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Lack of Detection of XMRV in Seminal Plasma from HIV-1 Infected Men in The Netherland

IamME

Too sick for an identity
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I am not concerned how my moderation style is perceived by those who don't agree with my decisions.
Maybe that's a problem? No-one is infallible.

Believe me, there are plenty of people who do!
As I am sure psychiatry loves it when people tell patients to shut up... doesn't prove anything.

I am not sitting here reading through every post on this forum. Posts only come to my attention when they are reported, so there has to be at least one other person who finds a given post offensive for any action to be even considered, let alone taken.

Now, you can continue to argue with my decision or you can go back to the discussion. What I am not about to do is to engage in argument with you over a moderating decision.
I hadn't said I expected anything else. None of that explains on why you agreed that the quote about the WPI was "offensive", so I'm not surprised you sidestep what you are incapable of defending.
 

Martlet

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I hadn't said I expected anything else. None of that explains on why you agreed that the quote about the WPI was "offensive", so I'm not surprised you sidestep what you are incapable of defending.
If you need specifics, such phrases as "get over yourself" and "are you, some hotshot lawyer for incompetent researchers or are you just naturally pompous?" are personally insulting and are against forum rules. The rest of the message was filled with sarcasm. Now you may find that acceptable behaviour, but it is not acceptible in this forum and this is my final word on that post.

And saying to me "so I'm not surprised you sidestep what you are incapable of defending" is also offensive. As Cort said some months ago, moderators will not be subjected to these types of attack. Please see your inbox.
 

thegodofpleasure

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PlosOne strikes again

Under the sub-heading "Ethics" I read the following:

The MSM were enrolled in a study protocol on the effect of HAART on semen quality.
Patients of the MSM group were not treated with antiretroviral therapy, before or at the sampling moment, while most men in the second group were treated with diverse regimens of antiretroviral drugs. Patient characteristics are summarized in Table 1.
So, the 25 heterosexual men were already on anti-retroviral treatment then ? :confused:

Little wonder that they didn't exhibit any signs of XMRV infection.

Also, a very small cohort, which, on the basis of background XMRV prevalence rate - 4% - could only have been expected to have yielded two XMRV+ve patients

PlosOne appears to have played another blinder !!!- what on earth do the Peer Reviewers think they were doing when they allowed this little gem to slip through their rather badly torn net ? :Retro mad:

TGOP
 

thegodofpleasure

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A better title for the article

The problem with the publication of "quickie" research papers like this one, is that the title can so often be misleading. Hence, if you don't read all of the detailed stuff, you can easily be drawn into making the wrong conclusions

Might it therefore be appropriate to rename this study :

Lack of Detection of XMRV in Seminal Plasma from a mere 29 HIV-1 Infected Men in The Netherlands ......... not suffering from prostate cancer and who aren't taking anti-retroviral drugs
 

Bob

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So, the 25 heterosexual men were already on anti-retroviral treatment then ? :confused:

Little wonder that they didn't exhibit any signs of XMRV infection.
90% of heterosexual men were taking anti-retrovirals, but none of the homosexual men were. (see the quotes from the study at the bottom of this post.)

I think what might be more relevant here is that this study, like all the other negative ones we've seen so far, was just unable to detect XMRV in the types of samples which they used, using the methodology which they used.


Also, a very small cohort, which, on the basis of background XMRV prevalence rate - 4% - could only have been expected to have yielded two XMRV+ve patients
A very good point. Such a small number of samples could be statistically insignificant. The researchers do not mention this in their conclusion.


PlosOne appears to have played another blinder !!!- what on earth do the Peer Reviewers think they were doing when they allowed this little gem to slip through their rather badly torn net ? :Retro mad:
From what I understand, researchers have to pay PlosOne to publish their studies, so there might not be much inclination for the journal to do very stringent peer reviewing.


Quotes from the paper regarding anti-retroviral drugs:

None of the homosexual men studied here were treated with anti-retroviral drugs, but from the heterosexual men, an argument for not detecting XMRV could be that 90% of them are taking antiretroviral therapy, resulting in HIV-1 viral RNA levels in blood plasma below the detection limit.
Although protease inhibitors specifically designed to inhibit HIV-encoded protease do not affect XMRV infection and replication, nor do non-nucleoside reverse-transcriptase inhibitors (NNRTI), XMRV is susceptible to the nucleoside reverse-transcriptase inhibitors (NRTI) azidothymidine (AZT) but not tenofovir in one study [22], or to AZT and tenofovir in another study [23].
I think that the authors are indicating that, with regards to levels of viral RNA in plasma, there might be a lower limit for detecting XMRV, just as there is with HIV (which seems obvious). It's a shame that the authors are not more explicit about this in their conclusions, and don't explicitly explain this as a possible reason for failure to detect XMRV.


