Domain: nih.gov
Stories and comments across the archive that link to nih.gov.
Comments · 5,290
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Meninist?
Perhaps not the best name: http://www.pubmedcentral.nih.gov/articlerender.fc
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Re:Cutting off nose to spite face
Great scientific pseudoachievements / pseudoadvances:
Phlogiston (a THEORY!! WOOO!)
http://www.jimloy.com/physics/phlogstn.htm
Montgolfier gas
http://www.chm.bris.ac.uk/webprojects2003/hetherin gton/final/montgolfier_bros.html
LSD as a mind control drug
http://www.mindcontrolforums.com/lsd-mc-cia.htm
(to be differentiated from drug addiction, which is certainly controlling)
Frontal lobotomies
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd= Retrieve&db=PubMed&list_uids=6379496&dopt=Abstract
Perpetual motion
http://burtleburtle.net/bob/physics/whythere.html
the 4^H5^H3 kingdom classification of organisms
http://encarta.msn.com/media_461530646/Classificat ion_of_Organisms.html -
I don't trust NCCAM
You're painting with far too wide a brush. Many alternative medicine practitioners and researchers are using the scientific method and expanding our knowledge of medicine. Take a look at the National Center for Complementary and Alternative Medicine - part of the U.S. National Institutes of Health. http://nccam.nih.gov/
I've already taken a look. I recommend you look at this.
GMD
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Re:Why is this modded Insightful?!?
>Alternative medicine is welcome to use the scientific method
>to verify their claims. Until that time, it belongs squarely
>in the "anti-science" camp.
You're painting with far too wide a brush. Many alternative medicine practitioners and researchers are using the scientific method and expanding our knowledge of medicine. Take a look at the National Center for Complementary and Alternative Medicine - part of the U.S. National Institutes of Health. http://nccam.nih.gov/ -
Re:"ergonomic" devices are not ergonomic at all
Have you ever heard of carpal tunnel syndrome? What you are describing is the worst possible thing to do to your wrists. The large muscles and ligaments in your shoulder and elbow can take some repetitive use. The delicate tendons in your wrist will swell from mousing all day using the method you described, pinching off the carpal tunnel nerve. Extremely painfull and debilitating. That's why ergonomic mice require macro-movements with the whole arm rather than the delicate micro movements used in fingertip mousing.
There are other conditions the position you mentioned can cause or aggravate, such as bursitis and tendonitis.
The best defense is to take a break every now and then and stretch out the wrist. General body stretching can also help back pain which can result from sitting in a chair all day. -
Re:Interesting...
...but probably not true. This has been soundly refuted (in my judgement) by a 2003 paper published at Berkeley. See reference below. CCR5-delta32 (the allele) does protect against HIV, but it's unlikely it's the result of the genetic mutations of plague survivors. More likely can be traced back to smallpox survivors from 700 years ago. Check out the ref, it's online. HIV has many strains, not just two. HIV is rapidly mutating. If you're into this topic, check out the many papers at www.cdc.gov. Marianne reference: Proc Natl Acad Sci 2003 December 9; 100(25): 15276-15279 Published online 2003 November 25. doi: 10.1073/pnas.2435085100. c2003 National Academy of Sciences "Evaluating plague and smallpox as historical selective pressures for the CCR5-[Delta]32 HIV resistance allele", by Alison P. Galvani* and Montgomery Slatkin, Department of Integrative Biology, University of California, Berkeley, CA 94720 *To whom correspondence should be addressed. E-mail: agalvani@nature.berkeley.edu. Edited by Robert May, University of Oxford, Oxford, United Kingdom Received August 8, 2003; Accepted October 3, 2003. http://www.pubmedcentral.nih.gov/articlerender.fc
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Re:but was it designed, and why??
Now to get back on topic, I've also heard that one caution people have about gene therapy (such as slipping in a gene that protects against HIV) is that if there are these ancient unexpressed viruses lying about in our DNA, what might we do if we muck around with it by slipping in some new genes?
There's problems enough in randomly inserting the desirable DNA into random locations in the genome. Like screwing up a regulatory gene and causing leukemia. The odds of a randomly inserted sequence being in exactly the wrong place in any one cell are pretty small, but when you're transfecting millions of cells at a time, the odds don't look so good: A Pubmed link: follow the "related articles" link for more detail
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I think what's more interesting
is how this mutation got into the general population in the first place.
