OMF(Open Medicine Foundation) OFFICIAL THREAD inc Q And A!

[Ben H]

in reading all of the posts I see the need to hire a project manager. Stanford has an excellent Business School; does Ron have any contacts there? Additionally, the private sector in Silicon Valley, holds a massive amount of talent. Also within the Phoenix Rising community, I suspect we have members with knowledge of Project Management, Systems Analyst, & Business Analyst.

Hey @Groggy Doggy

Can you clarify what you mean precisely by 'Project Manager' and the role (as it pertains) to OMF? Are you talking about the scientific side of things- Ron Davis leads the collaborative consortium on the scientific side. Or are you talking about the board for OMF which Linda is CEO of?


Thanks


B

 

[Gingergrrl]

Rituxumab and autoimmunity is a very popular topic!

For sure!

There are a couple of caveats however. For a definitive answer we would of course need Rons input, certainly for the first part. Whether he is able to (he will absolutely have ideas on it, the genius that he is) is based on a few things-having time for an answer that does it justice, professional courtesy (sometimes it is not appropriate to comment on other research, especially in certain stages) and confidentiality to name but a few.

I totally understand and definitely do not want him to comment on someone else's research vs. if he thinks those treatments could be effective in the autoimmune subgroup based on his research findings as of this point. I know I did not word my question as good as I would have liked to and apologize! Am just curious to hear his thoughts on those treatment modalities/techniques in general.

I will note this down and pass it on, but just putting it out there that some parts may be unanswerable for the time being.

Thank you so much and I totally understand.

Whether the Severely Ill Patient Study will ultimately include PAVAL I am not sure, but again will pass all this onwards. Prof. Davis and his team have an extremely logical way of working, and addressing all areas, but are led currently by where the Big Data and Severely Ill findings point at. It may be that anti-muscarinic auto antibodies are extremely relevant, or not at all. But be sure that if the data points them that way, they will be onto it. Currently afaik, it doesn't.

I have no doubt they will take what they find and head in that direction (vs. having any kind of pre-set agenda) which is why I really think this research will find the true answers. I was just curious if any of the severely ill patients seem to belong to an auto-immune sub-group (meaning that they never get sick- no flu, colds, fevers, malaise, lymph nodes, etc, but with all types of positive and irregular auto-immune markers and auto-antibodies yet ones that don't fit any known disease category like lupus for example.)

Thanks for the questions and I will pass them on as said

Thanks and very much appreciated.

I have one more question that I forgot to ask, do you know if any of the severely ill patients in the study also have a mast cell diagnosis or if any of their testing so far shows mast cell involvement? I am not sure what you are allowed to disclose and hope this is an appropriate question!

 

[Janet Dafoe]

I wondered if Ron was aware that another mecfs researcher, Ian Lipkin, had done just something very similar last year:
Diagnostics Breakthrough Brings Viral Sequencing to Doctors’ Toolkit | Columbia University Mailman School of Public Health
Research paper:
Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis



Which is potentially one less thing for Ron to do

from Ron: PCR is more sensitive than the capturing methods described above, meaning you have more sensitivity to find a virus at a low concentration of viruses in a sample. Lipkin's method is a great method for finding lots and lots of different viruses in a sample. What we've done is to change how the PCR is done so that we can detect multiple viruses in a single sample using a SINGLE PCR reaction. This is a much more sensitive method, so it's more likely to find a virus in a sample with few viruses. it's less expensive and it's much faster than the above "capturing" methods. This new technology allows for the PCR method to detect multiple viruses simultaneously, which hasn't been done before.

 

[Janet Dafoe]

Hey @Groggy Doggy

Can you clarify what you mean precisely by 'Project Manager' and the role (as it pertains) to OMF? Are you talking about the scientific side of things- Ron Davis leads the collaborative consortium on the scientific side. Or are you talking about the board for OMF which Linda is CEO of?


Thanks


B

Yes, a project manager would be good. We need more funding to be able to hire one. @NIHDirector Need funding!

 

[Janet Dafoe]

I saw the ceres nano is being employed for Lyme testing, which is very cool. I saw, too, the normal WB is also being used.

Since the usual caveats (antigenic variance, etc.) may apply here, I was wondering if there is anything being done to reduce problems associated with testing being pigeon-holed to a strain or two. Any Borrelia testing on a genus level? Or testing for as many species and strains as possible that we have knowledge of? For instance, testing to ensure no b miyamotoi or afzelii or garinii or any other very different species of Borrelia whose symptoms mimic ME/CFS and conventional Lyme - but are not picked up by US Lyme metrics - are culprits in a portion of our community?

