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  • April 28, 2014
  • 04:22 PM

Bugging city communities with impunity: this is the Staph of legend

by Kausik Datta in In Scientio Veritas

Whether we know it or not, the human skin is a veritable garden of micro-organisms. The outermost layer (‘epidermis’) of the skin, the shafts of hair follicles, as well as the soft surface inside the nose (‘nasal mucosa’), making up for approximately 1.8 square meter of surfaces, is home to about 1000 species of bacteria among other things. Most of these don’t ordinarily cause disease; some are there for the ride, and some even offer benefits by warding off other... Read more... Read more »

  • April 28, 2014
  • 04:00 AM

From Stone Darts to Dismembered Bodies, New Study Reveals 5,000 Years of Violence in Central California

by Blake de Pastino in Western Digs

From shooting their enemies with darts and arrows to crushing their skulls and even harvesting body parts as trophies, the ancient foragers of central California engaged in sporadic, and sometimes severe, violence, according to a new archaeological study spanning 5,000 years.... Read more »

Schwitalla, A., Jones, T., Pilloud, M., Codding, B., & Wiberg, R. (2014) Violence among foragers: The bioarchaeological record from central California. Journal of Anthropological Archaeology, 66-83. DOI: 10.1016/j.jaa.2013.11.004  

  • April 24, 2014
  • 04:39 PM

Cap and Trade Scientific False Positives?

by Neuroskeptic in Neuroskeptic_Discover

In a letter to Nature, University of Miami psychologists Michael McCullough and David Kelly propose A trading scheme to reduce false results. Neuroskeptic readers will know that concern over false-positive science is growing. Many solutions have been proposed, but McCullough and Kelly’s is quite novel: Cap-and-trade systems have proved useful in cutting pollutants such as […]The post Cap and Trade Scientific False Positives? appeared first on Neuroskeptic.... Read more »

  • April 22, 2014
  • 06:04 PM

SARS-CoV v. MERS-CoV: differences and similarities, what do we know?

by thelonevirologist in Virology Tidbits

Coronaviruses are important animal and human pathogens and are the causative agent of 30-40% community acquired upper respiratory tract infections, most of them mild diseases. Besides relatively benign infections, the infection of infants and children has been implicated in some cases to acute asthmatic attacks and the onset of croup (whizzing cough). With the identification of SARS-CoV in 2003 became associated with more severe pulmonary disease particularly in immunocompromised individuals. T........ Read more »

Barlan A, Zhao J, Sarkar MK, Li K, McCray PB Jr, Perlman S, & Gallagher T. (2014) Receptor variation and susceptibility to middle East respiratory syndrome coronavirus infection. Journal of virology, 88(9), 4953-61. PMID: 24554656  

Raj, V., Mou, H., Smits, S., Dekkers, D., Müller, M., Dijkman, R., Muth, D., Demmers, J., Zaki, A., Fouchier, R.... (2013) Dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-EMC. Nature, 495(7440), 251-254. DOI: 10.1038/nature12005  

Chu KH, Tsang WK, Tang CS, Lam MF, Lai FM, To KF, Fung KS, Tang HL, Yan WW, Chan HW.... (2005) Acute renal impairment in coronavirus-associated severe acute respiratory syndrome. Kidney international, 67(2), 698-705. PMID: 15673319  

Roper, R., & Rehm, K. (2009) SARS vaccines: where are we?. Expert Review of Vaccines, 8(7), 887-898. DOI: 10.1586/erv.09.43  

Payne DC, Iblan I, Alqasrawi S, Al Nsour M, Rha B, Tohme RA, Abedi GR, Farag NH, Haddadin A, Al Sanhouri T.... (2014) Stillbirth During Infection With Middle East Respiratory Syndrome Coronavirus. The Journal of infectious diseases. PMID: 24474813  

Drosten, C. (2013) Is MERS another SARS?. The Lancet Infectious Diseases, 13(9), 727-728. DOI: 10.1016/S1473-3099(13)70159-2  

  • April 21, 2014
  • 07:18 AM

What makes music groovy?

