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  • October 9, 2011
  • 03:46 AM

An ontology for QSAR and cheminformatics

by egonw in Chem-bla-ics

QSAR and QSPR are the fields that statistically correlate chemical substance features with (biological) activities (QSAR) or properties (QSPR). The chemical substance can be molecular structures, drug (which are not uncommonly mixtures), and true mixture like nanomaterials (NanoQSAR). Readers of this blog know I have been working towards making these kind of studies more reproducible for many years now.

Parts of this full story include the Blue Obelisk Data Repository (BODR), QSAR-ML, the CDK f........ Read more »

  • September 8, 2011
  • 11:28 AM

FUTON Bias. Or Why Limiting to Free Full Text Might not Always be a Good Idea.

by Laika in Laika's Medliblog

A few weeks ago I was discussing possible relevant papers for the Twitter Journal Club  (Hashtag #TwitJC), a succesful initiative on Twitter, that I have discussed previously here and here [7,8]. I proposed an article, that appeared behind a paywall. Annemarie Cunningham (@amcunningham) immediately ran the idea down, stressing that open-access (OA) is a pre-requisite for the TwitJC [...]... Read more »

Björk, B., Welling, P., Laakso, M., Majlender, P., Hedlund, T., & Guðnason, G. (2010) Open Access to the Scientific Journal Literature: Situation 2009. PLoS ONE, 5(6). DOI: 10.1371/journal.pone.0011273  

Matsubayashi, M., Kurata, K., Sakai, Y., Morioka, T., Kato, S., Mine, S., & Ueda, S. (2009) Status of open access in the biomedical field in 2005. Journal of the Medical Library Association : JMLA, 97(1), 4-11. DOI: 10.3163/1536-5050.97.1.002  

WENTZ, R. (2002) Visibility of research: FUTON bias. The Lancet, 360(9341), 1256-1256. DOI: 10.1016/S0140-6736(02)11264-5  

Murali NS, Murali HR, Auethavekiat P, Erwin PJ, Mandrekar JN, Manek NJ, & Ghosh AK. (2004) Impact of FUTON and NAA bias on visibility of research. Mayo Clinic proceedings. Mayo Clinic, 79(8), 1001-6. PMID: 15301326  

Carney PA, Poor DA, Schifferdecker KE, Gephart DS, Brooks WB, & Nierenberg DW. (2004) Computer use among community-based primary care physician preceptors. Academic medicine : journal of the Association of American Medical Colleges, 79(6), 580-90. PMID: 15165980  

  • August 31, 2011
  • 02:34 AM

Advice to become a refined self-plagiarist. (Disclaimer: it is not ethical and will not help your career)

by Pablo Artal in Optics confidential

Some comments on self-plagiarism practices in science that will damage your career... sooner than later... Read more »

  • August 26, 2011
  • 03:50 AM

Does internationalization change research content?

by Ingrid Piller in Language on the Move

Every linguistics undergraduate student is by now familiar with the fact of linguistic imperialism in academic publishing where the pressure to publish in international journals translates into the pressure to publish in English, leaving researchers from non-English-speaking backgrounds at a … Continue reading →... Read more »

  • August 26, 2011
  • 02:42 AM

A Whole New World: My Beginnings as a Student of Journalism

by Paige Brown in From The Lab Bench

This week, I started graduate classes for the first time as a student of Mass Communications at the LSU Manship School. Yahoo!
Thus begins my jump from a PhD in Biomedical Engineering to an advanced degree studying science journalism!
... Read more »

PH Longstaff. (2005) Security, resilience, and communication in unpredictable environments such as terrorism, natural disasters, and complex technology. Center for Information Policy Research. info:/

  • August 24, 2011
  • 09:00 AM

Taxonomy in decline or growth?

by Zen Faulkes in NeuroDojo

Earlier this year, Craig McClain from Deep Sea News wrote an editorial at Wired arguing that taxonomy as a scientific discipline was “going extinct.”

A short new paper challenges that view.

Joppa and colleagues looked at taxonomic research on cone snails (pictured), spiders, amphibians, birds, reptiles, and mammals. The number of taxonomists studying each group has gone up in every case, not down.

