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  • April 16, 2011
  • 12:02 AM

Citing versioned papers, robots and reviewers?

by Daniel Mietchen in Research Cycle Research

Established scholarly citation practices are tailored towards static documents. With the use of versioned documents spreading, citation formats have to follow suit. This requires to balance the need for proper identification of the source of a claim with the demands for cited information being up to date. Getting this right is particularly important in naturally versioned environments like wikis or GitHub. Continue reading →... Read more »

  • April 15, 2011
  • 02:21 PM

The Allure of Gay Cavemen

by Eric Michael Johnson in The Primate Diaries

The latest stop in the #PDEx tour is being hosted by Neuron Culture at Wired:In 1993 the reputable German weekly Der Spiegel reported a rumor that Otzi, the 5,300-year-old frozen mummy discovered in the Otztal Alps two years earlier, contained evidence of the world's earliest known homosexual act. "In Otzi's Hintern," wrote the editors, referring to the Iceman's hinterland, "Spermien gefunden worden." (If you require a translation, chances are you didn't want to know anyway.) The rumor quickly s........ Read more »

Will Roscoe. (2000) Changing Ones: Third and Fourth Genders in Native North America. Macmillan. info:/

  • April 15, 2011
  • 02:21 PM

The Allure of Gay Cavemen

by Eric Michael Johnson in The Primate Diaries in Exile

The latest stop in the #PDEx tour is being hosted by Neuron Culture at Wired:In 1993 the reputable German weekly Der Spiegel reported a rumor that Otzi, the 5,300-year-old frozen mummy discovered in the Otztal Alps two years earlier, contained evidence of the world's earliest known homosexual act. "In Otzi's Hintern," wrote the editors, referring to the Iceman's hinterland, "Spermien gefunden worden." (If you require a translation, chances are you didn't want to know anyway.) The rumor quickly s........ Read more »

Will Roscoe. (2000) Changing Ones: Third and Fourth Genders in Native North America. Macmillan. info:/

  • April 15, 2011
  • 12:43 PM

Great, now I’m yawning too.

by helikonios in The view from Helicon

From the annals of adorable research: You know how yawning is contagious? That’s not just a human thing. Chimpanzees, several other primates, and possibly dogs can “catch” yawns from others of their own species. This strange effect might be a byproduct of empathy—not the complex empathy that involves understanding and sharing someone else’s suffering, but [...]... Read more »

  • April 15, 2011
  • 11:45 AM

BIG Physics for small Science

by Paige Brown in From The Lab Bench

Metallic particles can be synthesized which are adequately small to be suspended in a liquid phase, where the particles exist on a size scale such that buoyancy in the medium and forces of gravity are balanced, and the particle solution, known as a colloid, is stable. In this state, these nanoparticles, named after their dimensions on the nanometer scale (1/billionth of a meter), will stay dispersed instead of precipitating out of solution. It might help to think of the similar way in which larg........ Read more »

Hutter, E., & Fendler, J. (2004) Exploitation of Localized Surface Plasmon Resonance. Advanced Materials, 16(19), 1685-1706. DOI: 10.1002/adma.200400271  

  • April 15, 2011
  • 11:43 AM

Development of first selective inhibitor of LRRK2 mutation found in Parkinson’s disease is progress on road towards new therapy

by Pieter Droppert in Biotech Strategy Blog

This month is Parkinson’s awareness month.  Following on from my recent interview (that you can read here & here) with Dr Todd Sherer of The Michael J. Fox Foundation for Parkinson’s Research, I was interested to read about progress being … Continue reading →... Read more »

Deng, X., Dzamko, N., Prescott, A., Davies, P., Liu, Q., Yang, Q., Lee, J., Patricelli, M., Nomanbhoy, T., Alessi, D.... (2011) Characterization of a selective inhibitor of the Parkinson's disease kinase LRRK2. Nature Chemical Biology, 7(4), 203-205. DOI: 10.1038/nCHeMBIO.538  

  • April 15, 2011
  • 10:50 AM

ENCODE Chromatin state data offers nice insights. Take this and run with it.

by Mary in OpenHelix

mmmmm….another “big data” paper illustrates a point I’ve been hammering on: there is terrific data coming out of these projects–but it’s not in the publications. So I’m going to talk about this paper in this post (1), but I’ll direct you to the database where the information is really available for your perusal–and to a tutorial that explains how to access it. Off we go….
The ENCODE project is one of the “big data” consortiu........ Read more »

Ernst, J., Kheradpour, P., Mikkelsen, T., Shoresh, N., Ward, L., Epstein, C., Zhang, X., Wang, L., Issner, R., Coyne, M.... (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. DOI: 10.1038/nature09906  

Birney, E., Stamatoyannopoulos, J., Dutta, A., Guigó, R., Gingeras, T., Margulies, E., Weng, Z., Snyder, M., Dermitzakis, E., Stamatoyannopoulos, J.... (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447(7146), 799-816. DOI: 10.1038/nature05874  