by Henkjan Honing in Music Matters

Last week PLOS ONE published an interesting study on rhythm, groove and syncopation that uses an often criticized methodology: questionnaire and web-based research...... Read more »

Witek, M., Clarke, E., Wallentin, M., Kringelbach, M., & Vuust, P. (2014) Syncopation, Body-Movement and Pleasure in Groove Music. PLoS ONE, 9(4). DOI: 10.1371/journal.pone.0094446  

Honing, H., & Reips, U.-D. (2008) Web-based versus lab-based studies: a response to Kendall (2008). Empirical Musicology Review, 3(2), 73-77. info:/

  • April 20, 2014
  • 03:34 PM

420: How Marijuana Messes With the Brain

by Alexis Delanoir in How to Paint Your Panda

Cannabis use has previously been associated with cognitive impairment, and Smith et al. (2013) showed that heavy marijuana use was associated with poor working memory and brain abnormalities. Now, Gilman et al. (2014) propose that even casual use of marijuana is associated with such negative effects. Is this an issue of correlation/causation, of funding bias, or are the world's weed smokers really in neurological danger? In this post, in celebration of 4/20, I provide context for the recent........ Read more »

Meier, M., Caspi, A., Ambler, A., Harrington, H., Houts, R., Keefe, R., McDonald, K., Ward, A., Poulton, R., & Moffitt, T. (2012) Persistent cannabis users show neuropsychological decline from childhood to midlife. Proceedings of the National Academy of Sciences, 109(40). DOI: 10.1073/pnas.1206820109  

  • April 19, 2014
  • 02:19 PM

Introduction to Traditional Peer Review

by Hadas Shema in Information Culture

Peer review was introduced to scholarly publication in 1731 by the Royal Society of Edinburgh, which published a collection of peer-reviewed medical articles. Despite this early start, in many...

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Biagioli, M. (2002) From Book Censorship to Academic Peer Review. Emergences: Journal for the Study of Media , 12(1), 11-45. DOI: 10.1080/1045722022000003435  

Benos DJ, Bashari E, Chaves JM, Gaggar A, Kapoor N, LaFrance M, Mans R, Mayhew D, McGowan S, Polter A.... (2007) The ups and downs of peer review. Advances in physiology education, 31(2), 145-52. PMID: 17562902  

Bornman, L. (2008) Scientific Peer Review: An Analysis of the Peer Review Process from the Perspective of Sociology of Science Theories. Human Architecture: Journal of the Sociology of Self-Knowledge, 6(2). info:/

Brown, R. (2006) Double Anonymity and the Peer Review Process. The Scientific World JOURNAL, 1274-1277. DOI: 10.1100/tsw.2006.228  

Callaham ML, Baxt WG, Waeckerle JF, & Wears RL. (1998) Reliability of editors' subjective quality ratings of peer reviews of manuscripts. JAMA : the journal of the American Medical Association, 280(3), 229-31. PMID: 9676664  

Spier R. (2002) The history of the peer-review process. Trends in biotechnology, 20(8), 357-8. PMID: 12127284  

  • April 18, 2014
  • 01:56 PM

Moving Beyond “Just-So Stories”: Young Children Can Be Taught Basic Natural Selection

by amikulak in Daily Observations

Spend more than a few hours with a child under the age of 10 and “why?” is a question you’re likely to hear a. Children are naturally curious explorers, and […]... Read more »

  • April 17, 2014
  • 12:34 PM

What makes music groovy?

by Henkjan Honing in Music Matters

Today PLOS ONE publishes a study that uses an often criticized research method: questionnaire and web-based research (cf. Honing & Ladinig, 2008). This study, however, is a good example of how an unspectacular method (i.e. compared to, e.g., controlled experiments, brain imaging techniques or computational modelling) can still be quite informative....... Read more »

Witek, M., Clarke, E., Wallentin, M., Kringelbach, M., & Vuust, P. (2014) Syncopation, Body-Movement and Pleasure in Groove Music. PLoS ONE, 9(4). DOI: 10.1371/journal.pone.0094446  

