Numbers arent enough

Click on the second link to see why I cannot deal with this, psychologically:

Oh no… Cedric died.

I am crying remembering Cedric… I saw him as Arnies brother-from-down-under… crap…

Anne-Marie Hodge from Endless Forms just wrote about new findings about Tasmanian Devils and their cancer:

Devil Dispatch: MHC the Key to Contagious Cancer Vaccine?

I took away another idea:

Reversible epigenetic down-regulation of MHC molecules by devil facial tumour disease illustrates immune escape by a contagious cancer

Further, we show that loss of MHC molecules from the cell surface of DFTD cells is due to coordinated down-regulation of genes essential to the antigen-processing pathway, and that this loss is by regulatory mechanisms including epigenetic modifications rather than structural mutations.

I dont think giving HIV+ patients epigenetic modifiers is a good idea. But Id definitely be trying them in infected Devils.

*heaviersigh*

One of the many problems we have when treating HIV patients is that HIV can hide (latent). So a cell can be infected with HIV, but not show any signs of being infected. The HIV provirus is just chillin in the host cell DNA, not making any viral proteins/babby viruses, so the individuals immune system doesnt even have a chance to kill it.

Periodically, those ‘hidden’ proviruses will activate, and make more viruses.

Its fun to look at in a phylogenetic tree– alovasudden, a virus collected at, say, 5 years post infection, looks like the viruses that were circulating 1 year post infection. Evolutionary time-traveling, evolutionary contingency, randomly exploring alternative evolutionary pathways than what were previously randomly explored– its added fun to the HIV-1 quasispecies.

… And an added complication to curing HIV infection.

So a lot of scientists have done a lot of work trying to figure out how to stop latency. Dont let HIV hide/time-travel.

The problem is (that is, of the many problems, this is one example), latency is not simple. Its not ‘BLOCK X = Activation!’ ‘ADD Y = Activation!”

So what some folks are trying is an epigenetic modifying drug (weird! theyre using pharmaceuticals, not religion or positive thinking to modify patients epigenetics! its as if epigenetics is just biochemistry and NOT MAGIC).

Even though there are *many* layers of epigenetic control of HIV, they are hoping that this one drug that does this one thing will knock all latent HIVs out of their slumber and then, I dunno, CTLs or something are supposed to kill the infected cells, and HIV CURED!

I welcome another weapon in our anti-HIV arsenal.

I do not welcome this:

Scientists on brink of HIV cure

That is so unhelpful, Mr. Simons.

My Debbie Downer take:

1– Does the drug get to where it needs to be? Apparently Panobinostat can cross the blood-brain-barrier, which was my first concern. Lots of HIV hiding in immune cells in the brain. If the drug cant get there, it cant work.

2– Does the drug active all of the infected cells? All of them. ALL OF THEM. Because with HIV, 85%, 95%, 99% dont cut it. Go ask AZT how ‘Well, it stops most of the viruses?’ worked out for it. To quote Dr. Ian Malcolm, ‘Life… uh… finds a way.’

3– What else does this drug do? Epigenetic modifiers are no joke. Screwing around with epigenetics is a great way to get cancer (and who knows what else). HDAC inhibitors are not ‘only’ going to screw with HIV proviruses. So what are the side effects of this drug? Are we going to cure their HIV, activate an ERV, and give them MS?

4– Most importantly, for me as a virologist: Activated HIV proviruses mean lots and lots and lots of babby viruses… Lots of babby viruses that all look and behave slightly different from all the other babby viruses, aka, a quasispecies. The patients immune system cant neutralize all of them immediately. I mean, that is the reason (again, one of the reasons out of many) why you never get better. Red Queen. Your adaptive immune system is reactive. By the time it reacts to the virus, its gone. Its changed. So your immune system has to adapt again.

What if you give patients these drugs, and all you do is turn 1000 infected cells into 100000000000000000000000000000 infected cells? What if all this treatment does is *rapidly* accelerate disease progression?

I hope it works. I hope its a cure. But if its not, I hope it does nothing.

Genital warts in young Australians five years into national human papillomavirus vaccination programme: national surveillance data.

In Australia, they started vaccinating girls/women against HPV in 2007.

In 2007, 11.5% of women under 21 (age-range most likely to get the vaccine before they were sexually active) were diagnosed with genital warts.

0.85% in 2011.

0% in women under 21 who got the HPV vaccines.

0%.

For women 21-30 (only maybe got the vaccine, and even if they did, maybe after they were sexually active), it went from 11.3% to 3.1%.

For women over 30, there was no drop.

In other words, the data suggests you need to get girls the HPV vaccine before they are sexually active, and then the vaccine does its job protecting them from the vax HPVs.

Whats more– Men were protected from HPV when the women got the HPV vaccine. Incidence in men dropped from 12.1% to 2.2%, and 18.2% to 8.9% in those same age ranges. None in the men over 30.

NO WAY!