Rosenbloom, K., Dreszer, T., Pheasant, M., Barber, G., Meyer, L., Pohl, A., Raney, B., Wang, T., Hinrichs, A., Zweig, A.... (2009) ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Research, 38(Database). DOI: 10.1093/nar/gkp961  

  • April 15, 2011
  • 10:16 AM

Hypsugines: an assemblage of 'pipistrelle-like non-pipistrelles' (vesper bats part XV)

by Darren Naish in Tetrapod Zoology

As we've seen throughout this series (see links below for previous parts), recent phylogenetic studies have found a number of 'pipistrelle-like non-pipistrelles' to form a novel clade previously unsuspected from morphological studies [composite above shows - l to r - Hypsugo cf. joffrei (from Kruskop & Shchinov (2010)), Neoromicia capensis (from Fernloof Nature Reserve), and Laephotis botswanae]. Following Roehrs et al. (2010), I'll refer to this as the 'hypsugine group'. Hypsugines occur ac........ Read more »

Volleth, M., & Heller, K.-G. (1984) Phylogenetic relationships of vespertilionid genera (Mammalia: Chiroptera). Journal of Zoological Systematics and Evolutionary Research, 11-34. info:/

  • April 15, 2011
  • 09:19 AM

that’s not what we meant by computer scientist

by Greg Fish in weird things

A while ago, there was some buzz on the pop sci circuit about scientists using machines to catch up with the constantly growing body of published papers and asking whether the machines could ever qualify as actual scientists proposing hypotheses of their own. Now there seems to be an affirmative answer since a robot- aided [...]... Read more »

King, R., Liakata, M., Lu, C., Oliver, S., & Soldatova, L. (2011) On the formalization and reuse of scientific research. Journal of The Royal Society Interface. DOI: 10.1098/rsif.2011.0029  

  • April 15, 2011
  • 09:01 AM

Hormonal therapy and cancer – the controversy rages on

by Sally Church in Pharma Strategy Blog

Hormone replacement therapy (HRT) is one of those subjects where many have a strong opinion either way and I suspect even if we have another dozen trials evaluating at the pros and cons, those opinions won’t change very much. That … Continue reading →
... Read more »

  • April 15, 2011
  • 05:56 AM

Natural selection and saving

by Jason Collins in Evolving Economics

In the academic literature at the intersection of economics and evolutionary biology, evolution of time preference (patience) is one area that has received much attention. This makes some sense, as most economic models that consider decisions over time include time preference. Time preference is normally included in the model through a discount rate of a [...]... Read more »

Hansson, I., & Stuart, C. (1990) Malthusian Selection of Preferences. The American Economic Review, 80(3), 529-544. info:/

  • April 15, 2011
  • 05:17 AM

A role for chromatin modifications and DNA repair in renal cell carcinoma

by Joana Guedes in BHD Research Blog

Following on from the blog last week, which described the identification of PBRM1 mutations in clear-cell RCC (ccRCC), other sequencing studies are also finding new genes that are mutated in ccRCC. For example, Dalgliesh et al. (2010) have identified mutations … Continue reading →... Read more »

Dalgliesh, G., Furge, K., Greenman, C., Chen, L., Bignell, G., Butler, A., Davies, H., Edkins, S., Hardy, C., Latimer, C.... (2010) Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes. Nature, 463(7279), 360-363. DOI: 10.1038/nature08672  

Komori, K., Takagi, Y., Sanada, M., Lim, T., Nakatsu, Y., Tsuzuki, T., Sekiguchi, M., & Hidaka, M. (2009) A novel protein, MAPO1, that functions in apoptosis triggered by O6-methylguanine mispair in DNA. Oncogene, 28(8), 1142-1150. DOI: 10.1038/onc.2008.462  

van Haaften, G., Dalgliesh, G., Davies, H., Chen, L., Bignell, G., Greenman, C., Edkins, S., Hardy, C., O'Meara, S., Teague, J.... (2009) Somatic mutations of the histone H3K27 demethylase gene UTX in human cancer. Nature Genetics, 41(5), 521-523. DOI: 10.1038/ng.349  

  • April 14, 2011
  • 02:28 PM

A rig by any other name, could it be an artificial reef?

by Southern Fried Scientist in Southern Fried Science

There are currently more than 7,500 offshore oil platforms actively probing the earth’s crust for black gold. Their relatively minimal appearance at the surface belies the shear magnitude of human construction beneath the waves. Oil platforms are among the world’s tallest man-made structures. Compliant tower platforms reach up to 900 meters in depth (in contrast, [...]... Read more »

Macreadie, P., Fowler, A., & Booth, D. (2011) Rigs-to-reefs: will the deep sea benefit from artificial habitat?. Frontiers in Ecology and the Environment, 2147483647. DOI: 10.1890/100112  

  • April 14, 2011
  • 01:41 PM

One Foot in Front of the Other

by Rob Mitchum in ScienceLife

There are few biological functions that we take for granted more than gait, the intricate symphony of motion that happens almost automatically when we walk or run. Gait is programmed deep into the nervous system of animals, an activity so robust that it is maintained even when large segments of brain are removed. Those crude, [...]... Read more »