Five percent of the seminal plasma samples from heterosexual men contained HIV-1
In our heterosexual patient group, at least 4 patients were taking drug regimens containing AZT, which could obstruct the detection of XMRV.
So only 5% of the heterosexual samples were testing positive for HIV-1. And these samples were all from HIV+ patients. So what chance is there for finding XMRV at this detection rate, when you'd only expect 4% of patients to be XMRV+ ?!
 

Bob

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Although HIV-1 was amplified from 25% of the seminal plasma samples, no XMRV was detected, suggesting that either the prevalence of XMRV is very low in The Netherlands, or that XMRV is not naturally present in the seminal plasma.
I think that they missed out a possible reason for not detecting XMRV... That they were using an inadequate methodology.
I notice that they froze the plasma samples to store them which, as far as I remember, the WPI had to stop doing with their samples when looking for XMRV.

Also, as far as I understand, the only detection method employed was PCR, which as we know, is not the most successful methodology for detecting XMRV.
I don't fully understand the WPI's methodology, but I would hazard a guess that this study doesn't come anywhere close to it.

Also, as thegodofpleasure mentioned in a previous post, the statistical likelihood of finding XMRV, in non-CFS patients, in such a small number of samples, where only 25% of samples (from HIV+ patients) tested HIV+, is almost zero.

A third alternative for the absence of XMRV in our samples could be that the XMRV found in other studies is an inadvertent laboratory contaminant, which has been reported before for other viruses, including another MuLV-related virus [25].
This demonstrates a lack of knowledge and understanding about the subject because, as we know, it is not possible for a person to have antibodies for a lab contaminant, and the genetic sequencing of XMRV shows that it is not a mouse virus, and the virus has been observed infecting human cells, and the genetic sequences of XMRV have variability which doesn't happen in contaminants, etc. etc. etc.


As a positive PCR control, we used diluted total nucleic acid extracted from the prostate carcinoma cell line 22Rv1, containing approximately 10 copies of integrated XMRV DNA and producing viral RNA, in each PCR reaction series.
They were looking for the type of XMRV which is found in prostate cancer, and this might not be the most prevalent strain of XMRV.


Quote taken from the Conclusion:
Taken together our results suggest that either XMRV has a low prevalence in this mainly Dutch patient group, as it cannot be found in seminal plasma of 54 HIV-1 infected men, a group with an increased possibility of acquiring sexually transmitted pathogens, or that it is not naturally present in the seminal plasma.
In my opinion, this is a strange and slightly dangerous conclusion, considering the limitations of the study.

Taking everything into account, these authors do not make any serious conclusions about XMRV at all, in my opinion...
This was just a small scale investigative research study, probably born out of curiosity, but not out of expertise in XMRV virology.
 

Rivotril

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Van der Meer/Kuppeveld get assisted by their Dutch friends from Amsterdam...
-Indeed still coming with the same Lake Tahoe crap (don't they read Science, where this misunderstanding was explained my mikovits/ruscetti)
-and again the main researcher is an "experimental Virologist" (Not a retorovirologist)
And same crap journals (PlosOne, Retrovirogy) in al this neg studies

Again total no cooperation: if they state that XMRV prelevance is lower in europe, let them test some US samples too...or ask at least WPI for some samples to be sure that their methodology is okay..

just some more crap to back up the recent CDC shit...

we may be happy that:
the co author of the paper who found the first human retrovirus and is 30 years in retrovirology (ruscetti), the author who " discovered" XMRV (Silverman) are on "our"side, and most likely also mr Alter (co discoverer hep c etc).
These are distinguished people in (retro)virolgy land, instead of people like kuppeveld, and this amsterdam bunch of experimental newby's

how could this crap still pass peer reviews?????

after all those weasly kuppeveld cdc etc shit...

why not use methods discribed by wpi? why no culturing

pfff in kuppeveld-like words :

i'm done with THEM
 

Rivotril

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http://www.plosone.org/article/comments/info:doi/10.1371/journal.pone.0012040

there is the possibility to comment on this study...i see one person has already made a comment

Would be nice to see a Parvo-unraveling the kuppeveld-study-like comment here..instead of all reacting with small comments..
one great fundamental and systematic analysis would be much better then just 100 small reactions from "complaining " me/cfs patients
 

taniaaust1

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http://www.plosone.org/article/comments/info:doi/10.1371/journal.pone.0012040

there is the possibility to comment on this study...i see one person has already made a comment

Would be nice to see a Parvo-unraveling the kuppeveld-study-like comment here..instead of all reacting with small comments..
one great fundamental and systematic analysis would be much better then just 100 small reactions from "complaining " me/cfs patients
nods yeah... and that is why im not going to comment there.
 

