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Lipkin Study - more concerns

Discussion in 'XMRV Research and Replication Studies' started by jace, Jan 8, 2012.

  1. jace

    jace Off the fence

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    This is basically Gerwyn's work, with a bit of sub-editing by me. I'll be interested to see how people respond to it.


    We all know that an MRV is only detectable by for a short time in the blood following innoculation. Thereafter it is readily found by PCR in lymphoid tissue, notably spleen, lymph nodes, tonsilluar tissue, lung tissue and intestines. We also know that for complex reasons the antibody response fades and also becomes undetectable.

    This is typical of the behaviour of many other gamma retroviruses. They infect B cells in the lymph nodes first and then spread to other secondary lymphoid tissues. They infect a class of B cell which ultimately resides in the peritoneal cavity. They also infect recycling CD20 B cells because those cells pass through the spleen and a very low percentage of them will become infected.

    The trouble is that these cells quite literally burst after a few days. Memory B cells are also a target for infection but after a short time in the blood they home in on lymphoid tissues again. The basic message is that multiple samples at multiple time points need to be taken from an infected patient to have any sort of chance of detecting a MRV in blood samples.

    The Lipkin study involves samples taken from a patient on the same day. We also know that the people have been "trying" to find a MRV in people with ME have set their tests to dectect a synthetic clone which does not exist in nature. Obviously they have no chance of detecting a real MRV in infected patients.

    They are going to be using this method again in the Lipkin study. Lipkin knows that XMRV (VP62) does not exist in nature so 75% of the researchers will be using tests which have no chance of working. This will leave Dr Mikovits and Dr Ruscetti attempting to detect an MRV in blood samples taken from chronically tired people on the same day. They are both brilliant scientists but contrary to their detractors views there is no evidence that they have magical powers!

    Even if by some incredible feat of ingenuity they are able to detect some virus in some people the difference between the number of ME positives and the numbers of CONTACT controls is certain to be obscured. Either way we lose. The Lipkin study has an excellent design for governments and corporate interests but a dire design for people with ME.
     
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  2. currer

    currer Senior Member

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    It is hard to second guess these decisions, jace we are so far removed from how they are made.....

    Dr Snyderman seems to trust Lipkin and I trust Dr Snyderman. That is the best I can do.

    I suppose they want a fairly close replication of the original paper and are not looking further yet. Perhaps extra ethical barriers would exist if they asked for permission to extend their study to look in tissues.

    It would be nice to get some tissue studies done.....but we are not being offered that now.
     
  3. snowathlete

    snowathlete

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    Personally i dont agree with that. I think the study is as well designed as we (or any disease group) is likely to get. The study is massive, and involves all the players - even the questionable ones, so that everyone is happy and can be a part of it. Even the people who Lipkin initially got slagged off for not including are involved - so in the end that was misinformation, because he had gone to great lengths to keep those people involved. If this study was any bigger, or more complicated, i wonder if it would ever get finished.

    Perhaps its sounds straightforward to some , but if you think about even just the logistics of running this study, what with all the different people and labs involved, and the number of samples being tested, its a massive task, and if you were to increase the number of samples, say by taking two from each patient, you double the work just to increase by one more data point per patient and how many would you need - where do you draw the line? 3, 5, 8?

    I also think that with all our ME/CFS experts involved, they must be pretty happy with the study and how its put together, else, why would they be in it, and i get the impression from the things that Lipkin has said that he really has respect for all the people involved, as they have worked in this area for a long time. I think they must have all had involvement in the setup of the study.

    If this study does find something conclusive, then clearly there will need to be more work focused in that area to nail the results down more accurately, and discover more about it, but that would be a follow on study that would be designed upon new knowledge and facts to help focus it and get more benefit out of it, and so im not particulary concerned that there are no tissue studies and stuff like that yet.
     
    Firestormm likes this.
  4. Esther12

    Esther12 Senior Member

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    Both the BWG and the Lipkin studies are well designed, and should allow anyone who had a blood test able to distinguish between samples from CFS patients and healthy controls to show that this is the case.

