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Different Brain Regions Are Infected with Fungi in Alzheimer’s Disease

nature.com

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Re: Different Brain Regions Are Infected with Fungi in Alzheimer’s Disease

#151
post #63

Earlier quoted context omitted.

It's known to be pretty difficult to treat a lot of fungal infections in the CNS. The agents we have are pretty nasty, with severe side effects.

I'm a hacker not a doctor but I've done some research into water purification, and here is what I've learned: The body is mostly water. The task of removing microorganisms and fungus from water has been well studied. Science knows of effective agents which are proven to purify water of micro-organisms like bacteria and also fungus. Some of these are being utilized in public water decontamination, and others while als…

Potassium iodide is not iodine; it is a compound of iodine, with the same relation to iodine that table salt (sodium chloride) has to chlorine gas, which is a chemical weapon. In fact, both potassium iodide and sodium chloride are alkali halides, compounds of the halogens iodine and chlorine, respectively. Iodine is extremely reactive and consequently toxic, not only to people, but even more so to bacteria, which is why it is useful in disinfecting water. Tincture of iodine typically contains both potassium iodide and elemental iodine, but it's the elemental iodine that does the work.

Iodine, on contact with electron donors, will rapidly reduce them and ionize to the same nontoxic iodide found in potassium iodide, rendering it nearly harmless. However, oxidizing your body cells causes chemical burns by killing them; oxidizing bacteria and fungi kills their cells too. Pure iodine will blister your skin on contact.

Essentially your optimism arises from confusing two related, but very different, substances. Don't feel bad; I've made similar errors any number of times. One out of every ten thousand times that you think you've found an easy way to hack around a difficult and important problem, it's a breakthrough. The other 9,999 times, you're overlooking a fundamental reason your idea won't work.

It's deeply unfortunate that HN is not the kind of place that people will correct your mistakes, as I've done above, instead of silently downvoting you.

If you are using CNS stimulants (amphetamines, methylphenidate, modafinil, cocaine, maybe even caffeine) you might want to cut down your dosage. The hyperfocus they facilitate can be counterproductive when it causes you to overlook your errors and get overexcited over a possible breakthrough. This can blossom into full-blown amphetamine psychosis, which is not an experience I recommend, especially for the people around you.

A useful tool in discovering errors like this is investigating consequences that would ensue should your reasoning turn out to be true. For example:

* Potassium iodide is a chemical that people have been dosed with many times, including soldiers under controlled conditions. If it cured everything from jock itch to acute bacterial meningitis, probably someone would have noticed.

* Bottles of iodine are labeled "for external use only". If it were nontoxic, it would not be labeled in this way.

* Many potassium iodide vendors and customers are enthusiastic promoters of colloidal silver, which actually is a broad-spectrum antimicrobial that is fairly nontoxic to human bodies. (By itself, it's not effective enough to disinfect water with, but in combination with the more toxic copper, ionized silver has been used to disinfect water.) If KI were effective for disinfection, they would be promoting it as such.

* Our bodies use iodide in certain thyroid hormones, so there are enzymes devoted to moving iodide ions around, keeping them from reacting with the wrong things, etc. This is different from e.g. lead, mercury, or tellurium, which have no known biological function and cause toxicity by acting as poor substitutes for other atoms. If iodide were nontoxic and effective at stopping fungal infections, we would have evolved to concentrate it in our bodies and direct it to areas suffering from inflammation. But we didn't.

Re: Different Brain Regions Are Infected with Fungi in Alzheimer’s Disease

#152
This article does NOT provide compelling evidence that fungi are the causative agent for AD. It merely reports correlative observations.

You may conclude that antifungal drugs could help patients with AD. You may also think that vaccination or some other mechanism of prevention could reduce the prevalence of AD. These conclusions are simply not supported by the data.

I am a biomedical data scientist, not a neuroimmunologist, so I asked a colleague in my MD/PhD program who has experience in the latter field. His thoughts:

"There are a number of concerning issues here:

1) They are using polyclonal antibodies. I don't think they addressed possibility of cross-reactivity. Comparing Alzheimer's disease vs control brain is like comparing apples and oranges. There can be very different inflammatory states between the two and yield different antigenic environments.

2) The possibility that neurofibrillary tangles or amyloid plaques are sticky and can non-specifically bind antibodies remains a possibility.

3) Only immunohistochemistry? Could have at least done some qPCR especially since they can grow these fungi for quantiation. The only other paper that observed fungus in CNS of AD patients is by the same group. The high possibility of artifact is has not been ruled out."

*edited grammatical typo

Re: Different Brain Regions Are Infected with Fungi in Alzheimer’s Disease

#154
post #29

Earlier quoted context omitted.

Depends on which way the arrow of causality points. If AD makes the brain vulnerable to fungal infection, probably not. But if fungal infection causes AD, then it seems likely. This might be a giant breakthrough, or it might be just a side effect. The uncertainty is not fun at all. But if the arrow points the right way, then yes it's possible that antifungals would be a big part of treatment.

Given that there is a low incidence of AD in India, i'd suspect that fungal infection is partly a cause. It would be interesting to plot food spiceyness vs AD rates and spiceyness vs fungal infection rates in the world population.

There was some promising research on using turmeric, the stuff that gives curry it's yellow colour, to treat Alzheimer's:

>We describe here three patients with the Alzheimer's Disease (AD) whose behavioral symptoms were improved remarkably as a result of the turmeric treatment...

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3665200/

Turmeric has strong anti fungal properties.

Re: Different Brain Regions Are Infected with Fungi in Alzheimer’s Disease

#155

Earlier quoted context omitted.