The current operating theory, as I understand it, is that it originated (uhhh
... mutated?) somewhere in southern Finland, made it's way across the Baltic Sea to Sweden, and from there fanned out across Europe and West Asia during the period of Viking expansion -- from about the 8th-10th centuries.The mutation is found in native populations as far away as Cyprus and North Africa; but the closer you get to Scandinavia, the more prevalent it becomes. So, really, the Vikings were doing the rest of Europe a public service while they were casually burning it into the ground.
Plunder. The gift that keeps on giving
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Gene linksThe CCR5 gene (which includes the CC5's with the delta 32 mutation) is on chromosome #3. You can look over the DNA code (nucleotides, codons etc.) and get more information on a number of sites:
UCSC Genome browser - has the whole gene, but you can zoom in on segments if you want.
NIH - this has links or links to links of everything you'd want to know.
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Re:medicine
Five to ten years or more? That's incredibly optimistic to put it that way, even with the "and more". Plus, he's not saying anything about a cure, just about treatment. Does anyone foresee gene therapy in action within the next decade?
Instead, what we'll see is early detection of genetic disease, and from a pharmacologicoprofitability standpoint, plenty of maintenance drugs to help keep the genes from being fully expressed or to mitigate the symptoms.
/cynicism
OTOH, early detection of as-yet uncurable genetic disease has led to marvelous increases in quality of life for people who are diagnosed. Let the research continue!
An earlier post that mentions Usher Syndrome is a great example. It's amazing that a ten-second Google can show an example of genetic testing providing early diagnosis and better treatment:
In April 2003, NIDCD researchers, along with their research collaborators from universities in New York, N.Y., and Tel Aviv, Israel, pinpointed a mutation, named R245X, of the PCDH15 gene that accounts for a large percentage of USH1 cases in today's Ashkenazi Jewish population. (The term Ashkenazi describes Jewish people who originate from eastern Europe.) Because of this finding, researchers conclude that Ashkenazi Jewish infants with bilateral, profound hearing loss who lack another known mutation that causes hearing loss should be screened for the R245X mutation. If a child's USH1 is discovered early on, before she loses the ability to see, then that child is more likely to benefit from the full spectrum of intervention strategies that are available to help her communicate and participate in life's activities.
From :http://www.nidcd.nih.gov/health/hearing/usher.asp #e
BTW, about 1% of Ashkenazi carry one copy of the R245X mutation... so about 1 in 400 Ashkenazi have Usher Syndrome by my calculation. -
Re:Patented
First of all, most SNPs are free information. dbSNP contains ~5 million validated SNPs and ~27 million reported SNPs in humans. Celera owns a lot of SNP finds, but most are junk (sequencing errors) and they will be giving them to the free databases soon.
However, the importance of this article has nothing to do with the number of SNPs available or the fact that the SNPs are common (because of the low sample size). The whole point is to have SNPs that exist in ~50% of the population so that the haplotype can be determined. The Haplotype shows which segments of the genome tend to be inherited together. This can be traced back for multiple generations of inheritance - essentially there are ancient haplotypes and more modern haplotypes. The importance of looking at haplotypes is that it allows researchers to see which region an important mutation relating to a disease may occur in. Note that just by knowing which haplotype the disease causing mutation occurs in does not let us know which SNP or insertion/deletion event causes the disease. -
Re:I don't get it...
and I think there is a use for magnesium oxide.
Use it when stuck in rush hour traffic! -
Link to 37CFR [Re:Not right!]
Here is a link for the 37CFR at s-edison.info.nig.gov
... Patents can be broken if a national interest demands it. -
Re:Source of creation, or evolution?
Eugene Koonin and William Martin just came out with a fascinating paper on the LUCA (Last Universal Common Ancestor). Link to Article on Pubmed
In brief: the RNA/DNA/protein worlds evolved at hydrothermal vents in inorganic chambers. At some point, the information molecules sheathed themselves in lipids and sugars, and free-living cells emerged from the vents.
In response to at least one of your questions: the LUCA to cell transition may have taken 500 million years (primordial soup = 3.5bya, 1st evidence of prokaryotes = 3bya). That's not very long on a geologic, or even evolutionary, time scale (about 20x the time for humans to diverge from apes). But it could have been happening at thousands and thousands of vents worldwide, in thousands and thousands of inorganic chambers per vent. All of that combinatorial power adds up.
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Re:Not right!
there is no Pandemic. It too is a fiction. Bird Flu is indegenous to the Americas. It in no way fits the profile of a "Pandemic." It is too lethal to be a viable pathogen. It kills itself off.