    Does Gerwyn really believe that Mikovits of Ruscetti have such a test? If so, then this should be shown in the Lipkin study. While perhaps multiple samples from different time points may be preferable, single samples should reduce the positive rates for both controls and CFS patients, meaning that clearly different rates of detection should still occur if there were really any association.

    It sounds like Gerwyn has realised the evidence is now strongly against an association between CFS and MRVs, but still wants to keep the story going for some personal reason.
     
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  5. currer

    currer Senior Member

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    The problem is that G is making claims about the assays to be used for the PCR testing.

    Now how does he know this and where is he getting his information from? Perhaps he cannot tell us. But we have to assume good faith on the part of the researchers unless we can prove otherwise...and thats it...proof.

    I feel equally dubious about the politicking I see, forced retractions etc. But unless G can show evidence, we cannot know how accurate his claims are either.

    The Lipkin study will not by itself lay the ghost of "XMRV" even if it is negative because of the history of manipulation of access to publication and the clear vested interests involved in a negative outcome.

    If "they" have the intention of "fixing" this study I am sure they will be able to do it easily so protests from us are futile. Sorry to be so cynical.

    Science itself is the real casualty.
     
  6. Andrew

    Andrew Senior Member

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    All this is well and good, but when blind testing shows a higher level of XMRV in controls than in patients, the reasonable conclusion is not that the XMRV is being evasive. It suggests that something is wrong elsewhere. Also, there was a flaw in the original Science study, which I never mentioned before. But now that things have progressed this far, I don't think this will change anything. Mikovits said that they tried harder to find XMRV in patients. They drew more blood, ran more tests, etc. This creates a built in bias. The tests should have been just as rigorous on subjects and controls. Because if there were false positives or contamination, this would give as much opportunity for this to show up in controls.

    But I do agree that blood tests are not necessarily revealing. The Rhesus studies demonstrated this. And so we really won't know until they start doing autopsies on CFS patients. And what I'd like to know is if any of the legitimate CFS researchers or funding foundations out there are willing to do this.
     
    oceanblue likes this.
  7. Daffodil

    Daffodil Senior Member

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    i've heard from 2 reliable sources now that retrovirus is being found...i pray this is true. so many lives hang in the balance.
     
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  8. Tony Mach

    Tony Mach Show me the evidence.

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    No, no, no. We don't "all know" that. First of all I suspect that you mean MLV-related viruses, when you write "MRV". And second of all, you provide no evidence for this supposed common knowledge. Whatever argument you want to make, it fails at your first argumentative sentence.

    And I have a question for Gerwyn: I thought when Dr. Mikovits tests the blood of 101 ME/CFS patients, she finds evidence for XMRV in the blood of 99 out of these 101 patients. How do you reconcile your statement with Dr. Mikovits' statements?

    And another question for him: Did you send your concerns to Dr. Mikovits? If yes, what did she answer? If no, why don't you warn her?
     
    Firestormm likes this.
  9. snowathlete

    snowathlete

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    I didnt know this before, but i cant say im surprised. The thing is, its sloppy. Very, very sloppy.

    As someone who made a living from designing tests and generating reliable end data from them across complex systems, I find it very annoying.
    Its fine to do that intially (sensible even) but when you then find something you need to start checking to the same degree in the controls. If you dont, then at best, you are taking a huge risk that others wont be able to replicate your results, or will find radically different numbers of positives, because they will treat the two groups the same, and you didnt.
    You are leaving yourself open to being discredited.

    And worse than that, you are creating a scenario where you might truely find something, but it wont be replicated, and subsequently, no one will believe you. This is worse, perhaps, than never finding it in the first place, because people are completely thrown off the trail by it.

    Given this new info, i feel very lucky that this big Lipkin study exists, because we could easily have got to this point, with lots of negative studies and no big Lipkin study at the end to try extra hard to replicate the results.