Give the vaccine to girls before they are sexually active?

Vaccines protect everyone?

Why, thats what those evil scientists have been saying from the very beginning! And a blatant, obvious example of herd immunity in action! Its as if the scientists… actually understand the science of vaccinations…

*cue Twilight Zone music*

He gets it.

I wish I had 5 minutes to talk to him. I dont. But we do have this ~21 min vid where he talks about some of the innovative things he and his crew are working on (phage therapy, faster ways to make influenza vaccines).

True Revolution in Medicine

 

(Im dissertation writing, posts will be sparse for the next couple of months- but to those of you sending me emails with ‘hey, what about ___?’ I will make sure to get to those!)

• H7N9 Bird Flu Cases Reach 21 In China; Death Total Unchanged At Six
•  More bird flu cases reported in China
•  New deadly bird flu virus infects at least 20 in China

The NPR article is quite good:

• Human Cases Of Bird Flu In China Draw Scrutiny

This ‘bird flu’ is not that bird flu. But many of the same basic principles still apply (srsly, read that article).

There is no reason to freak out about this ‘new’ bird flu yet. It does not appear to be transmitting human-to-human, and as I said in the previous article, ‘death rates’ from infection in impoverished regions of China are not necessarily analogous to the entire population.

However this bird flu is demonstrating quite nicely why scientists artificially evolved mammal-to-mammal transmissible ‘bird flu’ in the lab last year. Vaccinate people against these variants before they ever evolve. Nature is telling us ‘Hey, I know you guys were focusing on the H5N1 virus, but the H7N9 guys can cause trouble tooooo!’ We have the technology to do something about it. To stop it. We know how to make workable influenza vaccines.

… Or we can just worry about terrorists and wait for Nature to do what it does– Mutate, explore new uninhabited niches, and select.

Being there: examining the behaviour of Antarctic tourists through their blogs

*Very* fun idea! If you want to know how tourists are behaving/interacting with environment and wildlife of Antarctica when they visit, you could hitch a ride with a bunch of tour groups and spy on everyone– or you could sit at home in your warm office and study what these tourists have reported/posted on their blogs!

I was momentarily terrified I was quoted at some point for doing something wrong, as I fit the paper criteria– people who visited Antarctica 2007-2010 and visited Deception Island. Alas, they stopped collecting June 2010, so I wasnt (we really did try to do everything right). But I went there. I saw the ruins at Whalers Bay. Some in my group went ‘swimming’ (volcano powered hot-tub- but we didnt dig into the sand. they just ran into the water).

And thats what they found– Most people tried to do things according to the rules, but occasionally and briefly, tourists would screw up, either knowingly or unknowingly. Few/Tiny breaches add up when youre talking about 150,000 visitors a year. I wouldnt trade my Antarctica experience for anything, so I cant begrudge anyone else who wants to visit. So if you are going to Antarctica, try, try to follow the rules, and pressure your boat-mates to do the same… And make sure you blog about it for those of us who cant be there!

‘Its the mercury in vaccines!’ ‘Its XMRV in vaccines!’ Wait wait wait– ‘TOO MANY TOO SOON!!!!’

If you know nothing about immunology, this claim might make sense.

‘Your immune system’ could be ‘overwhelmed’ by trying to fight off too many ‘invaders’/'vaccines’ at once.

Except thats not how your immune system works.

You have B-cells and T-cells that, due to random chance/mutations, kinda-sorta recognize proteins from pathogens as ‘foreign’. When they are actually exposed to those proteins, they go through even more random mutation to make B- and T-cells that are super good at stopping the pathogen.

But a B-cell that ‘sees’ a polio protein and a B-cell that ’sees’ a tetanus protein and a B-cell that ‘sees’ microscopic aliens from Mars are independent entities. They dont even know the other cells exist. So, the B-cell that ‘sees’ a polio protein will just derp around if you are infected with influenza. He dont care. He cant see it.

You can get several vaccines at once (and be naturally exposed to countless pathogens the same day), and it doesnt matter. Your B- and T-cells have a specific job, and they do what they do regardless of other B- and T-cells doing their jobs.

So from my perspective, the ‘best’ vaccine would be one mega vaccine that would contain ALL the antigens to protect you from ALL the pathogens. It would reduce pain, reduce risk of complications from shots, reduce waste, reduce exposure to the fillers and preservatives in vaccines, reduce reduced immunity due to people forgetting to come back for booster-shot 2/3/etc, etc.

If we could combine all vaccines into one shot, I would be happy as a clam.

Unfortunately, due to differences in production and necessary adjuvents and such, that is not currently possible, but if it were (in the future), I would not be concerned about ‘overwhelming’ Babbys immune system. I would be concerned about immunodominance– Babbys immune system would ignore most of the components in the vaccine, and fixate on, say, one of the mumps proteins. And then you wouldnt be protected from everything else in the mega-mix. Defeating the purpose of a vaccine mega-mix.