Honing, H., & Reips, U.-D. (2008) Web-based versus lab-based studies: a response to Kendall (2008). Empirical Musicology Review, 3(2), 73-77. info:/

  • April 16, 2014
  • 08:29 PM

What makes music groovy?

by Henkjan Honing in Music Matters

Today PLOS ONE publishes a study that uses an often criticized research method: questionnaire and web-based research (cf. Honing & Ladinig, 2008). This study, however, is a good example of how an unspectacular method (i.e. compared to, e.g., controlled experiments, brain imaging techniques or computational modelling) can still be quite informative.... Read more »

Witek, M., Clarke, E., Wallentin, M., Kringelbach, M., & Vuust, P. (2014) Syncopation, Body-Movement and Pleasure in Groove Music. PLoS ONE, 9(4). DOI: 10.1371/journal.pone.0094446  

Honing, H., & Reips, U.-D. (2008) Web-based versus lab-based studies: a response to Kendall (2008). Empirical Musicology Review, 3(2), 73-77. info:/

  • April 15, 2014
  • 11:59 PM

OYM 30: The Irreproducible Joe Rochford

by On Your Mind in On Your Mind

This week on the On Your Mind Neuroscience podcast we’re excited to share our microphones with Dr. Joe Rochford.  He’s the Associate Director (or as he prefers Ass. Director) of the Neuroscience program at McGill and the Director of Academic Affairs at the Douglas Hospital Research Center and he’s sharing his thoughts on the importance more
The post OYM 30: The Irreproducible Joe Rochford appeared first on On Your Mind Podcast.
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Collins FS, & Tabak LA. (2014) Policy: NIH plans to enhance reproducibility. Nature, 505(7485), 612-3. PMID: 24482835  

  • April 15, 2014
  • 08:00 PM

New Study Shows Surgical Checklists In Operating Rooms Are Less Effective Than Assumed

by Jalees Rehman in The Next Regeneration

Optimizing such tailored checklists, understanding why some studies indicate benefits of checklists whereas others do not and re-evaluating the efficacy of checklists in the non-academic setting will all require a substantial amount of future research before one can draw definitive conclusions about the efficacy of checklists. Regulatory agencies in Canada and the United Kingdom should reconsider their current mandates. Perhaps an even more important lesson to be learned is that health regulator........ Read more »

Urbach DR, Govindarajan A, Saskin R, Wilton AS, & Baxter NN. (2014) Introduction of surgical safety checklists in Ontario, Canada. The New England Journal of Medicine, 370(11), 1029-38. PMID: 24620866  

  • April 14, 2014
  • 04:00 AM

Sacrificial and Common Graves Alike Reveal Diversity in Ancient City of Cahokia

by Blake de Pastino in Western Digs

Whether they died from natural causes or as sacrificial offerings, the residents of America’s largest prehistoric city were surprisingly diverse, with at least a third of the population having come from communities up to hundreds of kilometers away, according to new research of the settlement’s ancient graves.... Read more »

  • April 11, 2014
  • 12:46 PM

Variant Annotation in Coding Regions

by Daniel Koboldt in Massgenomics

The analysis of NGS data comes with many challenges — data management, read alignment, variant calling, etc. — that the bioinformatics community has tackled with some success. Today I want to discuss another critical component of analysis that remains an unsolved problem: annotation of genetic variants. This process, in which we try to predict the […]... Read more »

Davis J McCarthy, Peter Humburg, Alexander Kanapin, Manuel A Rivas, Kyle Gaulton, The WGS500 Consortium, Jean-Baptiste Cazier and Peter Donnelly. (2014) Choice of transcripts and software has a large effect on variant annotation. Genome Medicine, 6(26). info:/doi:10.1186/gm543

  • April 10, 2014
  • 05:33 PM

Tamiflu and Zanamivir: are they effective in treating Influenza or not ?

