Archiv für Dezember 2005

Field-testing refdb-mode

Dezember 22, 2005 - Markus Hoenicka
When I stepped in as a maintainer of refdb-mode, the Emacs frontend for RefDB, Michael Smith left me what was an awesome framework but far from complete in terms of functionality. Unfortunately I did not grasp the potential of his work earlier, I might have pushed him to implement the rest as well :-) So I had the pleasure to reactivate my lisp skills and make refdb-mode a full-fledged frontend for RefDB. So far I had implemented what I thought users might need, but in the past couple of weeks I finally had a chance to run a field test myself when compiling a grant application with a serious bibliography.

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Watch out for toothpicks

Dezember 04, 2005 - Markus Hoenicka
There is a case report in the New England Journal of Medicine showing which odd ways an accidentally ingested toothpick may take (if you think the obvious now - this may be the least eventful outcome [no pun intended]). A 67-year-old woman showed up in the hospital with chest pain and signs of a cardiac tamponade (the accumulation of fluids in the pericardial space), which may be caused by a postinfarction rupture of the ventricle. After draining 150ml of blood from the pericardial space, the woman was taken to an emergency surgery. The doctors removed another 600ml of clotted blood from the pericardial space and finally found a wooden toothpick which had gone through the diaphragma and then perforated a coronary artery. The woman recovered. A statistic reports 3.6 toothpick incidents per 100000 person-years. Next time you find meat rolls secured with toothpicks on your plate, do yourself a favour and remove them in time.

Help is coming for us cowards

Dezember 01, 2005 - Markus Hoenicka
A recent article in Nature links anxiety to oxidative stress metabolism. Looks like overexpression of glyoxalase 1 and of glutathione reductase 1, two enzymes involved in detoxifying substances generated by oxidative stress, increase the anxiety in mice. This may of course lead to new approaches to cure anxiety-related disorders, but the interesting question is why there is a link. Are we supposed to avoid oxidative stress?
Abstract

Digital data and science

Dezember 01, 2005 - Markus Hoenicka
Nature carries a couple of interesting articles this week (Vol438, issue 7068, 2005-12-01), about the use of digital data in science. Here is a discussion how the linking of public data and the use of web services may help to make the fate of data independent of the fate of a particular lab. Although the technical means to share data are out there (think Google base), it will also require a new thinking about data, which are now held captive until published in order to get the next grant.

This article discusses the good and evil of digitizing books in science. Good would be of course the availability and searchability. Bad would be that even researchers might limit themselves to the snippets they find on the web (due to copyright issues, newer publications are likely to be available only as partial data), just like Joe Sixpack erroneously thinks himself well informed after watching those 20 second headline news instead of reading a newspaper. Apparently some publishers want to collect the digital data of current books and sell them online as well.

Another article evaluates the blessings of Google Scholar, a search engine meant for, well, scholars. This service has an edge over other databases like Pubmed as it tracks citations which you can explore at a mouseclick. However, due to the automatic scanning of only those papers which are currently available online somewhere, there is a huge bias towards publications since the mid '90 (this is where the full-text archives of many journals start), a fact that commercial databases avoid.

Finally, here is an article which explains how blogs and wikis may change the ways scientists cooperate, although it is agreed that these techniques will not replace the classic "paper".