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  • April 22, 2014
  • 06:04 PM
  • 22 views

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. To understand the pathogenesis, it is vital to compare various aspects of the disease, including but not limited to the receptor distribution, viral entry and affected organs as well the interference with antiviral signaling.... 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
  • 62 views

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
  • 104 views

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 study associating casual marijuana use with brain abnormalities and pose these questions.... 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
  • 83 views

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...

-- Read more on ScientificAmerican.com

... Read more »

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
  • 80 views

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
  • 18 views

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
  • 67 views

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
  • 08:00 PM
  • 47 views

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 regulatory agencies should not rush to enforce new mandates based on limited scientific data.... 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 11, 2014
  • 12:46 PM
  • 105 views

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
  • 147 views

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.
... Read more »

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 8, 2014
  • 11:45 AM
  • 88 views

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
  • 137 views

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
  • 91 views

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.
... Read more »

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
  • 86 views

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  

  • March 28, 2014
  • 09:57 AM
  • 33 views

Patching the Leaky Pipeline of Women in STEM

by amikulak in Daily Observations

March is designated Women’s History Month in the United States, recognizing “generations of women whose commitment to nature and the planet have proved invaluable to society.” And yet, as we […]... Read more »

  • March 26, 2014
  • 06:45 PM
  • 112 views

The Ugly Ducklings of Science

by Neuroskeptic in Neuroskeptic_Discover

A group of management researchers provide new evidence of a worrying bias in the scientific process – The Chrysalis Effect: How Ugly Initial Results Metamorphosize Into Beautiful Articles ( via Retraction Watch ) The issue they highlight – the ability of researchers to eventually squeeze support for a theory out of initially negative data – […]The post The Ugly Ducklings of Science appeared first on Neuroskeptic.... Read more »

  • March 26, 2014
  • 05:04 PM
  • 86 views

Encephalitis lethargica and Influenza: a case of mistaken identity with a twist

by thelonevirologist in Virology Tidbits

Following the Influenza epidemic in 1918, physicians observed an increase in cases of Encephalitis lethargica (EL), the acute (often lethal) phase followed by post encephalitic parkinsonism (PEP), the latter affecting patients for several decades.

Based on the observation that these patients might have been infected with the 1918 Influenza virus, the conclusion was reached that a long-term consequence of Influenza might be the development of a neurological disease. ... Read more »

Ward AC. (1996) Neurovirulence of influenza A virus. Journal of neurovirology, 2(3), 139-51. PMID: 8799206  

Nichols JE, Niles JA, & Roberts NJ Jr. (2001) Human lymphocyte apoptosis after exposure to influenza A virus. Journal of virology, 75(13), 5921-9. PMID: 11390593  

Dale RC, Church AJ, Surtees RA, Lees AJ, Adcock JE, Harding B, Neville BG, & Giovannoni G. (2004) Encephalitis lethargica syndrome: 20 new cases and evidence of basal ganglia autoimmunity. Brain : a journal of neurology, 127(Pt 1), 21-33. PMID: 14570817  

  • March 25, 2014
  • 12:02 AM
  • 98 views

“I am Working-Class”: Self-Identification as a Measure of Social Class in Educational Research

by Mark Rubin in Mark Rubin's Social Psychology Research Blog

Governments around the world are trying to open up higher education to working-class people. For example, in January this year, the White House released a report titled: "Increasing college opportunity for low-income students: Promising models and a call to action." In the context of this general push towards widening participation in higher education, my colleagues and I have been developing a research project that aims to investigate social class differences in social integration among students atuniversity. After all, we need to bring working-class people into our universities socially and psychologically as well as physically. As we developed our research project, we quickly realised that the measurement of social class is an extremely contentious issue, with different researchers often preferring different measures. In particular, we noticed that there was a clear divergence between social psychologists and educational researchers in the types of social class measures that they used. Following the recommendations of a 2006 American Psychological Association report on measuring social class, modern-day social psychologists use subjective, self-identification measures of social class alongside more objective measures of income, occupation, and education (for a good example, see Michael Kraus’work). In contrast, educational researchers have tended to restrict themselves to objective measures and to ignore the more subjective aspects of social class (for a recent review, see Rubin, 2012; for a notable exception, see Ostrove & Long, 2007). We have discussed this interdisciplinary discrepancy in a recent review article published online this month in Educational Researcher. In our article, we call for educational researchers to follow the lead of social psychologists and complement (not replace) their objective measures of social class with measures of subjective social class. We believe that subjective measures are not only valid and reliable but also more direct and sensitive in their assessment of social class compared with objective measures. Most importantly, subjective measures tap the social identity aspect of social class, and they give a voice to students’ own opinions about their social class.

