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Paolucci et al: 2 out of 12 CFS patients positive for MuLV

Discussion in 'XMRV Research and Replication Studies' started by natasa778, Jul 31, 2012.

  1. RustyJ

    RustyJ Contaminated Cell Line 'RustyJ'

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    Ah, you're referring to science by consensus, because to say Mikovits was not cautious would be a naive oversimplification, especially since the very same researchers who had been dabbling in tissue steeped with contamination for decades, not knowing it was there, are the ones crowing about MRVs not being in humans. Notwithstanding that Mikovits took two years to come to her conclusions. Certainly she did not make any sweeping statements that she could not support with her data.
    xrayspex likes this.
  2. natasa778

    natasa778 Senior Member

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    LOL spot on
  3. Tito

    Tito Senior Member

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    Do we know why only 12 patients were tested and not 50 or 100?
  4. RustyJ

    RustyJ Contaminated Cell Line 'RustyJ'

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    Presumably to limit the number of positives, lol. Sorry, couldn't resist. It is a good question. I also would like to know the answer to this.
    Tito likes this.
  5. Tito

    Tito Senior Member

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    Lol
    It is also what I thought but I did not want to publicly express my cynicism. Lol
    :)
  6. Firestormm

    Firestormm Guest

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    Hmmm... you could always ask the study authors I suppose...
  7. JT1024

    JT1024 Senior Member

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    While I agree with "Open Access and Open Data", taking all registered experiments and counting that data would be not be appropriate use of statistics. Assay design matters... unless there is political or financial motivation as seems to be the case in much of scientific literature today.

    In many cases, poor study design results in poor results. When negative controls are positive, something is wrong with your assay. That is why you utilize quality control. I work in a clinical laboratory and utilize this daily.

    To throw the control values (0/40) in with the cohort being studied (2/12) is deceptive IMHO.
    RustyJ likes this.
  8. Snow Leopard

    Snow Leopard Senior Member

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    Because this was a pilot study with limited funding...
  9. Tito

    Tito Senior Member

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    I understand but when a sample is so small, the whole study becomes irrelevant. And the money is completely wasted. Testing 48 patients instead of 12 does not cost 4 times the initial amount, because the setup of the protocol is the same, the statistical analysis of the results costs the same or almost the same, it is just the marginal cost of the "ingredients" and use of devices. So it might cost twice the cost of a 12-patient study but it would be much more relevant.
  10. Tito

    Tito Senior Member

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    What puzzles me is that on one side we have 12 patients and on the other side 40 controls. Why not taking 26 patients and 26 controls? It would have cost exactly the same.
    pollycbr125 likes this.
  11. natasa778

    natasa778 Senior Member

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    O`Keefe on Paolucci paper;

    http://okeefe-lab.blogspot.co.uk/2012/07/new-study-finds-low-levels-of-mlv-gag.html#comment-form


    in the comments she discusses again the curious case of everyone finding gag sequences only...

    RustyJ and currer like this.
  12. natasa778

    natasa778 Senior Member

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    Probably for the same reason that those with positive findings are not bothering or trying to publish at all, as mentioned by O´Keefe recently... Probably the same reasons that made them patent before attempting to publish, IF they do. The air is just too contaminated with reactionary noises at the moment.
    xrayspex and currer like this.
  13. natasa778

    natasa778 Senior Member

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    Yes would be good to know the reasoning, although it could be something as simple as them having quick access to that many stored samples in a fridge somewhere nearby... not having funds to collect fresh samples etc...
  14. asleep

    asleep Senior Member

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    I believe the probability is actually 12/52 * 11/51 = 4.97%, which by convention is statistically significant (if only by half a nose hair). It would be nice, though, to see more detail about their methods.

    As others have said, this result strikes me as about what one could expect from a positive study with a (possibly) less rigorous patient criteria, a (possibly) less sensitive test (considering known limitations of PCR esp. in the context of unknown sequence variation), and other issues such as transient blood viremia.

    It is becoming comical what lengths researchers are having to go to in order to get past the publication censors with results that run counter to the ordained "consensus." Coffin's hypothetically assumed recombination must be referred to as an established "fact" if you want to be published. Any positive findings must be presented in the absolute most negative light, often involving logical and semantic contortion that would make the average Cirque du Soleil troupe blush.
  15. Mark

    Mark Acting CEO

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    Ah yes, quite right, how foolish of me. :redface: Thanks for correcting that schoolboy error. :D
  16. Firestormm

    Firestormm Guest

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    Anyone care to explain or help me understand/interpret the highlighted parts below from the full paper please?

    'It is however intriguing that the only positive results were obtained in these patients. On the other hand, in both cases the positivity could not be confirmed by the amplification of a different virus gene. The proviral DNA amount was very low in our patients, which might explain the stochastic amplification of a single virus gene in each of the two positive patients. Another possibility is that only fragment of virus DNA might be present in biologic samples.

    In conclusion, while it appears established that XMRV/MLV sequences are not detectable in a significant proportion of CFS patients, the frequency and the role of evolutionary relic retrovirus sequences potentially detectable in the human chromatin remain to be further elucidated.'

    http://www.newmicrobiologica.org/PUB/allegati_pdf/2012/3/341.pdf

    Thanks.
  17. Wally

    Wally Senior Member

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    Currer,

    I believe you are looking in the right direction. Sometimes when one issue hits a roadblock, it may have more to do with its impact on other issues. I think it is worthwhile to keep exploring these potential connections.

    Wally
  18. alex3619

    alex3619 Senior Member

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    My best guess is that given the controversy this number of patients was about all they could get funding for. Though I think the suggestion to ask the authors is a good one. I have done that in the past on papers, and found them very receptive. Bye, Alex
  19. natasa778

    natasa778 Senior Member

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    see O´Keefe´s plus other comments on her blog
  20. Bob

    Bob

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    I've read it now, and the results don't seem very impressive.

    Firstly, the fact that no controls contained any sequences, is the first indicator that control subject samples and patient samples could have been handled differently. I would expect that at least one of the control samples might show up as positive, if the positive results were not based on contamination. (But this would not necessarily be the case, considering the low numbers involved.)

    Secondly, the sequences that they detected are not helpful, as per my current understanding. The first sequence, 'CFS Pavia-1', was similar to Lo's sequences, but not the same, but it was 100% identical to a polytropic mouse virus.
    And the second sequence, 'CFS Pavia-2', was 100% the same as XMRV VP-62.

    The fact that the sequences were 100% identical to XMRV VP-62 and an ERV is not helpful, with regards to proving it is a human virus. It suggests that it could be contamination.

    That's my understanding so far, but I might have misunderstood something.

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