SOC

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one great fundamental and systematic analysis would be much better then just 100 small reactions from "complaining " me/cfs patients
Agreed. It's hard to know the general intent or flavor of a study by just selecting individual sentences. A fundamental and systematic analysis would indeed be much more valuable.
 

SOC

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The defenders of the idnefensible seem to have spilled over from the CAA thread where it was (?) SickofCFS who initiated complaints that sufferers are not nice enough to the purportedly altruistic researchers (to which someone replied, it's just another job) and that we're <Wessely>deterring researchers</Wessely>. I was mindful of that sort of nonsense which is what Sam is repeating here. We get that on a daily basis from the psychobabblers, do sufferers think it's not enough?
Actually, I said that I think verbal abuse of anyone is counterpoductive and that destructive and hostile criticism of people who are trying to help us, even if they're not perfect, is likely to limit the number of high-powered researchers willing to get involved with ME/CFS. I stand by that opinion.

I don't know where you got your interpretation of my comments. Your own mind, I suppose.
 
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A lie is an intentionally deceptive statement -- ie. it is not a mistake or an error, it is a conscious attempt to deceive.

The authors of the paper are:

Marion Cornelissen, Fokla Zorgdrager, Petra Blom, Suzanne Jurriaans, Sjoerd Repping, Elisabeth van Leeuwen, Margreet Bakker, Ben Berkhout, Antoinette C. van der Kuyl.



I trust you can substantiate your allegation because, if not, you have libelled each member of the research group.
What allegation?
 

Rivotril

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it is a LIE

wpi told 100000000000000 times by now that the 101 samples came not from lake tahoe solely

and after that: Ruscetti/Mikovits, after telling this 1000000000000000 times, even answered questions from Kuppeveld and co in Science where the samples came from, that they came from entire usa/canada

after all this, nobody can be serious to put this outdated crap again in a paper........

"If you tell a lie big enough and keep repeating it, people will eventually come to believe it."- Goebbels

maybe this fellow has inspired the Amsterdam researchers...


only goal of this study:

-xmrv wasnt there in me/cfs
-it isn't there in other people in the netherlands
-it is not transmittable by sexual contact/blood (HIV patients dont get it, and they got HIV, and if it was transmissive they would also have XMRV) (this crap is not my way of logical reasoning but that of these "scientists")

so (kuppeveld and this study together) we don't need a blood ban in netherlands/europe,

because: blood ban means XMRV is serious, big news and panic. and XMRV in CFS means the end of the weasly/van der meer school
 
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A local outbreak of CFS in the USA in 1984 was postulated to be associated with XMRV [1], [8].
Ze peeps iz Nederlandische, not ze nativ-speekern. If they'd said "has been" it would be better, but it's awfully rare to be perfect in a second language and this is par for the course in a middling journal (only Nature is said to fix every single grammatical mistake via editing). Maybe I'm sensitive to this because I've been trying to learn German for 11 years, with pitiful results.

The other mistake about the source of samples is non-trivial to be sure. You certainly don't want to see an error like that in a paper, it is usually avoided... but it sometimes happens. Are they the first to come up with this mistake or might they be propagating it from another source - wasn't there a "thing" bout this before?
 
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Yes, it is a lie that keeps getting repeated. I forget who started it, but it appeared in the BMJ article from McClure & Wessely.
 
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Re: peer review in PLoS One - PLoS One is not reviewed in any normal sense. In-house editors, who are not specialists in what they are reviewing, review the papers briefly just to make sure they are not TOTALLY cheezey.

Personally I like it that way - a lot. Scientists moan about peer review all the time - about cliques of established reviewers blocking new ideas. I suspect that this complaint has some merit. Everyone in research knows that PLoS One is non-refereed. That's good. No false pretenses. It would be best if it remains the only one. But even if other non-refereed journals start up, people are going to make convenient lists of them all over the net, and I think everyone in research will be aware of them.
 
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Yes, there is no perfect review system, humans get in the way. So it is a good idea to have a variety of journals out there. I wonder if they could use robots in the future.