Hidden feature at PUBMED

No, it is not really a hidden feature – but keep your mouse on “links” at the right part of the citation, wait for the drop-down, select “Link-out” and there is a good chance to jump directly to the publisher site, yea, yea.

Addendum

The nodalpoint blog” writes about MEDIE, a new PUBMED parser:

…is an “intelligent” semantic search engine that retrieves biomedical correlations from over 14 million articles in MEDLINE. You can find abstracts and sentences in MEDLINE by specifying the semantics of correlations; for example, What activates tumour suppressor protein p53? So just how useful is MEDIE and is it at the cutting edge?


CC-BY-NC

Who goes first?

A recent example of self-experimentation is the famous trial where Dr. Barry Marshall swallowed a tube full with Helicobacter pylori which led him to develop gastritis. Lawrence K. Altman, M.D. has written the story of self-experimentation in medicine covering the many facets of these heroic experiments. Published already in 1987, I discovered this book only now. Highly recommended, yea, yea.


CC-BY-NC

For some, the system is working well

Just received an email – the fall 2006 desk-to-desk message from Dr. Zerhouni, “Making it Work for our Emerging Scientists”
http://www.nih.gov/about/director/newsletter/Fall2006.htm. It says “For some, the system is working well. The best and brightest are reaching their full potential in solid, research careers. We have the evidence in the number of competitive grant applications being submitted. For others, the queue is backing up… Between 1980 and 2004 the average age of Ph.D. scientists earning their first R01 award went from 37 to 42 years… The problem appears to be largely the result of the ever-increasing age at which a researcher receives his or her appointment as an assistant professor.”
I would like to add that the average life expectancy also increased between 1980 and 2004, so the relative age remains the same. Yea, yea.

Addendum

Science magazine has different data on salaries of postdocs: academic salaries rose from $74,000 to $78,000 and industry salaries of $106,000 to $116,000 between 2005 and 2006.

Addendum

German salaries in biotech lab, research and marketing increased at the same time by 3.7% to €99,000 (for leading positions) and 3.3% to €74.000 (for specialists) according Laborwelt 1/2006 page 45.


CC-BY-NC

Is “vitamin” D a biological hub?

Folllowing up numerous emails to my recent review about allergy and vitamin D exposure, I wonder if there could be a quantitative relationship if we look at the vitamin D system as a major biological hub. This is not so much about connecting different playgrounds but of integrating signals (as shown in the hourglass blog). The East-West German difference, the farming studies as well as numerous other studies would even allow a quantitative effect. Yea, yea.

Addendum

Biospektrum will publish in their next issue a summary of the vitamin D story.

Addendum

4-07-2007 The list of vitamin D dependent genes that are associated with allergy (IL12B, IL12RB, SPP/OPN, CD14, CD23, VDR, TNF, GC, IFN, IL1RN, IL8, ADRB2, CARD15, IL4R, ALOX5, FLG, SOCS3) is expanding: TSLP and CD86


CC-BY-NC

Truth in science (and religion)

A recent interview of Jane Glitschier in PLoS genetics with Tom Cech nicely shows the relationship of truth and research: “There is a search for absolute truth in research. You never get there—but there are criteria by which you judge how close you are. You’re always criticizing yourself and criticizing your colleagues, and they’re criticizing you. And there is a test, very often, that you can do to decide who’s right.”

Addendum

Here is a difference between science and religion — Jesus told his disciples, “I am the way and the truth and the life” (John 14:6). Yea, yea.


CC-BY-NC

Living near highways

A new study now shows directly that personal exposure of particles is linked to asthma symptoms. Children carried pollution monitors in their backpacks on the way to school where PM2.5 ranged from 20 to 50 micrograms per cubic meter. Although only around 10 percent of the total mass of particles was diesel soot, it was this that was most closely linked to the children’s asthma. This nicely complements results of our study in Munich in 1989/1990 which was the first survey indirectly linking car exhaust and airway symptoms in children. Mechanisms how this happens are not very well known – for a discussion of the biphasic response see our paper of a mouse model, yea, yea.


CC-BY-NC

On display – the masterclass

During my professional career I have never been told how to make good graphics although extracting essential information from datasets is an advanced (and necessary skill). Fortunately, however, there are some excellent books that cover graphical display. The first one I came across was Michael J Campbell and David Machins’ “Medical Statistics – A commonsense approach” (see pages 44ff and 58 for “increasing data ink”) that gives a lot of useful advices how to improve figures. The next book that I found influential was Bill Cleveland’s 1993 book “Visualizing Data” who introduced into R and S multidimensional lattice graphics (also covered 2005 in “R Graphics” of Paul Murrell published by Chapman & Hall/CRC). I used this technique extensively in my 2005 PLoS paper on the worldwide distribution of allergy. At the moment I am reading the new book “Graphics of large datasets” by Antony Unwin, Martin Theus, Heike Hofmann which seems to be finally the masterclass of displaying data. Yea, yea.

