Monday, January 23, 2006 

For Koufax Award voters...

Aetiology has been nominated for a Koufax Award for Best new blog. First, if you're stopping by via that link, welcome, and thanks for checking out this site. I hope you'll take some time to stroll through the archives here, and to check out recent activity on my new site, located here. Sorry for the confusion!

Wednesday, January 11, 2006 

Aetiology is moving!

Well, it looks like it's official, so I might as well spill the beans. Seed Magazine has launched a new feature, Science blogs, and Aetiology is one of the inaugural blogs. If you take a look at the list of other blogs here, you'll probably notice some other familiar names. It's a good deal for me: they pay for everything *and* provide technical support. Everything else will stay the same--I still control everything I write, and there's no editorial control or anything from the higher-ups.

So, I hope you'll continue reading, and join me over at the new address:

For those of you who have this site on your blogroll (and allow me to take a moment to thank you for that in the first place), I'd appreciate it if you updated your link. I think there's some way I can do a re-direct eventually, but I'll keep traffic coming to this page for awhile before switching it over. Additionally, all old content will remain archived here, so if you've linked to a post here, it should be fine in perpetuity.

Tuesday, January 10, 2006 

H5N1--does it live up to the hype? Redux

Okay, one more quick post. I've talked quite a bit on here (and over on Panda's Thumb) about the importance of surveillance, and how the current death rates from H5N1 influenza ("bird flu") are likely to be artificially high, since we're more likely to diagnose the very ill cases than the mild or asymptomatic ones. (See here and here for the relevant posts). Indeed, that first post linked discusses a study carried out here at the Center for Emerging Infectious Diseases at the U of Iowa, which found that swine workers were much more likely to be infected with swine influenza viruses than those without significant swine contact--showing that there's likely a heckuva lot more sub-clinical or unrecognized cases of zoonotic influenza than ever pop up on the radar. A new study from Vietnam suggests the same thing, only surveying for "bird flu" and bird contact rather than swine. The abstract:
Background The verified human cases of highly pathogenic avian influenza in Vietnam may represent only a selection of the most severely ill patients. The study objective was to analyze the association between flulike illness, defined as cough and fever, and exposure to sick or dead poultry.

Methods A population-based study was performed from April 1 to June 30, 2004, in FilaBavi, a rural Vietnamese demographic surveillance site with confirmed outbreaks of highly pathogenic avian influenza among poultry. We included 45 478 randomly selected (cluster sampling) inhabitants. Household representatives were asked screening questions about exposure to poultry and flulike illness during the preceding months; individuals with a history of disease and/or exposure were interviewed in person.

Results A total of 8149 individuals (17.9%) reported flulike illness, 38 373 persons (84.4%) lived in households keeping poultry, and 11 755 (25.9%) resided in households reporting sick or dead poultry. A dose-response relationship between poultry exposure and flulike illness was noted: poultry in the household (odds ratio, 1.04; 95% confidence interval, 0.96-1.12), sick or dead poultry in the household but with no direct contact (odds ratio, 1.14; 95% confidence interval, 1.06-1.23), and direct contact with sick poultry (odds ratio, 1.73; 95% confidence interval, 1.58-1.89). The flulike illness attributed to direct contact with sick or dead poultry was estimated to be 650 to 750 cases.

Conclusions Our epidemiological data are consistent with transmission of mild, highly pathogenic avian influenza to humans and suggest that transmission could be more common than anticipated, though close contact seems required. Further microbiological studies are needed to validate these findings.
Though intriguing, there are some major weaknesses in the study. First, it's all self-reported, without any serological evidence, and "flu-like illness" ain't exactly definitive of actually having influenza. But it's certainly suggestive, and once again highlights what so many in public health have been trying to pound into the heads of those who control the funds: we need better surveillance, period.

Other scientists seem to be a bit more optimistic. According to this AP article:
"I would call this the smoking gun," said Dr. Gregory Poland, a Mayo Clinic flu specialist. "All of us have been concerned and have guessed that the data we have so far has been the tip of the iceberg."

The human cases counted so far likely have been the most severely ill patients treated at major hospitals, Poland said.