What package(s) did you use to create this?

I used http://r-fiddle.org to verify what was the intended function, then used built-in Artist Mode (M-x artist-mode) to draw an ellipse for function and square for axes, and finally cut it down in fundamental-mode and added labels. It's basically vanilla Emacs, but I admit to using multiple-cursors.el for some cleanup. It's an excellent addon mode offering a more interactive way to do some things you'd otherwise do…

Ah thanks, I was aware of artist-mode, I thought there was some ESS like package that could output ascii graphs of functions :) R-fiddle is new to me though, thanks for that.

Re: Different Brain Regions Are Infected with Fungi in Alzheimer’s Disease

#156

Earlier quoted context omitted.

I used http://r-fiddle.org to verify what was the intended function, then used built-in Artist Mode (M-x artist-mode) to draw an ellipse for function and square for axes, and finally cut it down in fundamental-mode and added labels. It's basically vanilla Emacs, but I admit to using multiple-cursors.el for some cleanup. It's an excellent addon mode offering a more interactive way to do some things you'd otherwise do…

Ah thanks, I was aware of artist-mode, I thought there was some ESS like package that could output ascii graphs of functions :) R-fiddle is new to me though, thanks for that.

There's also orgtbl-ascii-plot[0], there was a mode for writing out flow diagrams in Emacs that used a web backend to render them (I don't remember the name), and I'm pretty sure you could abuse some graphics-to-ascii or DOT file command line tools to get the required result in Emacs buffer - particularly via org-babel, which lets you invoke external programs to "evaluate" code blocks. I remember using some Java-based local tool to render graphs through org-babel, but again I don't recall the name or URL.

[0] - http://orgmode.org/worg/org-contrib/orgtbl-ascii-plot.html

Re: Different Brain Regions Are Infected with Fungi in Alzheimer’s Disease

#157
post #143

Earlier quoted context omitted.

Here's my problem, we know the outcome of Alzheimer's, surly we have the data to go ahead without a control group? We've had them before.

Without the control group, you don't know if the change you think you made is the change that made a difference.

I think it really comes down to the strength of the effect. If the anti-fungal has only a marginal effect on outcome, a large n control group helps tease out statistical significance. If the anti-fungal has a strong readily observable effect, the whole study gets un-blinded and everyone starts getting it pretty quickly anyway.

The reality is the control group and the test group are not the exact same people and often it's not even completely true everyone is dealing with the "exact same" disease (different genes, different mutations, different past treatment regimens, etc.). I definitely believe there are cases where a control is setup because "that's how it must be done" and not because it's going to actually provide any useful data at the end of the day to tell you anything about how the test group actually performed.

Another way I've seen this done which is a little less wasteful, and when you have high confidence in your new treatment, is to tweak the standard treatment marginally in some way you think might provide some small improvement in both groups, but in a way that could never justify its own full study. Like you modify the dosing schedule, add some vitimin, diet, or exercise change in some way you think will help both groups. But again you can only afford to do that if you are expecting a very strong effect from your new additive treatment which would blow away your tweak statistically, else you risk hiding a small benefit of the new treatment in your tweak.

In other words, you give every participant the best damn chance and the best care you can legally give them, and 50% of them know they are on something new which could be a blockbuster, and if it is, the whole group will get early access to it anyway.

Re: Different Brain Regions Are Infected with Fungi in Alzheimer’s Disease

#158
post #92

Earlier quoted context omitted.

Comparing old vs new is how it's done in cancer research. It's inhumane to prescribe placebo to someone in serious pain. You give them the old or the new, and they report how they felt. In this case, since there is no concept of old or new, it's an entirely new class of treatment. So you give the current best-practice treatment without anti-fungal, and you give the same with anti-fungal. Anyone in the study is agreei…

The place where I worked did a pretty good job at administering the studies. The cost was in all the sampling and shipping. When your study is doing 1,000 sample kits with 5 samples every week day for multiple years, its going to cost. I am still a bit clueless with all the research we have done with Alzheimer's why we need another control group?

Is that 1,000 patients enrolled each being tested daily? That is a heck of a lot of testing!

Obviously depends on the patient population (in/out patient) but IMO a huge component of the cost is pushed off on patients having to spend a day getting to the study facility to give blood and urine versus dropping it at a local lab.

Then again, if Theranos tells us anything about variability of lab results, you certainly have to take every precaution to protect the integrity of your data.

Re: Different Brain Regions Are Infected with Fungi in Alzheimer’s Disease

#159
post #143

Earlier quoted context omitted.

Without the control group, you don't know if the change you think you made is the change that made a difference.

Ok, but don't we have a body of knowledge on Alzheimer's that having another control group is redundant? Why do we keep needing new control groups for things that are going to kill people and we know are going to kill people? I cannot get by the ethical problem of knowing we're kill 50% of the people in the study to provide data we already have.

The problem is, if something related to how you run your test of the anti-fungal has an effect on the disease, you're going to assume its the anti-fungal; but maybe it's not. If you have a control group, and both groups do better than expected (compared to the body of evidence), then you've learned something you wouldn't have without a control group (and you'll have to work hard to figure out what changed in this study vs other studies). If anti-fungals are a clear winner, it's likely that the study protocol would be changed to give everyone the drug after early results.

Re: Different Brain Regions Are Infected with Fungi in Alzheimer’s Disease

#160

This is extraordinary. It means antifungal drugs like Fluconazole can possibly prevent AD.

No, it means that a researcher doing fourth rate science has successfully trolled HN.

Please stop posting unsubstantive comments to Hacker News.
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