All posts by admin

Vitamin D: A 18%! reduction in early infant mortality

A study published earlier this year in the Lancet found a 18% reduction in mortality when women obtained supplements during pregnancy until 90 days post partum including additional 800 ug retinol, 200 IU vitamin D, 10 mg vitamin E, 70 mg ascorbic acid, 1.4 mg vitamin B1, 18 mg niacin, 1.9 mg vitamin B6, 2.6 ug vitamin B12, 15 mg zinc, 2 mg copper, 65 ug selenium and 150 ug iodine. Much of the effect will be due to the vitamin D supplementation Continue reading Vitamin D: A 18%! reduction in early infant mortality

PDF Pubmed Finder

As announced earlier this week, here is a first version of the PDF Pubmed Finder.The Finder helps to identify an unknown paper within seconds and rename it within milliseconds. Although the Finder consists of a single page only it uses several areas to update the data. I have written the code for my local installation but you may try it also online with your own PDFs either by uploading them with the available form or by appending the PDF URL to the Finder address http://wjst.de/pubmed/finder.php?http://medicine.plosjournals.org/test.pdf
The last method is certainly better as it can be used within a scripting environment; note that my domain may not retrieve a PDFs that you can see at your local computer. PDFs also need to have some inline text (run an OCR on scans before submitting them).

zotero_c2.png
Here are some usage instructions: After selecting any article on the left (1.), clicking on relevant keywords (2., 3.) will lead to an immediate Pubmed search (4). Finish by clicking on “rename” or “Pubmed/Zotero” import of the correct reference. If your search doesn’t retrieve any useful hits, keywords will be automatically reset.
What I would like to know all from the AJAX experts who can inspect the sourcecode: I ran into deep problems described earlier with the prototype oncomplete function used in the links of the div2 container. They are checking how the div4 container was being updated. As you see it works, but I failed to clean up the code by having only one Javascript function in the beginning of the page with the div2 links calling this function. Your help would be greatly appreciated.

Not all that wheezes is asthma

A new abstract at the recent ATS congress now clears the 2007 controversy between the Camargo and Gale studies on the effect of vitamin D: Wheezing is not asthma (as the atopy component is missing?). Continue reading Not all that wheezes is asthma

CF and PHP at the same time

For a clinical research project I need a fast webserver that understands both COLD FUSION (for the existing database stuff) and PHP (for dokuwiki). As this is a non-commercial project, I decided for the RAILO 2.0 community version that works right out of the box as it includes the Resin webserver and the H2 database as well. Following some recommendations found on the net, php is running now with with the fastcgi option showing good acceptable performance with eAccelerator.

php.cmd

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@echo off

rem install php with this option
rem msiexec /i php-5.2.6-win32-installer.msi /q ADDLOCAL=cgi,ext_php_mysqli

rem check for right version
rem php-cgi -v

rem now run php on dedicated port
php-cgi -b 8002

rem let railo know in x:\railo\conf\app-default.xml
rem  <servlet servlet-name="php"
rem           servlet-class="com.caucho.servlets.FastCGIServlet">
rem    <init>
rem      <server-address>localhost:8002</server-address>
rem    </init>
rem  </servlet>
rem  <servlet-mapping url-pattern="*.php" servlet-name="php"/>

pause
exit

German Science blogging

The German blogosphere is now being mapped but with a few exceptions German science blogging doesn’ play a major role (in contrast to knitting that shows a large cluster Continue reading German Science blogging

CD 14 now also on the vitamin+allergy list

Just for curiosity I am collecting a list of allergy genes that are vitamin D dependent. The list is already rather long but now there is a prominent addition: CD14. Known as asthma gene for many years the vitamin D dependency isn’t such clear. A clever analysis, however, now shows that there is an intermediate step involved Continue reading CD 14 now also on the vitamin+allergy list

Placebo for placebo

or “Do placebo responders exist?” is a remarkable new review by researcher from the Harvard Medical School. I always wondered about the sheer size of the placebo effect (and its perception as nuisance parameter). The authors simply ask the question

… this paper also examines the evidence for the existence of a consistent placebo responder, i.e. a person who responds to placebo in one situation will respond in another condition or using a different type of placebo ritual….

Suggestibility is a human trait, yea, yea.

Vitamin D as an adjuvans to specific immunotherapy

Despite the known allergy promoting effect of vitamin D in early childhood, there is mounting evidence that it may have beneficial effects during specific immunotherapy. A paper on “IL-10-inducing adjuvants enhance sublingual immunotherapy efficacy in a murine asthma model” by researchers from a French allergen company Continue reading Vitamin D as an adjuvans to specific immunotherapy

Genome Browser now with GADview track

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

Orientation of genomic sequence and SNP allele designation

… permanently leading to errors – the plus / minus strand orientation and the consecutive sequence / allele designation of SNPs. Only recently I came across a fancy way how to define strand direction – from a tech note Continue reading Orientation of genomic sequence and SNP allele designation

Better suited to a more specialist journal

How many times did you hear that from an editor? At least I hear it 5 times every year … But have you ever heard of journal saying this is paper better suited to a more general journal? Never! So, this is a never ending loop, yea, yea.

Trans-border LD?

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?