"In the really rural areas, we know that this had to be occurring" too, and the study suggests that the prevalence "is pretty high," he said. "The data lines up biologically the way we would have expected it to."
I agree with a lot of that, but wouldn't call this a "smoking gun" in any way, shape, or form. Maybe it would have been if they'd definitively shown H5N1 seroconversion before and after bird exposure, but the "influenza-like illness" category is just too broad. Even other bird diseases that humans can acquire, such as psittacosis, can cause influenza -like symptoms--so I think Dr. Poland is overshooting. Hopefully this will help to get other studies funded, though.

I've not been writing much on the recent developments with H5N1, so for anyone who's not up to speed, check out Effect Measure, where they've been keeping up much better on the newest influenza news. And while those of us who report on the science are generally a bit more clinical about the suffering, Revere also reminds us of the more personal side, noting that one family in Turkey has now lost a son and two daughters to H5N1--a second son, age 6, survives. This is why it's so much easier to deal with stats--numbers, even when contemplating a large amount of deaths, are less difficult than the personal story of just one victim.

Edited to add this news story:
Two young brothers, ages 4 and 5, who have tested positive for the dreaded H5N1 avian virus but shown no symptoms of the disease were being closely watched at Kecioren Hospital here Tuesday. Doctors are unsure whether they are for the first time seeing human bird flu in its earliest stages or if they are discovering that infection with the H5N1 virus does not always lead to illness.

In any case, the highly unusual cluster of five cases detected in Turkey's capital over the last three days -- all traceable to contact with sick birds -- is challenging some of the doctors' assumptions about bird flu and giving them new insights into how it spreads and causes disease. Since none of the five has died, it is raising the possibility that human bird flu is not as deadly as currently thought and that many mild cases in Asian countries may have gone unreported.
Gee, no, really?? Why hasn't anyone considered that before? *smacks forehead, pulls out hair*

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New Grand Rounds!

Had a sick kid yesterday and am swamped today, so if you're jonesing for some good science reads, head over to Clinical Cases and Images for this week's Grand Rounds.


Aflatoxin found in pet food

I've been meaning to write something up about this for awhile, but keep forgetting. Anyhoo, because my own dog is currently ill and it's stressing me out watching her (not due to this, thankfully), I thought I'd do my own little part to get the word out to any dog owners who may not have heard of this recall.

Diamond Pet Food Recalled Due to Aflatoxin
Diamond Pet Food has discovered aflatoxin in a product manufactured at our facility in Gaston, South Carolina. Aflatoxin is a naturally occurring toxic chemical by-product from the growth of the fungus Aspergillus flavus,, on corn and other crops.

Out of an abundance of caution, we have notified our distributors and recommended they hold the sale of all Diamond Pet Food products formulated with corn that were produced out of our Gaston facility (see complete list below). Please note that products manufactured at our facilities in Meta, Missouri and Lathrop, California are not affected. The Gaston facility date codes are unique from other Diamond facility codes in that either the eleventh or twelfth character in the date code will be a capital "G" (in reference to Gaston). The range of date codes being reviewed are "Best By 01-March-07" through Best By " 11-June-07". Diamond's quantitative analysis records substantiate that Diamond's corn shipments were definitively clear of aflatoxin after December 10. As such, "Best By 11-June-07" date codes or later are not affected by this notice.

States serviced by our Gaston facility include Alabama, Connecticut, Delaware, Florida, Georgia, Kentucky (eastern), Maine, Maryland, Massachusetts, Mississippi, New Hampshire, New Jersey, New York, North Carolina, Ohio, Pennsylvania, Rhode Island, South Carolina, Tennessee, West Virginia, Vermont, and Virginia.

We are rapidly analyzing retained samples of all products produced in Gaston so we can isolate specific lot numbers impacted and provide this information to our distributors, retailers and customers as quickly as possible.

Meanwhile, if your pet is showing any symptoms of illness, including sluggishness or lethargy combined with a reluctance to eat, yellowish tint to the eyes and/or gums, and severe or bloody diarrhea, please consult your veterinarian immediately.
There's a list of the brands recalled, sold under the names Diamond, Professional, or Country Value. Unfortunately, several dogs have already died due to this contamination.