That logic is simply ridiculous, with the high population densities of cities and the speed and frequency with which people travel. You're seriously suggesting that a human-transmissible bird flu wouldn't be a "viable pathogen" because it would kill everyone in Taiwan too quickly to spread? Even if that were true, which is isn't, wouldn't you expect the Taiwanese to be concerned about that?
The idea that a human-transmissible bird flu would be dangerous has already been demonstrated by the 1918 flu epidemic that killed 20-50 million people. The 1918 virus was recently reconstructed, and it was found to be very similar to the bird flu viruses that are around in Asia today. The actual scientific paper, available here states:
"Until now, the exceptional virulence of the 1918 pandemic influenza virus has been a question of historical curiosity. Herein, we demonstrate the successful reconstruction of the 1918 pandemic virus in order to understand more fully the virulence of this virus and possibly of other human influenza pandemic viruses. Because the emergence of another pandemic virus is considered likely, if not inevitable (25), characterization of the 1918 virus may enable us to recognize the potential threat posed by new influenza virus strains, and it will shed light on the prophylactic and therapeutic countermeasures that will be needed to control pandemic viruses."
Tamiflu, assuming Bird Flu were to mutate into a dangerous flu "Pandemic", would be of no value. The disease kills in about 9 days. It is symptomatic only 2 of those days. By the time a person knew they were getting sick, getting a prescription would not save them. Its value is probably null anyway as it appears it is ineffective against the disease. Its only value would be prophalaxis and that is questionable.
A scientific paper demonstrating Tamiflu's effectiveness against the H5N1 virus is here .
A paper demonstrating Tamiflu's effectiveness against the 1918 flu virus (which is similar to the virus we fear will emerge) is here. -
Re:I don't blame them.
There are two, independent questions here:
a. The important question - can we save money by moving all drug R&D into the public sector,
and
b. The ancillary question - how much of the money spent to do drug R&D is really private, under the current circumstances.
I'm not that interested in point b, which is the only one you seem to want to talk about.
1. They're not well-established and credible journals.
Challenge is a bit odd, but Health Letter and Journal of Health Policy are both reputable - more importantly, you already complained about the bibliography being too long, and the Challenge article contains a great many citations which you can follow, if you really care about the question and aren't just arguing for the sake of it.
2. They weren't studies, they were op-ed and promotional pieces in the journals.
How exactly are you concluding that if you cannot read them? The *second three* (helpfully labeled as position papers) are indeed opinion articles.
If you actually knew anything about medline you'd know that it only returned recently published articles - no 19th century cadavers. If you know anything at all about biology and chemistry, you'd know why I find your whole line completely baffling - drug companies do hardly *any* fundamental research at all, they just develop drugs. This is simply common knowledge among all researchers, the drug companies don't even deny it.
Here is one example:
Telmisartan blocks the action of Angiotensin. As mentioned in this abstract. Angiotensin was discovered by this man, in the public sector. If you type angiotensin into medline (as I just did) you will find many examples of ongoing fundamental research on angiotensin, certainly useful to drug companies - of the ones I checked, all done by academic scientists. Comb the list for counter-examples, see if you can find any.
To be blunt, your assertion is from Mars. I'm not sure anyone even bothers to do a careful study of the question, it's regarded as so obvious. 40 years ago the situation was significantly different - private drug companies still depended heavily on public science, but it wasn't nearly so extreme as it is today.
Anyway, if you actually care about the question ask Dean for the articles, I have to go to bed. -
Re:I don't blame them.
There are two, independent questions here:
a. The important question - can we save money by moving all drug R&D into the public sector,
and
b. The ancillary question - how much of the money spent to do drug R&D is really private, under the current circumstances.
I'm not that interested in point b, which is the only one you seem to want to talk about.
1. They're not well-established and credible journals.
Challenge is a bit odd, but Health Letter and Journal of Health Policy are both reputable - more importantly, you already complained about the bibliography being too long, and the Challenge article contains a great many citations which you can follow, if you really care about the question and aren't just arguing for the sake of it.
2. They weren't studies, they were op-ed and promotional pieces in the journals.
How exactly are you concluding that if you cannot read them? The *second three* (helpfully labeled as position papers) are indeed opinion articles.
