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Comment: Tag #WhereIsTheFuckingPaper (Score 4, Informative) 74

by Guppy (#47716859) Attached to: Study: Seals Infected Early Americans With Tuberculosis

Oh, here it is: Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis (Paywall -- free Nature summary article here).

Modern strains of Mycobacterium tuberculosis from the Americas are closely related to those from Europe, supporting the assumption that human tuberculosis was introduced post-contact. This notion, however, is incompatible with archaeological evidence of pre-contact tuberculosis in the New World. Comparative genomics of modern isolates suggests that M. tuberculosis attained its worldwide distribution following human dispersals out of Africa during the Pleistocene epoch, although this has yet to be confirmed with ancient calibration points. Here we present three 1,000-year-old mycobacterial genomes from Peruvian human skeletons, revealing that a member of the M. tuberculosis complex caused human disease before contact. The ancient strains are distinct from known human-adapted forms and are most closely related to those adapted to seals and sea lions. Two independent dating approaches suggest a most recent common ancestor for the M. tuberculosis complex less than 6,000 years ago, which supports a Holocene dispersal of the disease. Our results implicate sea mammals as having played a role in transmitting the disease to humans across the ocean.

Comment: Re:Home fecal transplant went wrong (Score 1) 51

by Guppy (#47716225) Attached to: How To Read a Microbiome Study Like a Scientist.

While the clinical picture and timing suggests the possibility, it's far from certain that this was a primary infection stemming from his home fecal transplant. I would have liked to see an analysis of anti-CMV IgM titers, although in this case it's also possible that his case was recognized too long afterwards to determine whether or not it was an actual primary infection.

Comment: Re:Different colors (Score 1) 267

by Guppy (#47637205) Attached to: My degree of colorblindness:

Polycarbonate lenses drive me nuts because their Abbe number is too low; everything looks like an old-school 3-D movie (without looking at it through the red/blue 3D glasses) to me when I wear them.

I think there was some specialty lens company that sold a multi-layer achromatic eyeglass lens, but I believe they have since gone out of business, unfortunately.

The best commonly available material for chromatic dispersion is probably CR-39, followed by Trivex, but the index is too low for very high-powered prescriptions.

Comment: +1 for router on Uninterruptible Power Supply (Score 2) 426

by Guppy (#47637095) Attached to: Ask Slashdot: Life Beyond the WRT54G Series?

I have a Linksys E900 I've been running DD-WRT on for a while, and never had a lick of trouble with it until this week, when the WAN port fried thanks to a power surge (caused by some dumbass with a drill...).

That reminds me, one of the best things you can do for a home router is to put it behind a UPS. I put my father's Linksys wrt54g behind an old APC-300, it was up for over a year continuously afterwards, and only required a reboot when I had to move it around for some maintenance. Even a crappy $25 Belkin can be surprisingly stable when it has a nice clean power supply.

Comment: Physical structure of the phage? (Score 2) 100

by Guppy (#47549427) Attached to: Newly Discovered Virus Widespread in Human Gut

I'm the last author on the paper and it was discovered in my bioinformatics lab in the CS department at SDSU ...

Quick question -- I see from your paper, do you have an idea what it looks structurally? A bunch of media sites have pictures but are using what is obviously stock art (mostly of T-even phages), but from your paper I see that it has no close phylogenetic relationship to known phages (and if your group had e-microscopy or crystallographic data, it would have been in the paper already).

Still, I figured someone skilled in virology might be able to identify some capsid sequences or something, and be able to make a decent guess.

Comment: Re:cause and/or those responsible (Score 2) 667

by Guppy (#47497723) Attached to: Russian Government Edits Wikipedia On Flight MH17

Btw. does anyone here remember the USS Vincennes?

Funny thing, I once bought a used Science Fiction pulp novel from a used book store (up in State College, PA), sometime in the late 90's. Only later did I realize that "USS Vincennes" was stamped on one of the edges, indicating it must have come from some on-board library. It's a small world.

Anyway, to continue with your question -- yes, I remember it pretty well. And there were plenty of talking heads in the media trying to shift some of the blame onto Iran (that it must have been a martyrdom operation where Iran sacrificed it's own citizens to make us look bad, or that Iran shouldn't have operated civilian and military aircraft out of the same airport, or that the pilot should have known better than to fly on a path directly crossing that of a U.S. warship -- all bunk excuses).

But the U.S. government never denied that we were the ones who shot it down, they admitted it quickly and bluntly.

Comment: Re:I'll buy anything from China except food (Score 1) 431

by Guppy (#47258769) Attached to: Chinese-Built Cars Are Coming To the US Next Year

At this point, a majority of the apple juice and tilapia we eat in the U.S. is now imported from China -- as well as food additives such as citric acid, sorbic acid, some vitamin additives, and artificial vanilla flavoring.

And while they haven't yet reached a majority market share, frozen spinach, garlic, mushrooms, and cod have large fractions of the supply coming from China.

Comment: Predicting the next epidemic (Score 2) 172

by Guppy (#47220575) Attached to: Human Blood Substitute Could Help Meet Donor Blood Shortfall

Just force all blood donors to get tested for infection, regardless of orientation, then give the clean ones a certfification with expiry. Re-test as required to continue donating.

Back in the 80's, one of the things we learned from the opening stages of the AIDS epidemic is the possibility that a new disease agent will enter the human population, sight unseen. If such a new virus were to appear, it could spread silently for years before being identified (just has HIV did).

It is this risk which had led to the exclusion of the gay population. The elevated risk for HIV infection in that population serves as a marker -- it demonstrates that they have the epidemiological risk characteristics to become the initial host for such a new disease, should it ever appear. By excluding higher-risk groups, the idea is to slow down the opening stages of the next epidemic.

Every successful person has had failures but repeated failure is no guarantee of eventual success.