About aflatoxin: this is a fungal toxin made by several species of Aspergillus. You may have heard of it previously because it's a potential bioweapon. It's generally found in crops that have either gotten wet or have long been exposed to high humidity; like most fungi, Aspergillus grows best in moist conditions. When ingested, aflatoxin generally targets the liver, and can cause either acute effects (including death) or cause damage leading to cancer. Either way, it's nothing to mess around with, so please double-check your dog food and if you have the affected brand, contact Diamond pet foods. There was finally some news coverage of this last night (I think on NBC) and it was noted that Diamond would pay all vet costs related to treatment of affected pets (though as far as I know, dogs are the only ones affected so far, the Diamond site lists some cat foods as recall products as well).

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Friday, January 06, 2006 

South African AIDS activists sue denialists

South Africa has been a hotbed of AIDS denial, ever since President Thabo Mbeki invited noted HIV denialist Peter Duesberg and other HIV-deniers to his country to discuss "alternative" theories of AIDS. Though scientists and others (including prior president Nelson Mandela) in the country repeatedly spoke out against these ideas, they've lingered. Now, AIDS activists are taking it to the courts. In the current issue of Nature Medicine, they have a brief news report discussing the lawsuit.
Doctors and AIDS activists in South Africa have filed a joint lawsuit against the country's health minister and controversial vitamin supplier Matthias Rath as concerns mount over the government's lack of leadership amidst the country's worsening AIDS crisis.

The South African Medical Association (SAMA) and the prominent activist group Treatment Action Campaign (TAC), which together filed the lawsuit, say they aim to end the climate of what the TAC calls "politically-supported denialism" afflicting the country's fight against AIDS.

A key element of the lawsuit is the allegation that in at least two townships, Rath is running illegal medical trials for his multivitamins, which he markets to AIDS sufferers as an alternative to 'poisonous' antiretroviral drugs.
The lawsuit claims 5 deaths already due to this action, with reports of up to 12--while 2 people still living were found to be taking anti-retroviral drugs.

The saddest quote of the article:
A spokesman for Rath declined to speak to Nature Medicine about the case, saying he is convinced the journal is "funded to the hilt with drug money."
Man, these conspiracy theories are getting tiresome, and so hard to keep track of. Is Nature Medicine in bed with the EAC as well?

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Two potential rotavirus vaccines tested

Rotavirus, a member of the reovirus family, is one of the world’s leading causes of childhood death. This virus causes acute gastroenteritis and diarrhea, resulting in 600,000 fatalities every year in children younger than 5. Most of these deaths occur in the developing world, where there is poor sanitation and medical care, but even in the United States, about 40 deaths every year in children are attributed to rotavirus. Additionally, there are about 70,000 hospitalizations and billions of dollars in health care costs and missed work days for parents due to infection with this virus—-so the virus still causes a significant financial burden, even in a developed country.

A vaccine against the virus was first introduced in 1998 by Wyeth, with the name “RotaShield.” Based on a genetically engineered rhesus monkey rotavirus, the vaccine was withdrawn from the U.S. after only 11 months due to reports citing a potentially fatal intestinal blockage (intussusception) associated with use of the vaccine. Studies conducted following removal from the market showed that the risk of intussusception following vaccination with RotaShield was much lower than initially thought, and much lower than the risk of death from rotavirus, but the damage had been done and the virus remained shelved.

Two new vaccines may be able to take RotaShield’s place. Trials in a number of countries of these vaccines, GlaxoSmithKline’s Rotarix and Merck’s RotaTeq, showed that they worked well and had few side effects. In a trial involving 63,000 infants, the serially passaged, attenuated human rotavirus vaccine Rotarix reduced serious illness by 85% and hospitalizations for diarrhea by 42%. (Details here in the current issue of the New England Journal of Medicine). The RotaTaq vaccine, a genetically modified cow rotavirus, was given to 68,000 infants and was found to reduce severe disease by 98% and diarrhea-related hospitalizations by 63%. (Full study available here).

A current problem, however, is the cost of these vaccines. These new vaccines are projected to cost approximately $100 each, or more, putting them far out of the reach of most third world countries, where even $1 for a vaccine is often more than most people and the government can afford. More widespread use in countries that can afford them, such as the United States, could serve to drive these prices down, but this will still take time—-and meanwhile, over half a million children are dying each year from this virus. (To give some numbers for comparison, about 4 million babies are born each year in the U.S.--imagine waiting for a vaccine for a disease that killed 15% of them every year. ) Not surprisingly to anyone who follows global health issues, the Bill and Melinda Gates Foundation, among others, are working to accelerate this process, and get this vaccine to those who need it most.