Addendum 1

An examples how to improve a barchart (yes – I resisted to start with a 3D barchart but the cluttering colors and grids are hopefully good to see).

demo.gif

Addendum 2

A new Nature Nascent entry: “The way we present genomic and proteomic data on the web sucks


CC-BY-NC

Foucault pendulum

I visited the Deutsche Museum yesterday, where one of best attractions is the Foucault pendulum a 30 kg weight at a 60 m rope (the original at the Panthéon was 67 meter long and weights 28 kg). We could see, that the pendulum swings on a an elliptic course, hitting the conses always from the back. As we were told, the deviation of the pendulum is a function of latitude. The horizontal axis is the latitude from 90 degrees to 0 degrees latitude. The vertical axis shows the rate of precession in degrees per hour; positive for clockwise precession, negative for counterclockwise precession (the Coriolis effect seems to have a minor role). I wondered what might be the reason for the spin or chirality seen so often in nature. Most DNA has a right-hand screw (nevertheless there are hundreds of images on the net and many scientific papers) that show left-handed DNAs). Yea, yea.


CC-BY-NC

Ethnographic studies at Oktoberfest

Having many years of experience with ethnographic studies at Oktoberfest München, I am fascinated by a new Cell paper that shows distinct behavioral responses to ethanol. This is something that I alread assumed (although I did not known about this particular RhoGAP18B isoform only about ADH deficiency). Will the knowledge of more and more mutations in the lifestyle area raise ethical problems? Yea, yea.


CC-BY-NC

False Memory

The German magazine Spiegel has a nice paper about the false memory debate and the “implanted” memory of events that never happened. They cite Hans Markowitsch from Bielefeld that the autobiographical memory is not very good in recalling past events, being much much more adapted to orientation of current and future events. Has anyone examined blogs and if their content can be recalled by the author? Nai, nai.


CC-BY-NC

Once again genetic testing

I have argued earlier that the free decision of an individual to allow genetic testing, will also reveal data on genetic relatives that have never consented to that procedure.
A new review by Bruce Weir now confirms that “it is reasonably straightforward to find the probability of the genotypes of individuals when their relationship is known…” My current work lets me also assume that with 500,000 SNP data at hand, much individual characteristics of the donor can be reconstructed – there are no anonymous DNAs datasets as some people still believe.
I even fear that genetic testing will increase for example in “homeless” (in vitro fertilized) individuals as these people will want to prevent sibling marriage – see for example the a-China DNA project. Other people may be curious about their genealogy, others about drug side effect prediction, lifestyle, assurance questions…
With every new dataset, available datasets will gradually decrease their anonymity level. I fear that anonymity is not so much a dichotomous property, it is much more a likelihood ratio to stay unknown under the probability to be known. Yea, yea.

Addendum

Time online of Dec 17, 2006 reports that the British police is holding the DNA records of more than 1m innocent people — eight times more than ministers have previously admitted. I wonder if this will affect participation rate of the UK Biobank that targets health of lifestyle, environment and genes in 500,000 people.


CC-BY-NC

Sleep well

Just came to my attention that there is research of sleep related genes, the usual stuff of protein kinases, dopaminergic receptor, and serotonine transporter. Also this research community seem to have the common difficulty of the complex disease gene mappers – to understand a phenomenon (not a trait) as systemic function, an intrinsic property of a multicellular and multiwired brain, yea, yea.

Addendum

More strange phenotypes orgasm frequency, pain, human memory performance.

Addendum

Read also the what-we-could-have-learned-from-linkage-studies.


CC-BY-NC

Heritable mutation or not?

moblog – Tsun Leung Chan is now reporting a heritable germline epimutation of MSH2 in a family with hereditary colorectal cancer another case of “paranormal” inheritance. They find a mosaic germline methylation pattern (which might even be a symptom of another mutation that affects the demethylation-de novo methylation pattern of MSH2 during embryogenesis?). If my hypothesis is true these families should even show more genes with different methylation patterns, yea, yea.

Addendum 28/5/08

Another attempt to answer this question comes by a study of the MLH1 promotor

Pro: MLH1 promoter methylation was found in a patient and his mother giving evidence for a familial predisposition for an epimutation in MLH1. Contra: a de novo set-up of methylation in one patient, a mosaic or incomplete methylation pattern in six patients, and no evidence for inheritance of MLH1 promoter methylation in the remaining families.


CC-BY-NC