by thelonevirologist in Virology Tidbits

A recently published report from the Cochrane Colloboration suggested that two drugs which are used in the treatment of human Influenza are not as effective as reported in clinical studies, so it is worth to pause a moment and recapitulate how these drugs work and take a closer look at the report before rushing to any judgment.
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Moscona, A. (2005) Neuraminidase Inhibitors for Influenza. New England Journal of Medicine, 353(13), 1363-1373. DOI: 10.1056/NEJMra050740  

Rossman JS, Jing X, Leser GP, Balannik V, Pinto LH, & Lamb RA. (2010) Influenza virus m2 ion channel protein is necessary for filamentous virion formation. Journal of virology, 84(10), 5078-88. PMID: 20219914  

Rossman JS, Leser GP, & Lamb RA. (2012) Filamentous influenza virus enters cells via macropinocytosis. Journal of virology, 86(20), 10950-60. PMID: 22875971  

van Riel D, den Bakker MA, Leijten LM, Chutinimitkul S, Munster VJ, de Wit E, Rimmelzwaan GF, Fouchier RA, Osterhaus AD, & Kuiken T. (2010) Seasonal and pandemic human influenza viruses attach better to human upper respiratory tract epithelium than avian influenza viruses. The American journal of pathology, 176(4), 1614-8. PMID: 20167867  

Loregian A, Mercorelli B, Nannetti G, Compagnin C, & Palù G. (2014) Antiviral strategies against influenza virus: towards new therapeutic approaches. Cellular and molecular life sciences : CMLS. PMID: 24699705  

  • April 10, 2014
  • 11:18 AM

Why do dogs lick people?

by Cobb & Hecht in Do You Believe In Dog?

Just Wow. Photo: Chris Sembrot PhotographyHi Julie,Yes, but WHY? I loved Claudia Fugazza's guest post about drawing on dogs' social imitation capacities to learn as copy-cats in the Do as I do training technique. Good stuff! A few things collided this week that resulted in me deciding to look into why dogs lick people. The first was the Huffington Post 'This Is What Happens When You Ask People To Kiss Their Dogs In Front Of A Camera' (example above from Chris Sembrot's 'For the love o........ Read more »

Bradshaw John W.S., Blackwell Emily J., & Casey Rachel A. (2009) Dominance in domestic dogs—useful construct or bad habit?. Journal of Veterinary Behavior: Clinical Applications and Research, 4(3), 135-144. DOI: 10.1016/j.jveb.2008.08.004  

  • April 8, 2014
  • 11:45 AM

Scientists Like Some Animals Better than Others (Hint: Bears)

by Elizabeth Preston in Inkfish

In the fight for attention from researchers, there are winners and there are civets. That’s what researchers found when they analyzed almost 16,500 published papers about animals from walruses to weasels. They saw clear trends in which animals are the most popular to study. And it matters because the most popular animals aren’t necessarily the […]The post Scientists Like Some Animals Better than Others (Hint: Bears) appeared first on Inkfish.... Read more »

  • April 4, 2014
  • 04:41 PM

MERS-CoV orf4a -an antagonist of antiviral signaling

by thelonevirologist in Virology Tidbits

As mentioned in a previous entry MERS-CoV is capable to inhibit antiviral signaling by antagonizing interferon signaling pathways which are induced by the recognition of dsRNA by intracellular pathogen-associated molecular pattern (PAMP) receptors. Although having a ssRNA genome, dsRNA is produced during Coronavirus replication as an intermediate and thus can be recognized by Toll-like receptors -3 and -9 (TLR-3/TLR-9). ... Read more »

Niemeyer D, Zillinger T, Muth D, Zielecki F, Horvath G, Suliman T, Barchet W, Weber F, Drosten C, & Müller MA. (2013) Middle East respiratory syndrome coronavirus accessory protein 4a is a type I interferon antagonist. Journal of virology, 87(22), 12489-95. PMID: 24027320  

Yoneyama M, Kikuchi M, Natsukawa T, Shinobu N, Imaizumi T, Miyagishi M, Taira K, Akira S, & Fujita T. (2004) The RNA helicase RIG-I has an essential function in double-stranded RNA-induced innate antiviral responses. Nature immunology, 5(7), 730-7. PMID: 15208624  