If you actually knew anything about medline you'd know that it only returned recently published articles - no 19th century cadavers. If you know anything at all about biology and chemistry, you'd know why I find your whole line completely baffling - drug companies do hardly *any* fundamental research at all, they just develop drugs. This is simply common knowledge among all researchers, the drug companies don't even deny it.
Here is one example:
Telmisartan blocks the action of Angiotensin. As mentioned in this abstract. Angiotensin was discovered by this man, in the public sector. If you type angiotensin into medline (as I just did) you will find many examples of ongoing fundamental research on angiotensin, certainly useful to drug companies - of the ones I checked, all done by academic scientists. Comb the list for counter-examples, see if you can find any.
To be blunt, your assertion is from Mars. I'm not sure anyone even bothers to do a careful study of the question, it's regarded as so obvious. 40 years ago the situation was significantly different - private drug companies still depended heavily on public science, but it wasn't nearly so extreme as it is today.
Anyway, if you actually care about the question ask Dean for the articles, I have to go to bed. -
Fallacies
"The majority of the expenses associated with new drug discovery are actually made in the public sector - by Universities and so forth."
Private R&D spending on pharmaceuticals exceeds public R&D spending. This is actually true for R&D in general ($132 billion federal vs. $190 billion industry), and it's true for pharmaceuticals ($30 billion federal vs. $49 billion industry). For the first 3 figures, see here:
http://www.aaas.org/spp/rd/rd06main.htm [chapters 2 & 4]
For the last figure, see here:
http://www.phrma.org/publications/publications//20 05-03-17.1145.pdf
The last is an industry organization, but r&d spending is part of companies' public SEC filings and the figures are in line with the aggregate numbers.
It's a fallacy that public and private pharmaceutical r&d are substitutes. Public r&d tends to focus on basic science while private r&d focuses on specific drug development and testing. Here it is from the horse's mouth:
http://ott.od.nih.gov/Reports/211856ottrept.pdf
The public sector would be just as good at developing drugs as it would be at making cars and televisions (see Union, Soviet).
"these additional resources are a *fraction* of the total increase in drug prices that result from the patents they are awarded"
If patents over-compensate drug companies, then we'd see a lot more entry into the (apparently very lucrative) drug business by new firms until these extra-ordinary returns are competed away. Even with patent protection, lucrative business models attract entry by competitors until excess profits are competed away. -
Re:Not right!
Actually, the U.S. government wouldn't have to invoke eminent domain if they wanted to do something like this. Most of the basic research that leads to these drugs, vaccines, etc. is paid for by the federal government. The gov't then licenses this technology to biotech and pharmaceutical companies to develop a practical application, like a drug. The private company keeps IP rights to the developed drug/vaccine/whatever.
In these licensing agreements, however, is a clause that allows the government, in an emergency, to manufacture the drug/vaccine/whatever, or give a license to another manufacturer to increase supply of the product. So they're not invoking eminent domain to seize IP, they're availing themselves of a contractual provision. Among other things, this means the gov't doesn't have to compensate the IP holder.
See, for example, section 5.04(b) of the Model PHS Patent License Aggreement--Exclusive, available here. -
Re:Although I haven't read TFA...
It used to be that abortions were legal in the U.S. up until 'quickening' or fetal movement. Now groups want to say that life begins before an embryo has even implanted or differentaited.
RU-486 results in 1 death in 200,000 making it twice as safe as penicillian. Those people who have suffered the worst side effects were those who took it despite being having contra-indicating factors warning against its use.
(from religioustolerance.org)
RU-486 still has complications in 8-10% of cases requiring surgical follow up, which I think is what you're alluding to.
http://www.americanpregnancy.org/>
But I thought these folks were ALL ABOUT women's health!
I used to think doctors were all about health too, but most of them don't seem to care.
I'm saying this as a guy who has met a fair number of doctors who were simply unable or unwilling to do simple diagnostic work. Apathy and negligence are problems throughout the medical profession. The number of unreported incidences of malpractice is high. A significant accident occurs in one out of three major operations, if memory serves. I could be off on this, I don't have time to google it. All I know is that I've had one friend injected with so much insulin that they went into a coma, and my mom had her teeth filed down by the dentist when she specifically asked for them not to be.
Vaginal administration of RU-486 isn't contra-indicated, however. It's an off-label use, which is different. You haven't really supported the notion that it should be banned (though from what I've googled on the NIH research, oral administration is far more effective.), or even supported the notion that that was in fact the cause of these women dying.