I know Mark Davis is working on some Lyme stuff, but that effort is restricted to the San Fran area - which means strain(s) will likely be indiginous, and potentially different than, say, Connecticut or Kansas.

Sooooo, how does one discount Borrelia, if only one or two Borrelia, out of 36 Species and 300 strains already known to be on the table, are being tested for?

btw, similar strain issues also beset Bartonella testing, a disease that also is fond of chronicity.

I do realize there are costs here, and the testing already proposed is extra-ordinarily comprehensive and ambitious. It's just that, how can we rule in or out any pathogen if we are not adaquetly sweeping the field for it? I am hopeful that this team which is doing so much already, is trying to resolve this dilemma.

from Ron: We are testing for ALL viruses, bacteria, funguses and parasites. We are even testing for organisms that have never been seen before by doing elaborate sequence comparisons. First we eliminate the human DNA in the sample. Then we compare sequences of DNA (not human - those are gone) that we find in the individual to every sequence that's ever been done in the entire world. We do not require a perfect match, which means we can find organisms that have never been seen before because every organism is related to some organism that HAS been found. We are using very heavy computational analysis to do this.

 

[Kati]

@Rose49 Hppy birthday to Ron, I will be making an extra donation in his honor. I invite everybody to do the same. His work and approach to research is what will get out of this ginormous hole we're in.

 

[Sasha]

from Ron: PCR is more sensitive than the capturing methods described above, meaning you have more sensitivity to find a virus at a low concentration of viruses in a sample. Lipkin's method is a great method for finding lots and lots of different viruses in a sample. What we've done is to change how the PCR is done so that we can detect multiple viruses in a single sample using a SINGLE PCR reaction. This is a much more sensitive method, so it's more likely to find a virus in a sample with few viruses. it's less expensive and it's much faster than the above "capturing" methods. This new technology allows for the PCR method to detect multiple viruses simultaneously, which hasn't been done before.

from Ron: We are testing for ALL viruses, bacteria, funguses and parasites. We are even testing for organisms that have never been seen before by doing elaborate sequence comparisons. First we eliminate the human DNA in the sample. Then we compare sequences of DNA (not human - those are gone) that we find in the individual to every sequence that's ever been done in the entire world. We do not require a perfect match, which means we can find organisms that have never been seen before because every organism is related to some organism that HAS been found. We are using very heavy computational analysis to do this.

 

[aimossy]

I'm certainly stoked to have both Lipkin and Davis working hard on our illness!!
https://www.mailman.columbia.edu/pu...ough-brings-viral-sequencing-doctors’-toolkit

 

[aimossy]

Happy belated birthday to Ron Davis! I've donated to OMF and CII I'm counting the days to the replication of work and also seeing how all the work they do ties in together which will happen - in my view. We need these great teams.

 

[Biarritz13]

from Ron: We are testing for ALL viruses, bacteria, funguses and parasites. We are even testing for organisms that have never been seen before by doing elaborate sequence comparisons. First we eliminate the human DNA in the sample. Then we compare sequences of DNA (not human - those are gone) that we find in the individual to every sequence that's ever been done in the entire world. We do not require a perfect match, which means we can find organisms that have never been seen before because every organism is related to some organism that HAS been found. We are using very heavy computational analysis to do this.

Between this and the last finding, does that mean pathogens can cause an issue with metabolites?

 

[Ben H]

@Rose49 Hppy birthday to Ron, I will be making an extra donation in his honor. I invite everybody to do the same. His work and approach to research is what will get out of this ginormous hole we're in.

Thankyou so much Kati (and I agree totally).

If you would like to make the extra donation, you can here:

http://forums.phoenixrising.me/inde...-and-send-a-message-to-him-to-celebrate.45688

Where you can also send a personalised message to Ron!


Thanks so much!


B

 

[Ben H]

Between this and the last finding, does that mean pathogens can cause an issue with metabolites?

I am not Ron ofcourse, or @Rose49 Janet, but I believe this to be a 'yes'.

In the recent conference in London, it was reported that one patient of Ron's had a issue with Tryptophan metabolism due to an infection which affected the normal metabolic pathway.




B

 

[Biarritz13]

I am not Ron ofcourse, or @Rose49 Janet, but I believe this to be a 'yes'.

In the recent conference in London, it was reported that one patient of Ron's had a issue with Tryptophan metabolism due to an infection which affected the normal metabolic pathway.

B

Thank you. Do we know what was the pathogen involved with this patient?

 

[Ben H]

Thank you. Do we know what was the pathogen involved with this patient?