For further information, please see the following article: Rubin, M., Denson, N., Kilpatrick, S., Matthews, K., Stehlik, T., & Zyngier, D. (2014). "I am working-class": Subjective self-definition as a missing measure of social class and socioeconomic status in higher education research. Educational Researcher DOI: 10.3102/0013189X14528373... Read more »

  • March 24, 2014
  • 04:30 PM
  • 104 views

Molecular aspects of Ebola and other Filoviruses

by thelonevirologist in Virology Tidbits

In the last few days news organizations reported an outbreak of Ebola in West Africa, leading (as of March 24th) to a death of 59 out of 80 infected people. The Ebola virus and its variant Marburg virus are known to be one the most lethal viruses infecting humans. Once infected patients die of hemorrhagic fever, a painful and agonizing death characterized by fever, excessive blood loss and diarrhea. There is no effective therapy, except replacing fluids, blood, coagualnts as well as relatively generic measures such as the administration of Immunoglobulin or antiviral pharmaceuticals such as Ribavirin or S--adenosylhomocysteine (SAH) hydrolase inhibitors. Antibiotics are also given to prevent secondary infections should the patient survive. Novel treatments include the use of antisense RNA, which has been shown to treat infections in non-human primates under experimental conditions. The application of a recombinant vesicular stomatitis virus expressing the Glycoprotein from Ebola has been developed as well and might prevent death of the patient.  In order to prevent the infection from spreading into the community, patients have to be quarantined and caregivers have to wear protective clothing. The mortality is high, varying from 90% in the case of Ebola Zaire to 34% to Ebola Bundibugyo; a special case might be Ebola Reston, which did not cause any fatality among humans –although it is not clear if humans can get infected in the first place.The following strains of Ebola virus have been identified during past epidemics:Ebola Zaire (1976)Ebola Sudan (1976)Ebola Côte d'Ivoire (1994; also known as Tai Forest Virus and may only be a close relative to Ebola)Ebola Reston (1994; Simian Hemorrhagic Fever Virus, not infectious for humans)Ebola Bundibugyo  (2007)The prototype of Ebola, Marburg Virus (closely related to Ebola but distinct from) was identified in the 1960s to be the causative agent of a small epidemic of hemorrhagic fever among animal care workers in Marburg/Germany and Yugoslavia with a fatality rate of 23-90%. In general the first symptoms of disease include a general malaise with Influenza-like symptoms, including fever/chills, chest pain, and phryngitis. If the central nervous is affected symptoms include severe headache, depression, confusion, fatigue, and coma. The most visible symptoms include hemorrhagic symptoms - such as bleeding at injection sites, and hematomas. Death generally occurs because of low blood pressure, tissue necrosis and multiple organ dysfunction. 0 0 1 16 94 East Carolina University 1 1 109 14.0 Normal 0 false false false EN-US JA X-NONE ... Read more »

Mühlberger E. (2007) Filovirus replication and transcription. Future virology, 2(2), 205-215. PMID: 24093048  

Kiley MP, Bowen ET, Eddy GA, Isaäcson M, Johnson KM, McCormick JB, Murphy FA, Pattyn SR, Peters D, Prozesky OW.... (1982) Filoviridae: a taxonomic home for Marburg and Ebola viruses?. Intervirology, 18(1-2), 24-32. PMID: 7118520  

Hoenen T, Shabman RS, Groseth A, Herwig A, Weber M, Schudt G, Dolnik O, Basler CF, Becker S, & Feldmann H. (2012) Inclusion bodies are a site of ebolavirus replication. Journal of virology, 86(21), 11779-88. PMID: 22915810  

Iwasa A, Halfmann P, Noda T, Oyama M, Kozuka-Hata H, Watanabe S, Shimojima M, Watanabe T, & Kawaoka Y. (2011) Contribution of Sec61α to the life cycle of Ebola virus. The Journal of infectious diseases. PMID: 21987770  

  • March 23, 2014
  • 02:30 PM
  • 121 views

Nanopillars of nanotubes! A novel method to drastically improve charge transport in hybrid nanotube devices

by Jonathan Trinastic in Goodnight Earth

A new article demonstrates a method to drastically increase the conductivity of hybrd CNT-polymer devices using nano-engineering!... Read more »

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