So the ‘TOO MANY TOO SOON’ claim doesnt make sense from a scientific perspective (not even mentioning the ‘and then some kind of magic happens, and then, AUTISM!’ part…???).

But it gets repeated all over the internet, so some scientists investigated.

Increasing Exposure to Antibody-Stimulating Proteins and Polysaccharides in Vaccines Is Not Associated with Risk of Autism (pdf)

Press release

SPOILER: Getting the recommended schedule of vaccines (TOO MANY!) at the recommended time (TOO SOON!) is not associated with autism rates.

I am so shocked.

• South Africa: ‘Over 25% of schoolgirls HIV positive’
• 28 Percent Of South African Schoolgirls Have HIV Because Of ‘Sugar Daddies,’ Health Minister Says

The good news is, this statistic is WRONG:

Media get it wrong on SA schoolgirls’ HIV statistics

Last week the Mail & Guardian used a South African Press Association (Sapa) article on its site incorrectly stating that 28% of South Africa’s schoolgirls were infected by HIV, compared with 4% of schoolboys.

But the fact-checking organisation, Africa Check, reported that Motsoaledi’s speech at a “taking Parliament to the people event” in Carolina in Mpumalanga was misinterpreted by a Sowetan journalist and was then re-reported by other news companies and agencies.

Oh thank god. 28% of girls infected? My brain couldnt handle that.

Yeah, now for the bad news– The 28% figure wasnt right for all of South Africa. It was right for a specific group of school kids in South Africa.

Motsoaledi said on Friday the statistics that were incorrectly quoted were on an HIV testing and counselling campaign, which actually found a small number of schools in the Natal Midlands were particularly hard-hit by HIV. Of the group of children tested there, 28% of girls were infected by the disease compared to 4% of boys.

Uuuuuuugh *headinhands*  Uuuuuugh. Dammit.

Theres also this:

Media mis-reporting HIV rate among SA schoolgirls. True rate is 12.7 percent

The most recent statistics, compiled as part of a 2011 HIV and syphilis survey, which was published last year by the Department of Health, indicate that HIV prevalence among young women aged between 15 and 19 was around 12.7% in 2011, a decrease on the previous year’s figure of 14%.

This is less than half the figure in the Sowetan’s headline.

It is even less than the figure (20.5%) for HIV prevalence among pregnant women aged 15-24, a population group who are always likely to have a higher prevalence rate than all schoolgirls, for obvious reasons.

Uuuuugh. Uuuuugh the ‘real’ stats dont make me feel any better. Dammit. Uuuuuuuugh…

Reasons for Not Vaccinating Adolescents: National Immunization Survey of Teens, 2008-2010

Our findings across 3 years show that, even as clinicians are increasingly recommending HPV, increasing numbers of parents, >40% in 2010, do not intend to vaccinate their adolescent female children with this vaccine. Parents intending to refuse are increasingly concerned about vaccine safety and seem less willing to accept clinician recommendations.

Yeah, what do us stupid virologists and immunologists and physicians know. Better just let your kid get a preventable disease that can cause a deadly cancer cause some idiot on the internet told you vaccines are made of Satans spooge.

Whatever.

*walksaway*

YAWN!

Thats childs play, at this point.

Lets give those GMO viruses a real challenge.

Lets get them to fight a real bastard form of leukemia– B-cell Acute Lymphoblastic Leukemia (B-ALL) in adults.

In kids, B-ALL has high cure rates (>80% cured).

In adults, things are more difficult (38% are alive 5 years post-diagnosis). Things get much more difficult if the adult has relapsed (7% alive 5 years post-diagnosis).

Can a GMO HIV-1 do better than 7% in relapsed adult B-ALL patients?

CD19-Targeted T Cells Rapidly Induce Molecular Remissions in Adults with Chemotherapy-Refractory Acute Lymphoblastic Leukemia

There are five patients in this study. Four were >50 years old. One was only 23.

One had bone marrow that was 70% tumor. Yeah…

Four of the five patients went into remission and were eligible for bone marrow transplants. One died of unrelated issues, but the other three are doing just fine.

The fifth patient just couldnt get the bone marrow transplant because of other heath problems, and the cancer came back.

But four out of five went from “My bone marrow is basically just tumor and Ive got a 7% chance of surviving” to “Thanks to GMO HIV, I could get a bone marrow transplant and now Im fine.”

The side-effects?

All that dead tumor really pissed off their homeostasis and they had high fevers/high cytokine levels for a while, but it was easily treated with some steroids (but unfortunately would impair the tumor slaughterfest). They gotta improve that. But as far as ‘cancer treatment side-effect’ profiles go, Ill take it.

So Im happy about this, right?

Well, Im sick of writing about the papers. Im sick of writing about four patients, five patients, six patients. I *know* this is a process, but this kind of protocol *WORKS*. We need this therapy to be fast-tracked into the clinics. We need this to be normal.