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Not gotten enough PZ Myers at Pharyngula?

Just in case you're not getting enough of everyone's favorite "mad scientist," today over at DailyKos, DarkSyde's published an interview with Pharyngula's PZ Myers. Love him or hate him (and I can already see some of his quotes in there again being mined by the Discovery Institute...), you gotta admit he's an interesting fella. And I won't even dig at him too badly for this quote regarding the administration at his university:

They don't agree with everything I say -- in particular, I suspect my anti-religious stance might give a few of our administrators' ulcers -- but they're also committed to the principles of academic freedom.

That "stress-->ulcers" thing ain't ever gonna die, is it? :)

Thursday, January 05, 2006 

What a difference a molecule makes...

Microbial ecology, and its relation to the development of infectious disease, is an ever-growing field of study. Of course, there are a vast number of bacterial species living amongst us, most of which do not cause us any harm. Others may infect us only when, so to speak, the stars align in a certain manner: when a number of factors collide that result in the development of a diseased state. For instance, we may already be immunocompromised due to the presence of another infection—something minor, such as a rhinovirus, or something more serious, such as HIV—and this chink in our armor allows another organism to more easily infect, and potentially damage, us.

Other agents in the environment also play a key role in the ecology of potentially pathogenic microorganisms. A recent study in Science highlighted one of these that appears to play an important role in the ecology and evolution of Vibrio cholerae, a major human pathogen of the past several centuries.

V. cholerae is the bacterial agent of cholera, a deadly water-borne disease. The bacterium itself is somewhat of a boomerang or kidney bean shape, and can be found in a number of aquatic environments of varying salinity. Cholera has killed millions over the past 200-odd years, frequently re-appearing in pandemic form after initially emerging from India in the early 1800s. Infection with the bacterium can lead to severe gastrointestinal problems, and the production of copious amounts of "ricewater stool." Death is generally due to severe dehydration. It’s also a bacterium that has played a key role in the development of the very science of epidemiology. John Snow, considered the “grandfather” of epidemiology, became famous for tracing a 1854 outbreak of cholera in London to a contaminated well, introducing the basic principles of epidemiology along the way.

More recent research has shown that in nature, the bacterium uses the polymer chitin as both a food source and an anchor. Chitin is the second most common polymer on earth (beaten only by cellulose), and is the most abundant in the marine environment, where V. cholerae thrives. Chitin can be found in a number of diatoms, in the exoskeletons and fecal material of arthropods, and in fungi, just to name a few sources.

Why does this matter? V. cholerae that are associated with chitin have been found to be more highly resistant to acid—a primary defense mechanism against food (including water)-borne pathogens. Chitin surfaces can also serve to concentrate these bacteria. Biofilms of V. cholerae on a single chitin-containing plankton, for example, may be enough to constitute an infectious dose of the organism-—meaning you’d have to ingest an incredibly small amount of contaminated water in order to develop disease. If this wasn’t all bad enough, the new study by Meibom et al. shows that chitin causes V. cholerae to become naturally competent—-it makes it take up DNA.

Previously, V. cholerae wasn’t thought to be naturally competent (also referred to as "naturally transformable"). Though it was known that there was a large amount of genetic diversity within the species, it was thought this was largely due to transduction--movement of genetic material between bacteria by viruses, since in laboratory culture, V. cholerae didn't readily take up DNA. Meibom et al. showed that when V. cholerae were grown in the presence of chitin polymers, they took up a Kanamycin resistance gene at much higher rates than isolates grown in the same medium without chitin--the chitin caused them to become competent.

Now, to return to microbial ecology and evolution. I already mentioned that chitin is the most abundant polymer in the aquatic environment, and that the results of this new study show that chitin can greatly increase the possibility of horizontal gene transfer in V. cholerae. Imagine, now, what can happen when there’s a copepod bloom (literally "oar foot;" this is simply a general name for a number of aquatic crustaceans)—-a giant increase in the population of these (chitin-containing) animals, in water that’s contaminated with V. cholerae. Under these conditions, the potential for rapid evolution of these populations of bacteria--and hence, the transmission of novel strains to humans--may be immense, if the laboratory findings hold up under natural conditions.