The number of species being described is also going up, but it is actually not keeping up w........ Read more »

  • August 18, 2011
  • 04:59 AM

Retractions correlate better with 'Impact Factor' than citations

by Björn Brembs in

Thomson Reuters' Impact Factor (IF) is supposed to provide a measure for how often the average publication in a scientific journal is cited and thus a quantitative basis for ranking journals. However, there are (at least) three major problems with the IF:The IF is negotiable and doesn't reflect actual citation counts (source)The IF cannot be reproduced, even if it reflected actual citations (source)The IF is not statistically sound, even if it were reproducible and reflected actual citations (so........ Read more »

  • August 16, 2011
  • 02:28 PM

It was twenty years ago today . . .

by Marco Frasca in The Gauge Connection

With these beautiful words starts a recollection paper by the founder of arXiv, Paul Ginsparg. This is worth the reading as this history spans a number of years exactly overlapping the computer revolution that definitely changed our lives. What Paul also changed through these new information tools was the way researchers should approach scientific communication. [...]... Read more »

Paul Ginsparg. (2011) It was twenty years ago today .. arXiv. arXiv: 1108.2700v1

R. Aouane, V. Bornyakov, E. -M. Ilgenfritz, V. Mitrjushkin, M. Müller-Preussker, & A. Sternbeck. (2011) Landau gauge gluon and ghost propagators at finite temperature from quenched lattice QCD. arXiv. arXiv: 1108.1735v1

Axel Maas, Tereza Mendes, & Stefan Olejnik. (2011) Yang-Mills Theory in lambda-Gauges. arXiv. arXiv: 1108.2621v1

  • August 15, 2011
  • 05:42 AM

Wikipedia: I Fought the Lore and the Lore Won

by Duncan Hull in O'Really?

Fighting the lore of wikipedia is an increasingly futile battle but there are people who resist using and improving the online encyclopedia. The remarkable thing is that some of this resistance comes from the scientific and academic communities, two groups of people who are supposedly concerned with the dissemination of knowledge. Wikipedia is the lore With [...]... Read more »

Neil L. Waters. (2007) Why you can't cite Wikipedia in my class. Communications of the ACM, 15-17. DOI: 10.1145/1284621.1284635  

Patricia L. Dooley. (2010) Wikipedia and the two-faced professoriate. WikiSym '10 Proceedings of the 6th International Symposium on Wikis and Open Collaboration. DOI: 10.1145/1832772.1832803  

Logan DW, Sandal M, Gardner PP, Manske M, & Bateman A. (2010) Ten simple rules for editing Wikipedia. PLoS computational biology, 6(9). PMID: 20941386  

  • August 1, 2011
  • 07:47 AM

“Your Science Reporting Truly Sucks…” – The Editor’s ‘Apology’

by Stuart Farrimond in Dr Stu's Science Blog

It’s not just tabloids that are having their pants pulled down at the moment. Medical journals are too. A few weeks the BJGP – Europe’s leading general practice journal – heralded apparently ground-breaking research on the benefits of acupuncture. On closer inspection, the research was poorly constructed, drew dubious conclusions and biased in extremis. I … Continue reading »... Read more »

Paterson, C., Taylor, R., Griffiths, P., Britten, N., Rugg, S., Bridges, J., McCallum, B., & Kite, G. (2011) Acupuncture for ‘frequent attenders’ with medically unexplained symptoms: a randomised controlled trial (CACTUS study). British Journal of General Practice, 61(587), 295-305. DOI: 10.3399/bjgp11X572689  

Jones, R. (2011) Editor's response. British Journal of General Practice, 61(589), 495-495. info:/10.3399/bjgp11X588367

Farrimond, S. (2011) Acupuncture for `frequent attenders' with medically unexplained symptoms. British Journal of General Practice, 61(689), 494-495. info:/10.3399/bjgp11X588349

  • July 29, 2011
  • 09:00 AM

Taxonomist as science survivalists

by Zen Faulkes in NeuroDojo

Just over a week ago, a vote by botanists at the International Botanical Congress decided to allow species names to be considered valid if they are published only electronically. Nature talks about this in this editorial. (Not only were botanists wedded to paper publication, but having species descriptions in Latin. Latin? I had no idea.)

Zoologists, from what I’ve read so far, think that botanists made a bad decision.

Because zoologists are bitter about their floppy disks.

Okay, perhaps n........ Read more »

  • July 25, 2011
  • 02:48 AM

Social Media Use By US Hospitals

by Dr Shock in Dr Shock MD PhD

Buffer From a structured review of websites of 1800 US hospitals focusing on their Facebook, Twitter and Youtube accounts: 21% used social media More likely to be large, urban hospitals run by nonprofit, nongovernment organisations More likely to participate in graduate medical education Used social media to target a general audience (97%) Provide content about [...]