Bacterial infections are treatable, though some strains of S. Aureus are now resistant even to vancomycin, and starting to become resistant to the various fluroquinolones. But considering that they don't know the facts related to these women's cases, and that the infections weren't treated properly, it would seem that these women simply weren't receiving proper medical care to begin with in terms of follow up visits. That, rather than a pill, was the cause of their death. The "human at conception" camp opposes RU-486 for reasons that have nothing to do with protecting women's health.
When it comes down to it, abortion is still far safer than pregnancy. There were 399 deaths from pregnancy in 2001 alone.
Up until the late 1800s, 'quickening' or the time when fetal movements could be felt, was the point of no return for a pregnancy. The notion that 'life has always begun at conception' according to religious doctrine is simply not true. If you ask someone to show you a biblical passage that makes the claim that life begins at conception, I promise you they'll show you a passage that says somthing else entirely. Without fail. The notion that "people are fully human at conception" is literally the belief that undifferentiated cells are people.
But when even Bill Frist tried to argue that it should be slightly later, he was essentially shouted down by his own party who didn't want to hear it. -
Re:Akin to bicycle riding?The article describes how activity in the basal ganglia changes when the subject experiences new situations, vs. how it behaves when following a pre-established pattern in response to a set of contextual cues.
Riding a bike, on the other hand, has a lot more to do with motor control patterns which I believe are established in the cerebellum. There have been studies on people with brain damage (gunshot wounds to the head, etc.) which lead to a model where the cerebellum is the center of memory and learning for things like riding a bike or playing piano. Not being a neuroscientist, I don't know the present state of research, but I think these motor-control "habits" are processed differently from habits like wanting to eat, drink, smoke, etc. in response to stimuli.
There's an article that would shed a lot of light on the discussion if it wasn't hidden behind subscription mechanisms (a pox on scientific journals that don't give open access to publicly-funded research!)
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Ok how about this
Earlier today I ate a lot of rice. Just now, I took two gigantic shits about 15 minutes apart. Anyway, I was thinking, "what's up with that?" because I am usually very regular. Anyway I googled the terms rice and fiber together. You know what I found? This:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd= Retrieve&db=PubMed&list_uids=3035151&dopt=Abstract
Note what country this came from. Now this fecal recognition phone story appears on Slashdot. Coincidence? I think not.
Think about it. -
personally i dont believe it but..
here are some studies that show there isnt a link between mesothelioma and smoking.
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cmed .section.21842
"Although asbestos exposure and cigarette smoking act synergistically to produce bronchogenic carcinoma, smoking is not a factor for mesothelioma.183,192,238,291" -
Re:which scientific survey
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Re:which scientific survey
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Re:It is still in doubt actually
Marijuana has certainly received some unfair press in the past, but that does not mean that we should glorify it to the other exreme: smoking marijuana is not harmless.
Smoking anything is bad for your lungs, whether by carcinogens or just damaging chemicals. Marijuana smoke has been found to depress the local immune system (read: your lungs). Studies have been done correlating marijuana smoking with schizophrenia (example), although rarely is there any claim of causality.
Admittedly, I am an occasional smoker, but while I appreciate the positive effects, I also recognize the negative ones. Ultimately, I believe that to smoke or not is simply a personal decision, like the rest of the human diet. It will be great to know more about the ways that the cannabinoid family of chemicals affect the brain, but it's unfair to portray them either as a villain or a hero. They're simply chemicals whose effects are still widely undetermined. I applaud the fact that people are researching the topic, however, and I too wish that research into such topics wasn't so tightly controlled. Perhaps when the political pendulum swings back towards the liberal (and hopefuly more research-and-science-oriented) end of the spectrum we will see more and less obstructed research on topics like this and many others. -
Re:The American Antibiotic Addicts
I take it that you are neither a doctor nor a pharmacist. Azithromycin is an antibacterial agent (not an antifungal) that is chemically similar to the more widely prescribed erythromycin. While Azithromycin may be used in conjunction with antifungal agents, it in and of itself has no antifungal activity.
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Re:Isn't that a bit like
Not to mention deforestation so they have somewhere to put cows. Y'know, until the ground becomes unusable because it no longer has forest to protect it from the weather.
The big efficiency issue with cows, however, is people putting them on land that would be fine for growing more or less anything directly consumable by humans, which happens a lot more due to the increased demand for meat, because everyone seems to have this belief it's a good idea to eat lots of it. Actual recommended daily intake of meat is 5-7 ounces/140-200 grams.