I do not I am afraid. It was reported as an 'infection' from the London conference.


B

 

[justy]

I have one more question that I forgot to ask, do you know if any of the severely ill patients in the study also have a mast cell diagnosis or if any of their testing so far shows mast cell involvement? I am not sure what you are allowed to disclose and hope this is an appropriate question!

I would also like to know the answer to this question. There seem to be quite a lot of PWME who ALSO have MCAS, and of those who have ME and MCAS another proportion of us also have EDSIII. I suspect many I have spoken to who have an MCS diagnosis actually have Mast Cell issues.

Will they be looking for this in any way? I guess this may be another subset, or another reaction to a pathogen of some sort - my MCAS seems to be secondary to a whole host of chronic infections found so far.

 

[GreyOwl]

@Ben Howell do you know any more about the patient's issue with tryptophan metabolism? What the issue was? How it manifested?

 

[Groggy Doggy]

I am not Ron ofcourse, or @Rose49 Janet, but I believe this to be a 'yes'.

In the recent conference in London, it was reported that one patient of Ron's had a issue with Tryptophan metabolism due to an infection which affected the normal metabolic pathway.




B

I have been taking 5 HTP (non time release) when needed for sleep for 15 years. It helps with my overall mood too. But my health went into downward spiral 3 years ago. So for me, the tryptophan/serotonin mechanisim is not the cause of my ME nor the reason I still have ME. Many people in the general population suffer from depression, but they don't have ME.

I am grateful to hear about new research, but my preference is to focus it on what treatments will improve the core ME symptoms (IOM report, especially PEM). We need greater collaboration among doctors that have treated severly ill patients (ME or closely related biological dysfunctions) to decipher what the severely ill patient 'big data' means.

I worked with data for 20 years. Having more data is not always helpful. Data must be organized and structured in a way that is meaningful. This is why seasoned health care providers with severely ill "hands-on" experience need to be assembled.

I appreciate this thread and being able to express my opinion. But I can't ignore the knowledge I gained in my career and what I have learned about ME.

Thank you for reading this.

GD

 

[Simon]

Thanks to Ron for taking the trouble to provide an answer.

PCR is more sensitive than the capturing methods described above, meaning you have more sensitivity to find a virus at a low concentration of viruses in a sample

As far as I can tell, the key point about the new method from Ian Lipkin using high throughput sequencing is that it matches PCR for sensitivity [the Columbia site says "(VirCapSeq-VERT) is as sensitive as the gold standard polymerase chain reaction (PCR) assays while enabling simultaneous testing for hundreds of different viruses", which seems to be backed up by the published paper.]

However,

What we've done is to change how the PCR is done so that we can detect multiple viruses in a single sample using a SINGLE PCR reaction. .... it's less expensive and it's much faster than the above "capturing" methods

can't argue with cheaper and faster! Good to hear Ron is moving the technology forward like this.

Like @aimossy I'm delighted we have to have such great researchers working on our case. My best to Ron for his birthday tomorrow (I made my donation to mark his birthday yesterday).

 

[duncan]

"

"from Ron: We are testing for ALL viruses, bacteria, funguses and parasites. We are even testing for organisms that have never been seen before by doing elaborate sequence comparisons. First we eliminate the human DNA in the sample. Then we compare sequences of DNA (not human - those are gone) that we find in the individual to every sequence that's ever been done in the entire world. We do not require a perfect match, which means we can find organisms that have never been seen before because every organism is related to some organism that HAS been found. We are using very heavy computational analysis to do this."

1. 
   
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That sounds incredible. This is very exciting. Thank you so much for responding to me.

Quick question: Since it is highly likely that DNA sequences from all sorts of bacteria and viruses will surface, how will it be decided which positive results signify mere historical exposure, vs sequences or traces that signify active or contributory pathogens?

Lyme might be a good example. How will it be determined if the DNA, if found, represents an active infection vs debris? Oh, as this is serological testing, I think, how does one deal with the paucity of Bb DNA in serum? ( Current PCR sensitivity for Lyme can run as low as 10-20%.)

Sorry, that's like three questions - but in my defense, they are related.

 

[A.B.]

"

That sounds incredible. This is very exciting.

Quick question: Since it is highly likely that DNA sequences from all sorts of bacteria and viruses will surface, how will it be decided which positive results signify mere historical exposure, vs sequences or traces that signify active or contributory pathogens?

I don't think genetic material from bacteria and viruses stays around for long. Maybe in some places, but not in the easily accessible body fluids.

Antibodies against bacteria and viruses can stay around for many years but these are not measured in PCR.

My 2 cents, which could be wrong.