the SNPxSNP landscape as well as a disease traits and apply such an algorithm to that picture. I did some research but didn’t find any example exploiting that idea; maybe it’s even more useful with the current shift to full genomes?
Hopefully the auto-loader at the bottom will pick some previous posts here about calcium, vitamin D and allergy; these may be necessary for the background of a new study published in the American Journal of Respiratory and Critical Care Medicine last week
We looked for Cav1 channel expression in Th2 and Th1-cells by real-time PCR and Western blotting. We sequenced the isoforms expressed by Th2-cells and tested whether Cav1 antisense oligodeoxynucleotides (Cav1AS) affected Ca2+ signaling and cytokine production […] mouse Th2 but not Th1-cells expressed Cav1.2 and Cav1.3 channels. Th2-cells transfected with Cav1AS had impaired Ca2+ signaling and cytokine production, and lost their ability to induce airway inflammation upon adoptive transfer.
This highlights again the close connection of the calcium system to immunology. While the earlier TRPM4 story was basically about mast cells, we now arrived at Th2 cells, yea, yea.
It took some time. Science has a paper on Calcium-sensing receptor antagonists abrogate airway hyperresponsiveness and inflammation in allergic asthma” by Yarova et al. writing about antagonists of the calcium-sensing receptor
We show that polycations and elevated extracellular calcium activate the human recombinant and native calcium-sensing receptor (CaSR), leading to intracellular calcium mobilization … These effects can be prevented by CaSR antagonists, termed calcilytics. Moreover, asthmatic patients and allergen- sensitized mice expressed more CaSR in ASMs than did their healthy counterparts … Thus, calcilytics may represent effective asthma therapeutics.
I don’t know, if the last statement is really warranted but – as written 5 years ago – there is a super tight connection of calcium and vitamin D to allergy.
and if I have a faith that can move mountains, but have not love, I am nothing. 1 Corinthians 13:2
Yesterday’s farewell sermon of Joachim Funk in Gröbenzell reminded me to the chapter that I once learned by heart (in Greek) and let me today go for some pictures of Kapuzinergasse in Munich, where the walls of St. Anton hold this inscription in big letters (Schmerzhafte Kapelle und Kapuzinerkloste, St. Anton).
Wikipedia describes the last year’ financial crisis as “an economic bubble (sometimes referred to as a speculative bubble, a market bubble, a price bubble, a financial bubble, or a speculative mania) as a “trade in high volumes at prices that are considerably at variance with intrinsic values”. A new and excellent Embo Report (thanks to WK) arrives at the same description of current science, a
dangerous cocktail of short-term gains prevailing over long-term interests, herding, increasing pressure to deliver results, the absence of effective oversight, and blind trust that the system would regulate itself Continue reading The science market bubble
… quoting Nature Medicine this week
All of this is well and good, but it will hardly be news to those who have pondered these issues. At the Nature journals, for example, data sharing has long been a requirement for publication, and we have gone as far as directly urging authors to fulfill their commitment to sharing when other researchers have requested our involvement.
Ok, I would like to get this full dataset …
From Slashdot today:
Scientific discovery is fraught with false starts and blind alleys. As a result, labs accumulate vast amounts of valuable knowledge on what not to do, and what does not work. Trouble is, this knowledge is not shared using the usual method of scientific communication: the peer-reviewed article. It remains within the lab, or at the most shared informally among close colleagues. As it stands, the scientific culture discourages sharing negative results. Continue reading Blind alleys
From a recent email that I received
In theory, science research laboratories are always peaceful places, where pure knowledge is being pursued. However, in recent years some tragic episodes of workplace violence have disturbed this tranquility. Continue reading Lab violence
We had Aulchenko here a year a go or so – now here comes his new paper Predicting human height by Victorian and genomic methods
In a population-based study of 5748 people, we find that a 54-loci genomic profile explained 4–6% of the sex- and age-adjusted height variance, and had limited ability to discriminate tall/short people, as characterized by the area under the receiver-operating characteristic curve (AUC). In a family-based study of 550 people, with both parents having height measurements, we find that the Galtonian mid-parental prediction method explained 40% of the sex- and age-adjusted height variance.
yea, yea.
What do all these places share? Spitalfriedhof Basel, Roopkund Lake, Catacombes de Paris and Central Yakuts are all examples where remains are available for genetic studies (even Tutankhamun was undergoing a paternity test recently).
More relevant will certainly be an empirical investigation if reduced selection is leading now to immune disease.
Finally, a really important paper (at least for me ;-)
Here we show that habitually barefoot endurance runners often land on the fore-foot (fore-foot strike) before bringing down the heel, but they sometimes land with a flat foot (mid-foot strike) or, less often, on the heel (rear-foot strike).
The forefoot has lower collision forces! while the forces are excessive according to an earlier study. These new studies support the recent development of a running shoes (currently under development in Magdeburg) with no heel Continue reading Collison forces during distance running
Here is another tech tip to overcome a frequent task – resetting printers and mailers when moving a Macbook around the world: Location X is a perfect solution with a built in autolocate function (depending on airport network! which is superior to IP detection)
Unfortunately Continue reading Change location
Being tired from entering several books into an Endnote library, I found a better way – just enter “GKV” as the remote library where you can select ISBN search…
While some of my earlier co-workers continue to praise the achievements of GWAs, some other earlier co-authors now show that the common variants thrown on the current GWA chips are leading to false associations (politely called “synthetic” associations)
We propose as an alternative explanation that variants much less common than the associated one may create “synthetic associations†by occurring, stochastically, more often in association with one of the alleles at the common site versus the other allele. Although synthetic associations are an obvious theoretical possibility, they have never been systematically explored as a possible explanation for GWAS findings. Here, we use simple computer simulations to show the conditions under which such synthetic associations will arise and how they may be recognized. We show that they are not only possible, but inevitable…
The proof comes with a sickle cell anemia study Continue reading True, false, true, false, true, false, false
What happens when looking at that video?
The neuroanatomy view this week in Nature
we predict[…] a macroscopic signal visible to functional magnetic resonance imaging (fMRI) in humans. We then looked for this signal as participants explored a virtual reality environment, mimicking the rats’ foraging task: fMRI activation and adaptation showing a speed-modulated six-fold rotational symmetry in running direction. The signal was found in a network of entorhinal/subicular, posterior and medial parietal, lateral temporal and medial prefrontal areas. Continue reading Tear Down the Walls