No related posts.... Read more »

Thaker SI, Nowacki AS, Mehta NB, & Edwards AR. (2011) How U.S. hospitals use social media. Annals of internal medicine, 154(10), 707-8. PMID: 21576547  

  • July 24, 2011
  • 02:01 PM

Blogs/Twitter in Medical Publications: Too Unreliable to Quote or A Change Waiting to Happen?

by Pranab Chatterjee in Scepticemia

Just a few days ago, I was co-authoring a submission for a journal on the issue of handling social media with care and needed to cite a bunch of blogs and non-traditional online sources of information (including Tweets and Friendfeed … Continue reading →... Read more »

Mandavilli A. (2011) Peer review: Trial by Twitter. Nature, 469(7330), 286-7. PMID: 21248816  

  • July 20, 2011
  • 07:04 AM

Autotune the Abstract: Singing in the Brain

by Ben Good in B Good Science

As a science communication student I find myself constantly coming across new and different ways people try and get across scientific data and knowledge. It can range from typical things such as news articles and blog posts to knitted representations of science. Whilst some of the crazy ways people try and get out their research may [...]... Read more »

  • July 1, 2011
  • 09:50 PM

Q&A's with a Science Journalist: 'It's All Relativity'

by Paige Brown in From The Lab Bench

This week I am interviewing Louise Ogden, a science blogger on our own community blog Student Voices, which is hosted on Scitable by Nature Education. Louise also has her own science blog, It’s All Relativity, where she talks about space missions, climate change, exoplanets, solar eclipses, and much more! Louise is currently finishing up her Masters project at City University in London, which will earn her an (exciting!) degree in science journalism.... Read more »

Alison Wright. (2010) High-energy physics: Top of the class . Nature Physics, 6(644). info:/10.1038/nphys1783

  • June 28, 2011
  • 04:31 PM

Impact Factor Boxing 2011

by Duncan Hull in O'Really?

[This post is part of an ongoing series about impact factors] Well it’s that time again. The annual sweaty fist-fight for supremacy between the scientific journals, as measured by impact factors, is upon us. Much ink (virtual and actual) has been spilt on the subject of impact factors, which we won’t add to here, other [...]... Read more »

  • June 21, 2011
  • 05:44 PM

More magic numbers

by nuclear.kelly in Miss Atomic Bomb

I was alerted to some interesting work by a recent report in the IoP's Physics World magazine. Researchers have finally worked out that there is, in fact, a correlation between group size and quality of research.The paper (available on arxiv and published in Scientometrics, which is apparently the research of... research) took information from a survey of UK universities (and a few French) and determined the "quality vs quantity" of the research output (the "quality" metric is described in more ........ Read more »

  • June 9, 2011
  • 08:41 PM

Coverage of common causes of death in the UK media

by Hadas Shema in Information Culture

Is there a correlation between the diseases you read about in the news and what is actually likely to kill you?Williamson, Skinner and Hocken (2011) studied the 10 most daily read newspapers in the UK s (The Sun, Daily Mail, The Mirror, The Telegraph, The Times, Daily Express, Daily Star, The Guardian, The Independent and the Financial Times) for a year, in order to see whether there's a correlation between the media reporting of illness and death and actual statistics.Most common causes of dea........ Read more »

Williamson, J.M., Skinner, C. I., & Hocken, D.B. (2011) Death and illness as depicted in the media. International journal of clinical practice, 65(5). info:/21489079

  • May 30, 2011
  • 12:00 PM

Prelim Finding The Holdouts: Who Is Required To Publicly Archive Data But Still Doesn’t?

by Heather Piwowar in Research Remix

Knowing who is least likely to publicly archive data, even when required to do so, could help us uncover unrecognized hurdles in data archiving tools, policies, practice, and culture. The results could be used to study these issues and direct educational and policy resources as necessary.... Read more »

Piwowar HA. (2011) Data from: Who shares? Who doesn’t? Factors associated with openly archiving raw research data. Dryad Digital Repository. info:/doi:10.5061/dryad.mf1sd

  • May 27, 2011
  • 09:45 PM

Filtering Out Propaganda from the Medical Literature

by Michael Long in Phased

A checklist can help scientists who evaluate technical medical manuscripts to recognize medical propaganda, thereby helping to prevent unwarranted hype from becoming mainstream knowledge.... Read more »

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