Domain: plospathogens.org
Stories and comments across the archive that link to plospathogens.org.
Comments · 6
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Re:Good, but not for the reasons I had hoped for.
I don't think there's any reason to believe that being out in miserable weather will make you sick -- not if you're maintaining proper body temperature, at least. That's some wives' tale that has lived way past its expiry date.
When was that expiry date, again?
Turns out Influenza, at least, depends a lot on air temp and humidity. Regardless of your body temperature...
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As a flu researcher...
The linked summary article is so much technobabble. Slashdot is full of smart people who can handle a link to an open access journal article...
Go to http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1001034 to find out that the lack of a Lysine (K627) in the PB2 gene would normally prohibit this virus from replicating in humans, but is compensated for by the presence of a Arginine (R591) residue. These are both basic amino acids, and are located near each other on the structure. So, just a standard compensatory mutation - the sort of thing flu does all the time.
This is a nice bit of science, but it hardly explains the cause of the whole pandemic (this was a Franken-virus cobbled together from 4 other viruses). More science, less sensationalism, please!
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Re:Sounds good...
Based on a few papers I found and a few quick, back-of-the-envelope calculations, it should help at least 10.3% of the infected population and at best will help 96%. The huge amount of variability comes from not knowing much about superinfection in HIV. I'd also like to know what strains VRC01 and VRC02 specifically
/don't/ target; if the researchers are referring to HIV-1M, O, and N and HIV-2, then "over 90%" means 23/25 is covered, so I'm betting HIV-1N [see http://commons.wikimedia.org/wiki/File:HIV-SIV-phylogenetic-tree.svg ]---but, who knows.Anyway---for every 100 person-years, there will be a few HIV reinfections in HIV-positive individuals, sometimes by viruses of the same exact subtype, sometimes by viruses of differing subtypes. Sometimes the viruses are more virulent than the original infecting strain of HIV. The time elapsed since the original HIV infection does not seem to make an impact on the distribution of times of second HIV infections. (Yes, I know that sentence could use re-wording, but exactly how is eluding me atm.)
http://jama.ama-assn.org/cgi/content/full/292/10/1177 suggests 5.0 reinfections per 100 person-years (population size 78) in SoCal, http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.0030177 suggests 3.7% reinfections (population size 36) per 100 person-years in Kenya, and http://jvi.asm.org/cgi/content/full/79/16/10701?ijkey=30fccead91569e63031af4357a242da634620d52#SEC3 suggests 10.3 reinfections per 100 person-years (population size 20). A weighted average of these numbers, where the weights are the population sizes (not the best approach, but given the sparse amount of data found in the literature about this particular topic in general, it's better than no weighting, perhaps), comes out to 5.0 reinfections [reinfection or superinfection is very hard to define for HIV---see the methodology in the second article for more information about this] per 100 person-years. So if we look at http://en.wikipedia.org/wiki/File:HIV_time.png a timeline...If we assume the number of reinfections a year is simply the reinfection rate (5.0/100 to get per-year) multiplied by the HIV-positive population that year, and guess that none of the population in 1980 (where the timeline starts) was superinfected, we get 22.7 million in 2008. If the population in 1980 had all been superinfected, we get 30.0 million in 2008.
On the other hand, if we assume that only the increment in HIV-positive population is eligible for reinfection (a lousy assumption, but with how little is known, it's as good as any---actually, I'm partly going off of the notes in the introduction of the second article about the known information about reinfection rates), and just multiple the difference from year-to-year in the HIV-positive population by the reinfection rate, we get 1.31 million. (It would not make sense to include the 1980 population here, based on the assumption made.)We don't really know enough to guess, but we can probably assume there would be at least an easily noticeable impact. A 10% drop in HIV population would be very obvious---that's a few million people.
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Re:change is a comin'
I'm a biochem post-doc working in a molecular-microbiology lab. We're studying E.coli O157:H7 and attempting to inhibit intimin formation.
intimin is a protein on the surface of the cell membrane which allows the bacteria to adhere. no intimin and the bacteria stay in solution, therefore no more quorum sensing, no more bio-film and no infection! voila!
Sounds easy, right? Those little critters just won't cooperate though!
But, back to papers. At the institutions I've been at it's quantity first, quality 2nd, and brand-name distant 3rd. Quantity is easy. Quality is harder - it's best judged over time by the number of cites. If your peers cite your papers as the basis for their work, you're doing something right. Scientists are being rated by their citations now.
As for brand - no one really cares if you publish in Cell, Journal of Bacteriology, Molecular Microbiology or PLoS Pathogens. (unless, of course it's top-tier Science/Nature/PNAS, etc. any guess as to what percentage of submitted papers those top tiers represent?)
Why would you give your work away to some publisher so they can make a buck? What do you get out of it? You give them your paper. Signing the copyright over to them. You work for them for free, peer-reviewing papers so they can have a peer-reviewed journal. And then they make $$$ money selling them, restricting their audience, and give you nothing. That seems right to you? Just so you can say your insignificant little paper [>90% are] was published in XXX journal?
I don't care if I never make a major discovery, but if the guy/gal who "cures" EHEC cites my work on intimin formation my scientific dreams would have been fulfilled. I will have participated in what Newton described with "If I have seen further it is by standing on the shoulders of giants".
rho
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Re:How to filter low impact sciencePLoS Pathogens has an Impact Factor of 6.0 in Journal Citation Reports. Less than the 29.2 of Cell, 30.0 of Science or 26.7 of Nature, but close to the 9.6 of PNAS (bigger is better). That's certainly not low impact; the vast majority of journals are closer to 1.0 Impact Factor. And it's a journal that's less than three years old (started September 2005)!
Seriously, have you not heard of the Public Library of Science? It's the attempt to break the stranglehold of the for profit publishers. The content is published under the Creative Commons attribution license, and anyone can download it -- unlike most scientific publications, which require a subscription. It's completely peer reviewed, and been extremely successful. The oldest journal, PLoS biology (from 2003), has a 14.1 impact factor. They are, very definitely, peer-reviewed -- you wrote this without apparently even reading the webpage for PloS Pathogens?
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How to filter low impact science
I'm always suspicious whenever I see ostensibly "high-impact" summaries that link to press releases of work that is either unpublished or published in low impact journals. In this case, I haven't looked up the impact factor of the journal PLoS pathogens (article), but I do biophysics research on HIV and I've never heard of this journal. As a useful general rule, science articles shouldn't appear on here (and waste everyone's time) unless they've been submitted through a peer-reviewed journal (not the case here), and I think they should hit high-impact journals like Science, Nature, Cell, PNAS,
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