    Of course, it might just turn out that XMRV exists, and is in almost everybody - we just dont know until all the samples are tested to the same degree.

    I still hope that something positive will come off this and that we are found to have a retrovirus at much higher levels than controls, but i suppose we will just have to wait and see! Lets hope!
     
    ukxmrv likes this.
  10. RRM

    RRM

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    Gerwyn is now thinking the Lombardi study was false then, surely?

    After all, they had no problem finding it in the blood of 68 out of 101 patients, and Mikovits later reported that it had actually become 99 out of 101. Also, from the 8 blood samples they received from Lo, Mikovits has reported that they've detected XMRV in all 8 samples.

    This is a rather bizarre argument, in my opinion. Gerwyn is apparently basing his opnion on the macaque study, in which the monkeys were injected with VP62.

    So the artificial lab construct VP62 is totally useless and not reflective of actual infection.....unless you like the results (which don't even suport his position by the way)?

    I am sure this all sounds pretty nice but it is not a valid argument. Again, like Esther basically explained, the Lipkin study is designed to specifically test the earlier claims by Lombardi et al. and Lo et al. that there are gammaretroviuses to be found in the blood of ME/CFS patients.

    When you don't believe the virus is in the blood, the original studies are wrong and there is no basis to test for them in tissue in the context of a validation study.

    Of course, any scientist (including Mikovits) can hypothesize that a gammaretrovirus is to be found in (for instance) lymphoid tissues of ME/CFS patients. The correct way to follow up on this is for that scientist to get some patients' lymphoid tissues (and of course some controls' tissues), do PCR/serology/whatever other test you have, and see if you can discriminate between patients and controls. If your data is looking robust enough, I am sure that plenty of editors will be happy to publish such a finding.

    And then other scientists can try to validate and/or follow up on that work.

    Again, there is really no need for this. No "positive" study had to take samples at multiple time points to reliably discriminate between patients and controls. Mikovits and colleagues even published an addendum to the Science paper that was specifically created to "further detail the multiple detection methods [Lombardi et al.] used". There is absolutely no mention of having to take multiple samples at multiple time points in the paper.

    There is (to my knowledge) actually no published evidence whatsoever that any scientist has "set" their tests to detect the synthetic clone VP62. Most scientists do indeed include a sample spiked with Vp62 (or 22Rv1) as a positive control, and that is perfectly regular and acceptable.

    In fact, in light of the new "problems" about finding XMRV in blood, the whole argument (while already being invalid) about using "known positives" becomes moot. After all, which sample(s) can you then really use as "calibration" when any positive sample may actually be negative at any given time? The "calibration" will essentially become a detection test in itself, because a negative outcome on a positive calibration sample may be either due to a) this sample really being negative at this time point or b) your test not being "optimized" to detect the virus (so you'd have to find a "true positive" to check on this, which "true positive" might not be actually...etcetera)

    Without first providing any criticism of the study's cohort, suddenly this study will be investigating "chronically tired people". Weasel words, really.

    I guess I am being seen as the "enemy" by some, but (besides it being a baseless argument because the same physicians as the ones from the original studies are involved, as well as Mikovits herself) I find this insulting to the patients involved in this study, some of which are posting on either of the main two (or three) ME/CFS forums. Damn those scientists who don't think this is a purely physical disease, but the people who are selected for this study by Montoya, Peterson, Komaroff and three other pretty well respected physicians, must surely be misdiagnosed fatigued lazy people? Sure.

    The only labs involved are Lo, Switzer and Ruscetti/Mikovits, so it's either 66.7% or 33.3%, by the way.

    There is to my knowledge no information whatsoever on "contact controls"

    And "some incredible feat of ingenuity"?

    It didn't seem to be needing "some incredible feat of ingenuity" to perform these experiment when Mikovits criticized the likes of McClure and Van Kuppeveld (and several others after that). All it needed was perfect replication and/or "known positives" as controls. Now, two years after they began telling everyone that they were doing it wrong, Mikovits and Ruscetti can do everyting the same as in their original study and use as many "known positives" as they want, invloving a cohort that has been carefully selected and approved by them (and the other authors)....