Crone SA, Zhong G, Harris-Warrick R, & Sharma K. (2009) In mice lacking V2a interneurons, gait depends on speed of locomotion. The Journal of neuroscience : the official journal of the Society for Neuroscience, 29(21), 7098-109. PMID: 19474336  

McLean DL, Fan J, Higashijima S, Hale ME, & Fetcho JR. (2007) A topographic map of recruitment in spinal cord. Nature, 446(7131), 71-5. PMID: 17330042  

  • April 14, 2011
  • 11:32 AM

Mitochondria and Hypertension

by Jon Wilkins in Lost in Transcription

So, here's a new thing.
Best URL for sharing:
URL for hotlinking or embedding:

This is based on a recent paper (citation below) where they identify a point mutation in the mitochondrial DNA that appears to result in hypertension.

So why is this interesting? Well, for me, as an evolutionary theorist who works on intragenomic conflict, it is interesting because the mitochondrial DNA is, in principle, subject to s........ Read more »

  • April 14, 2011
  • 11:02 AM

Origins of Life: General RNA Polymerases

by ogremkv in Cassandra's Tears

Yesterday, I discovered a new set of studies that I had not previously known about.  I may write about all of them, but I definitely want to talk about this particular study for two reasons.  The first reason is that … Continue reading →... Read more »

Wochner A, Attwater J, Coulson A, & Holliger P. (2011) Ribozyme-catalyzed transcription of an active ribozyme. Science (New York, N.Y.), 332(6026), 209-12. PMID: 21474753  

  • April 14, 2011
  • 11:01 AM

Birds Inherited Strong Sense of Smell From Dinosaurs

by Brian Switek in Dinosaur Tracking Feathers, air sacs, nesting behavior—the earliest birds owed a lot to their dinosaurian ancestors. The first birds also inherited a strong sense of smell. Modern birds have not been thought of as excellent scent-detectors, save for some super-smellers such as turkey vultures, which detect the scent of rotting carcasses. We typically think of avians [...]... Read more »

Zelenitsky, D., Therrien, F., Ridgely, R., McGee, A., & Witmer, L. (2011) Evolution of olfaction in non-avian theropod dinosaurs and birds. Proceedings of the Royal Society B: Biological Sciences. DOI: 10.1098/rspb.2011.0238  

  • April 14, 2011
  • 10:46 AM

Tales from the Intestinal Crypt

by Sanford- Burnham in Beaker

Doctors have noticed for decades that people with Down Syndrome seldom develop cancers. Down Syndrome results from an extra copy of chromosome 21, leading scientists to wonder if something about that particular piece of the genome could protect against cancer. A few years ago, researchers at Johns Hopkins University tested that hypothesis. They added several [...]... Read more »

Múnera, J., Ceceña, G., Jedlicka, P., Wankell, M., & Oshima, R. (2011) Ets2 Regulates Colonic Stem Cells and Sensitivity to Tumorigenesis. STEM CELLS, 29(3), 430-439. DOI: 10.1002/stem.599  

  • April 14, 2011
  • 09:30 AM

Eptesicini: the serotines and their relatives (vesper bats part XIV)

by Darren Naish in Tetrapod Zoology

A group of mostly mid-sized pipistrelle-like bats of Africa and the northern continents are known as the serotines (Eptesicus) [species shown here is the one generally known simply as the Serotine E. serotinus: photo by Mnolf, from wikipedia]. Here in Europe this is - along with pipistrelles, noctules and long-eared bats - one of the most familiar of vesper bat groups. As we'll see, this group is anything but boring: it includes some weird big-eared species as well as the only bats known to ........ Read more »

Roehrs, Z. P., Lack, J. B., & Van Den Bussche, R. A. (2010) Tribal phylogenetic relationships within Vespertilioninae (Chiroptera: Vespertilionidae) based on mitochondrial and nuclear sequence data. Journal of Mammalogy, 1073-1092. info:/

  • April 14, 2011
  • 09:22 AM

Biology of indolent B-cell lymphomas and chronic lymphocytic leukemia

by Sally Church in Pharma Strategy Blog

We all know the importance that inflammation and the immune system plays in the early development of many cancers, but this is not a ubiquitous finding.  Indeed, some hematologic malignancies arise out of immunodeficiency, such as myelomas and chronic lymphocytic … Continue reading →
... Read more »

Christopoulos P, Follo M, Fisch P, & Veelken H. (2008) The peripheral helper T-cell repertoire in untreated indolent B-cell lymphomas: evidence for antigen-driven lymphomagenesis. Leukemia : official journal of the Leukemia Society of America, Leukemia Research Fund, U.K, 22(10), 1952-4. PMID: 18385751  

Wendtner CM. (2011) Lenalidomide in CLL: What Is the Optimal Dose?. Clinical advances in hematology , 9(3), 220-4. PMID: 21475128  

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