Indeed, it was already known that weather conditions that can lead to these copepod blooms played a role in cholera outbreaks--and scientists have been working on modelling the conditions that may lead to cholera outbreaks, as well as testing additional potential environmental conditions that play a role in disease. Will this help prevent--or at least provide advance warning of--cholera outbreaks in the future? Time will tell. In the meantime, I wonder how many other bacteria that aren't considered to be naturally transformable (such as Group B strep, which I discussed here) would be if we only found the right set of conditions.

Biology, Cholera, Evolution

Wednesday, January 04, 2006 

2005 Medical weblog awards--voting open

Voting's open at you can go here to vote. Aetiology is up for best new blog and best clinical blog. I don't have a chance in hell 'cause my readership's still pretty low compared to some of the other sites listed, but I'd appreciate it if y'all could help me not get my ass kicked *too* badly. Thanks muchly to those of you who nominated this blog in the first place, and more thanks to those of you who take the time to head over there and vote. This certainly isn't the biggest place in the blogosphere, but it's cool to be appreciated by those of you who do check in regularly.


This view of life

Over my "vacation" (which unfortunately ended up being more work than play), I was at a dinner with two of my best friends from the past 15-odd years. For whatever reason, the topic turned to evolution--and we quickly realized that we had, erm, differing opinions on whether evolution actually occurred or not. Now, this was pretty depressing to me, as both of them are very intelligent women, and one happens to work in a scientific field. So, we retreated to a coffee shop for some animated conversation on science, religion, and politics. I don't know if I changed any minds or not, but that wasn't really my goal anyway--rather, just to talk about the evidence that supported evolution, and to discuss their own reservations and objections. Obviously there were only so many things we could cover, but it was an interesting chat (and I hope I wasn't too harsh. It's a topic that makes me a bit...excitable.)

Anyhoo, I wish I'd had this op-ed on me. Written by evolutionary biolgist Olivia Judson, it highlights just a few things that make evolution so amazing:
Organisms like the sea slug Elysia chlorotica. This animal not only looks like a leaf, but it also acts like one, making energy from the sun. Its secret? When it eats algae, it extracts the chloroplasts, the tiny entities that plants and algae use to manufacture energy from sunlight, and shunts them into special cells beneath its skin. The chloroplasts continue to function; the slug thus becomes able to live on a diet composed only of sunbeams.

Still more fabulous is the bacterium Brocadia anammoxidans. It blithely makes a substance that to most organisms is a lethal poison - namely, hydrazine. That's rocket fuel.

And then there's the wasp Cotesia congregata. She injects her eggs into the bodies of caterpillars. As she does so, she also injects a virus that disables the caterpillar's immune system and prevents it from attacking the eggs. When the eggs hatch, the larvae eat the caterpillar alive.

It's hard not to have an insatiable interest in organisms like these, to be enthralled by the strangeness, the complexity, the breathtaking variety of nature.
This is what I find so incredibly cool about biology. It's not quite like any other science--life makes it messier.

In Jurassic Park, Jeff Goldblum's character, skeptical of the measures that have been implemented to control the park's dinosaur inhabitants, notes that "life will find a way." And indeed, it does--in nature as well as in the movies. And for me, it's so interesting to learn about, as Judson describes it, the "breathtaking variety" of those ways. Hairworms making their grasshopper hosts take a dive. Tiny molecular changes that can result in drastic effects on an outcome, or even lead to a cultural phenomenon. Sure, sometimes it's gruesome; the dearly departed WinAce's collection of organisms that look designed has a plethora of fascinating--if somewhat nasty--organisms that are part of this variety. Life ain't always beautiful butterflies and flowers--it's also parasites, and bacteria, and a whole lot of "kill or be killed" situations. And while biology doesn't rely as much on equations and formulas as some of the other natural sciences, Judson notes:
It's that small facts add up to big pictures. For although Mother Nature's infinite variety seems incomprehensible at first, it is not. The forces of nature are not random; often, they are strongly predictable.