  • April 2, 2014
  • 05:52 PM

MERS-CoV and SARS-CoV: two members of a divergent family

by thelonevirologist in Virology Tidbits

Coronavirus infections are commonly associated with relative benign respiratory and enteric diseases in humans, such as the common cold, and with outbreaks among agricultural livestock -chickens, swine or cattle. The outbreak of a novel disease in humans, severe acute respiratory syndrome (SARS), in 2003 however highlighted the potential lethal consequences of Coronavirus (CoV) induced disease in the human population.
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Pyrc, K., Berkhout, B., & van der Hoek, L. (2006) The Novel Human Coronaviruses NL63 and HKU1. Journal of Virology, 81(7), 3051-3057. DOI: 10.1128/JVI.01466-06  

Golda A, Malek N, Dudek B, Zeglen S, Wojarski J, Ochman M, Kucewicz E, Zembala M, Potempa J, & Pyrc K. (2011) Infection with human coronavirus NL63 enhances streptococcal adherence to epithelial cells. The Journal of general virology, 92(Pt 6), 1358-68. PMID: 21325482  

Ge XY, Li JL, Yang XL, Chmura AA, Zhu G, Epstein JH, Mazet JK, Hu B, Zhang W, Peng C.... (2013) Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature, 503(7477), 535-8. PMID: 24172901  

de Wilde AH, Raj VS, Oudshoorn D, Bestebroer TM, van Nieuwkoop S, Limpens RW, Posthuma CC, van der Meer Y, Bárcena M, Haagmans BL.... (2013) MERS-coronavirus replication induces severe in vitro cytopathology and is strongly inhibited by cyclosporin A or interferon-α treatment. The Journal of general virology, 94(Pt 8), 1749-60. PMID: 23620378  

  • March 29, 2014
  • 06:50 PM

Human cancers and viruses: 50 years of Epstein Barr Virus

by thelonevirologist in Virology Tidbits

March marked the 50th anniversary of the discovery of Epstein-Barr Virus (EBV) - an anniversary which the author of this blog almost missed, wouldn’t it have been for an article published Science on March 21st.... Read more »

Butel, J., & Fan, H. (2012) The diversity of human cancer viruses. Current Opinion in Virology, 2(4), 449-452. DOI: 10.1016/j.coviro.2012.07.002  

Hammerschmidt, W., & Sugden, B. (2013) Replication of Epstein-Barr Viral DNA. Cold Spring Harbor Perspectives in Biology, 5(1). DOI: 10.1101/cshperspect.a013029  

Daikoku T, Kudoh A, Fujita M, Sugaya Y, Isomura H, Shirata N, & Tsurumi T. (2005) Architecture of replication compartments formed during Epstein-Barr virus lytic replication. Journal of virology, 79(6), 3409-18. PMID: 15731235  

Tsurumi, T., Fujita, M., & Kudoh, A. (2005) Latent and lytic Epstein-Barr virus replication strategies. Reviews in Medical Virology, 15(1), 3-15. DOI: 10.1002/rmv.441  

Arnaud F, Varela M, Spencer TE, & Palmarini M. (2008) Coevolution of endogenous betaretroviruses of sheep and their host. Cellular and molecular life sciences : CMLS, 65(21), 3422-32. PMID: 18818869  

Allison AB, Kevin Keel M, Philips JE, Cartoceti AN, Munk BA, Nemeth NM, Welsh TI, Thomas JM, Crum JM, Lichtenwalner AB.... (2014) Avian oncogenesis induced by lymphoproliferative disease virus: a neglected or emerging retroviral pathogen?. Virology, 2-12. PMID: 24503062  

Fuentes-González, A., Contreras-Paredes, A., Manzo-Merino, J., & Lizano, M. (2013) The modulation of apoptosis by oncogenic viruses. Virology Journal, 10(1), 182. DOI: 10.1186/1743-422X-10-182  

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