    ...and now it apparently needs a miracle for even the original scientists to discriminate between patients and controls?
     
  11. currer

    currer Senior Member

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    Thanks daffodil,
    I hope the rumours are true. I am tired of listening to malicious criticisms of Drs. Mikovits and Ruscetti. They make me feel ashamed of the human race.

    The contention that virologists with the experience and expertise of the Ruscettis do not know how to find a retrovirus and have made elementary mistakes in their research is self-evidently absurd.

    It is only the power of the opposing side to continually publish and reiterate its propaganda that can make people confused and doubtful.

    The scientific evidence is still unrefuted as proper replication studies have not been done.
    The mandate of the BWG was to create rapid throughput assays, no more. It cannot be used, as it has been, to go beyond its' original design to try to undermine the Lombardi research and to state that HGRVs do not exist.

    This is a political, not a scientific statement.

    I agree with Gerwyn's analysis of the scientific issues at the beginning of this thread - I just want to say that, - as I feel his analysis has been unfairly criticised - but I doubt that the design of the study can be changed at this stage, and although it is right to point out the potential pitfalls of the design, we also have no choice but to accept the decisions of those running the study.

    The Lipkin study can only show two things.
    It will either prove that there is a retrovirus associated with ME or it will be inconclusive.

    It cannot end the debate because sufficient doubt has been generated by the manipulation of evidence and the attempts to restrict free unbiased debate and access of both sides to publication that we have witnessed, that trust in the veracity of the scientific process has been undermined.

    The power of political and financial considerations to interfere with the search for scientific truth and to silence dissent has been amply and disturbingly demonstrated and will not be forgotten.
     
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  12. Firestormm

    Firestormm Guest

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    I actually queried whether this came from Gerwyn on the other forum. Simply because I couldn't believe it had. Now it seems it did I am actually rather stunned: http://www.mecfsforums.com/index.php/topic,11084.0/topicseen.html

    Great breakdown there RRM and from others above as well. The original post is a fallacious argument and contains too much supposition presented as fact by the author(s). The Lipkin Study is about Lombardi and Lo - as has been said - period. Anything else - including anything that is 'found' as a result of this study - or any avenues of research resulting thereof - will need new papers to be published.

    We also know next to nothing about the Lipkin Study and certainly not enough to jump to the conclusions exhibited in the first post. But we do know - and there are several threads now about this that contain the following information - a little about how the samples will be treated. Enough perhaps to not be able to conclude that the odds are somehow staked against Mikovits and/or Ruscetti or even Lo and/or Alter for that matter:

    September 2010: http://blogs.wsj.com/health/2010/09/08/world-class-virus-hunter-to-head-up-the-latest-xmrv-study/

    November 2010: http://blogs.wsj.com/health/2010/11/17/gearing-up-for-the-big-search-for-xmrv/

    The study has grown in size - in relation to patient samples - and also the 'WPI' are no longer involved of course.
     
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  13. Firestormm

    Firestormm Guest

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    This is another old, old, old, old, 'argument'. Replication does not mean reproducing the exact same methods, the exact same conditions, the exact same environment, as supposedly happened in the Mikovits, Silverman, et al. labs. It means replication of the results - and of the conclusions reached.

    I know you won't buy that. I read the other day a reply to this very same point from 'Lance' someone I have come to respect as a scientist who comments on TWiV on occasion. This was how he put it:

    'A word on replication. In science, replication means asking the same question and getting the same answer. It does NOT mean using the same brand of Taq polymerase and having the annealing temperature within 0.1 C of the original experiment etc etc. It really doesn't matter about the miniscule differences between the papers in this field. These differences are far less than those you find in other fields - if you really want to see variability have a look at how flavivirus labs do their antibody neutralization assays. There are more methods than you've had hot dinners, yet the fundementals of the results are reproducible using the different assays. There is no reason why XMRV should be a special case. The arguments against XMRV infecting humans are way bigger/better than this.'

    http://www.virology.ws/2012/01/01/twiv-164-six-steps-forward-four-steps-back/

    No. The 'mandate' was to test whether or not the assays created by those who authored the paper alleging XMRV/MLVs could be found in the blood of patients and - don't forget - the healthy population (!). Those assays couldn't. Period.