For example, if you were to discover a new species and you told me that the male is much bigger than the female, I would tell you what the mating system is likely to be: males fight each other for access to females. Or if you discover that the male's testicles make up a large part of his weight, I can tell you that the females in his species consort with several males at a time.

Suppose you find that a particular bacterium lives exclusively in the gullets of leeches and helps them digest blood. Then I can tell you how that bacterium's genome is likely to differ from those of its free-living cousins; among other changes, the genome will be smaller, and it will have lost sets of genes that are helpful for living free but useless for living inside another being.
And while we find much that is predictable, many interesting areas of research seek to discover why we see something that, on the surface, *doesn't* fit those patterns. Why would some populations, for example, have a higher rate of the gene that causes sickle cell anemia, an often-fatal condition in people who possess 2 mutant copies of the gene? It didn't seem to fit--until it was noted that the heterozygotes had greater resistance to malaria, and thus, there was a reason for this unexpected pattern.

It truly is humbling to think about all that we've discovered about the variety of life on this planet, and even more humbling to consider the vast amount we know little or nothing about. Alas, the experience of Judson is all too common:
When I was in school, I learned none of this. Biology was a subject that seemed as exciting as a clump of cotton wool. It was a dreary exercise in the memorization and regurgitation of apparently unconnected facts. Only later did I learn about evolution and how it transforms biology from that mass of cotton wool into a magnificent tapestry, a tapestry we can contemplate and begin to understand.
I think I've mentioned before that this my high school bio class was like this as well--lots of memorization, a good dose of anatomy, but no emphasis on evolution to tie it all together. In fact, I thought biology was boring before I took an intro course in college. I'm happy to admit I was totally wrong (something I don't do very often!).
Some people want to think of humans as the product of a special creation, separate from other living things. I am not among them; I am glad it is not so. I am proud to be part of the riot of nature, to know that the same forces that produced me also produced bees, giant ferns and microbes that live at the bottom of the sea.

For me, the knowledge that we evolved is a source of solace and hope. I find it a relief that plagues and cancers and wasp larvae that eat caterpillars alive are the result of the impartial - and comprehensible - forces of evolution rather than the caprices of a deity.

More than that, I find that in viewing ourselves as one species out of hundreds of millions, we become more remarkable, not less so. No other animal that I have heard of can live so peaceably in such close quarters with so many individuals that are unrelated. No other animal routinely bothers to help the sick and the dying, or tries to save those hurt in an earthquake or flood.
I very much agree with this. Elsewhere online, I was involved in a discussion about evolution with a number of people with a host of different beliefs, from atheist to a self-described fundamentalist Christian. One Christian (who actually happens to be in seminary) stated his view on the topic:
And for me, there is something deeply spiritual about that idea, of connectedness to all of the planet on some level. I don't find that evolution challenges my spirit; rather, learning more about how nature interconnects allows me to find more footing with my own life and walk with God.
This feeling of interconnection is something any of us can experience, regardless of our religious beliefs (or lack thereof). To steal a quote from Darwin, there is grandeur in this view of life--and I'm happy I evolved.


Tuesday, January 03, 2006 

Back from the net void...

I love heading home and seeing family, but man, does it get exhausting. I'm ready for a vacation from my "vacation" now (in scare quotes 'cause I spent way too much time working on a book manuscript), but alas, it's time to get back to the real work--after I wade through a mountain of email. Ugh.

About me

  • I'm Tara C. Smith
  • From Iowa, United States
  • I'm a mom and a scientist, your basic stressed-out, wanna-have-it-all-and-do-it-all Gen Xer. Recently transplanted from Ohio to Iowa, I've spent most of my life in the midwest (with 4 years of college spent out east in "soda" territory). My main interest, and the subject of my research, is infectious disease: how does the microbe cause illness? What makes one strain nasty, and another "avirulent?" Are the latter really not causing any disease, or could some of those be possible for the development of chronic disease years down the road? Additionally, I've spent a lot of time discussing the value of teaching evolution, and educating others about "intelligent design" and other forms of creationism. My interest in history of science and medicine is also useful as a way to tie all of the above interests together. [Disclaimer: the views here are solely my own, and do not represent my employer, my spouse, that guy who's always sitting by the fountain when I come into work, or anyone else with whom I may be remotely affiliated.]
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