    Not even going to go there :rolleyes:

    We don't know enough about the 'design of the study'. Are you saying that you do not 'trust' the experts involved in this MASSIVE undertaking to do their jobs? Or that - I don't know - they are somehow being forced NOT to do their jobs perhaps? I mean wasn't that another 'argument' levelled at the BWG study?

    As we don't know the 'study design' how on earth can anyone 'point out the pitfalls'? But RRM covered this much better than I. Far more eloquently.

    Yes and No. The 'Lipkin Study' will attempt the 'replicate the results' alleged by Lombardi et al. and Lo et al. That is pretty much all we know - so XMRV/MLVs.

    It will end the debate about Lombardi and Lo et al.'s 'associations' I think. Finally. And this is what I believe Mikovits herself (and others) was referring to in her statement about 'definitive' and being wrong and how science works.

    'That will be the definitive answer, she said. If were wrong and we cant reproduce it, then well be wrong, and thats how science works. '

    http://www.nytimes.com/2011/12/23/h...-retracts-chronic-fatigue-syndrome-paper.html

    Currer do you honestly believe that in response to the publication of Lombardi and the associations alleged by that paper that a new retrovirus was discovered in blood not only of patients but also of healthy people - did not prompt a MASSIVE and IMMEDIATE reaction from the scientific and federal/government authorities?

    Even Racaniello has been at pains to point out that none of this marks the 'end' of any future associations. And neither does it mean that scientists will stop looking - whether in CFS patients for a retrovirus or in other populations. It was and remains about the associations alleged by a single paper (in the main) that of Lombardi.
     
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  14. currer

    currer Senior Member

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    Firestormm, Dr Bieger's research in Germany carefully replicated the METHODS used by Dr Mikovits and succeeded in finding the virus.

    "Major advice throughout the experimental period came from J. Mikovits who was extremely helpful with methodological advice and testing of parallel samples including sequencing of XMRV specific viral DNA sections."

    http://forums.phoenixrising.me/showthread.php?15611-Dr-Bieger-and-XMRV&p=232418#post232418

    I remember Dr Lo saying in his talk how his tests had initially been negative, until he modified his protocols to adhere closely to Mikovits own ones...and then he found virus.

    So I do not find the quote you use on replication at all convincing, sorry.

    If Dr Mikovits is correct there will be serious consequences for the way medical care is delivered. We have seen corruption in other areas where large amounts of money and profit are at stake. Why not here?

    I suppose we differ on how willing we are to trust authority figures.
    I used to believe in the good faith of our representatives and institutions...I do not now after following the XMRV debate.

    Dr Yes is always good to read.
    http://www.mecfsforums.com/index.php/topic,11084.45.html?PHPSESSID=unjnfm36k8rfs7ogvmhvb76nr3

    "HGRVs do not exist" is a political statement because the prostate cancer studies are still unretracted. Even Switzer found HGRVs in his prostate cancer study.
     
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  15. currer

    currer Senior Member

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    (Quote) "Currer do you honestly believe that in response to the publication of Lombardi and the associations alleged by that paper that a new retrovirus was discovered in blood not only of patients but also of healthy people - did not prompt a MASSIVE and IMMEDIATE reaction from the scientific and federal/government authorities?"(Quote)


    Check out this link to the National Whistleblowers Centre
    http://www.whistleblowers.org/index.php?option=com_content&task=view&id=1220&Itemid=190

    "Most scientists have never been targeted for retribution by government, industry or academia. Usually, such treatment is reserved for researchers who gain public attention and directly threaten important government policies or corporate profits. To stop researchers who publish unwanted results, institutions have resorted to using false allegations of research misconduct as a weapon of choice. Scientists who are targeted in this manner suffer lifelong consequences, and the chilling effect it has on other scientists is profound. Few, if any, scientists are willing to step into the firing line of government or big industry and risk being martyred."


    "Unfortunately, there is no place for researchers targeted by government and industry to hide. Scientific societies and scholarly journals will broadcast allegations of research misconduct throughout the scientific community and to the mass media. Government inquiries and academic proceedings designed to protect scientists from false allegations of research misconduct are useless when government agencies and academic institutions are the source of the allegations. And, protections afforded under the law do not even recognize that research misconduct exists at the institutional level."
     
  16. alex3619

    alex3619 Senior Member

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    I am yet to be convinced of any corruption re XMV, but the allegation has been made that the BMJ has engaged in activities that can be considered a danger to public health. This is of course unproven, only allegation, but there is a call to have the BMJ investigated. Please note that the BMJ is probably the journal most pushing evidence based medicine.

    http://niceguidelines.blogspot.com.au/2012/01/whistleblower-scientist-dr-lewis.html

    In most cases where corruption/bias has been claimed I think that failures of normal processes are more likely to blame. For example, the review process on papers for journals appears like it all to often a club - it depends on whether you are in or out. We know that enquiries into specific medical claims are often blinded by limited scope of what can be included (e.g. NICE and ME) - they appear to be aiming at proving their preconceved ideas and not giving any credibility to evidence that refutes those ideas. This is because they are not coming from a scientific standpoint but a political one in my view. Similarly scientists are rewarded with funding and acclaim if they publish according to vested interests liking (Zombie science). With such rewards, it might well be easy to become biased without even being aware of it. In most cases, but not all, I suspect that the scientists involved think they are doing normal science and the right thing.

    With regard to corporations, they have a duty to shareholders not society, although they are required to stay within the law. So they promote things that support them, and don't fund research or activities that don't. This is Zombie science again but perfectly justified for the corporation, and not illegal.

    This is more about systemic failings in society, the legal system, and checks and balances rather than corruption, more often than not.

    Without a whistleblower, its very hard to demonstrate corruption unless someone makes a mistake.

    Bye
    Alex
     
  17. snowathlete

    snowathlete

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    its true that corruption does occur in almost all walks of life, and sometimes it can be quite complex and deep. Indeed, it is often the case that people become corrupted by the norms of the system that they work in and maybe dont even realise it themselves, but are still part of the corupt system.

    Still, there needs to be motive, individual or group, and there are plenty of possibilities for such existing. So although i dont see any solid tell tale signs of this - yes maybe those who are worried about it are right.
    BUT there is also motivation for people to find XMRV (Whether it does exist or not) for personal benefit, and group benefit, as well a moral benefit to some degree, so i think if XMRV can be found, it will be, because there are more people out there who would benefit from this discovery, than just Dr M and the WPI.

    I hope that is comforting for people, it is for me.
     
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  18. pollycbr125

    pollycbr125 Senior Member

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    How can this be possible when any samples they may have tested will not have been unblinded yet ? well thats my understanding anyway . I dont know how the Lipkin study will pan out but please do not start rumours as to the results with no evidence to back it up . Patients had a tough year last year with all that went on I dont think many can cope with false hope again . Lets just see what happens , Hopefully the study will find something but at this moment in time that would be impossible to know . Rumour and speculation was rife last year and tbh did a lot of harm . lets have a year with just facts please . I know people like to post messages such as this to give people hope but it can also be damaging too .
     
  19. Firestormm

    Firestormm Guest

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    Dr Bieger provided an update and never published if I recall. Thread is here: http://forums.phoenixrising.me/showthread.php?15611-Dr-Bieger-and-XMRV&goto=newpost I don't have time now to re-read or remember the content but am sure you have read it by now.
     
  20. acer2000

    acer2000 Senior Member

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    http://jvi.asm.org/content/early/2011/02/16/JVI.02411-10.abstract
     

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