So, right, yeah, had a point. Cattle aren't efficient if used where vegatables/fruit could be grown, and eating less wouldn't do you us any harm. -
There is more than 1 genes for HGH ???
Hey. It looks there are two genes
... GH1 and GH2.
Some cut'n'pastes from http://www.ncbi.nlm.nih.gov/entrez/ ...
Official Symbol: GH1 and Name: growth hormone 1 [Homo sapiens]
Other Aliases: HGNC:4261, GH, GH-N, GHN, hGH-N
Other Designations: pituitary growth hormone
Chromosome: 17; Location: 17q24.2
GeneID: 2688
Official Symbol: GH2 and Name: growth hormone 2 [Homo sapiens]
Other Aliases: HGNC:4262, GH-V, GHL, GHV, hGH-V
Other Designations: placenta-specific growth hormone; placental-specific growth hormone
Chromosome: 17; Location: 17q24.2
GeneID: 2689 -
Re:Either that or....
For example, you'd expect to see animals with 1 arm, 2 arms, 3 arms, 10 arms, no arms, half an arm, round arms, and so on for every part of the body while evolution is fine tuning this stuff.
In high school, a friend of mine was born with only one small, withered arm. Three arms in a person would be difficult from a genetic standpoint, because we develop two arms due to the initial symmetrical division of the body during development. You could have three of lots of organs, but it sure would be difficult to get all the plumbing right and have a surviving person come out of that development.
On the other hand (no pun intended) polydactylism, having one or more extra fingers or toes, is probably the most common abnormality found at birth. The tendency to have offspring with polydactylism is possibly genetic in some instances.
Syndactylism, having no fingers or toes, can also be due to a genetic mutation. -
Re:Yeah it's flexibleVolatile has a few meanings, besides the popular "explosive", it also means to evaporate easily - the usual use in science.
Here is an example of a paper with the term "Non-volatile protein"
I'm not in this field, but I would assume that in the context in this thread it is not evaporating but used sort of incorrectly (IANABC) and probably what is meant is that the protein stays put and doesn't send out little pieces to alert the immune system that a foreigner is present, but then again, I am not a BioChemist.
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Re:I echo the above statements
My Pentium III test machine with 256Meg of Ram blew away a dual processor Intel system with 1Gig of Ram while parsing a 30Meg XML import/export file.
Heh, a little offtopic but - This is why I hate XML. It's so bloated. You take 1 to 6 hours parsing a 30 megabyte XML file in C? I was just tasked with parsing out some select data from a 37 gigabyte XML file (870 million lines). I tried all sorts of optimizations and parsers upon finding that it might take days to parse. My solution - 50 lines of perl using regular expressions. I run this on a dual processor 3.something with 2 gigs of ram. It takes 5 minutes. If I coded it in C it would probably take 10 seconds but it's not worth the time.
Here's the file and convertor if anyone wants to fuck around with nearly a billion (bloated XML) lines of genetic data:
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ASN_BINARY/Al l_Data.ags.gz
ftp://ftp.ncbi.nlm.nih.gov/asn1-converters/by_prog ram/gene2xml/ -
Re:I echo the above statements
My Pentium III test machine with 256Meg of Ram blew away a dual processor Intel system with 1Gig of Ram while parsing a 30Meg XML import/export file.
Heh, a little offtopic but - This is why I hate XML. It's so bloated. You take 1 to 6 hours parsing a 30 megabyte XML file in C? I was just tasked with parsing out some select data from a 37 gigabyte XML file (870 million lines). I tried all sorts of optimizations and parsers upon finding that it might take days to parse. My solution - 50 lines of perl using regular expressions. I run this on a dual processor 3.something with 2 gigs of ram. It takes 5 minutes. If I coded it in C it would probably take 10 seconds but it's not worth the time.
Here's the file and convertor if anyone wants to fuck around with nearly a billion (bloated XML) lines of genetic data:
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ASN_BINARY/Al l_Data.ags.gz
ftp://ftp.ncbi.nlm.nih.gov/asn1-converters/by_prog ram/gene2xml/ -
Great, but... bone loss still a problem
Not saying the bone loss problem can't be solved, but ever since hearing about the bone loss problem I've felt that radiation would be easier to solve than bone loss.
A simplistic source, (http://www.factmonster.com/ipka/A0778174.html) has this easy to digest quote
"... And because the gravity on Mars is only 38% of Earth's, ways to counteract any damaging effects of the weak gravity on their bodies, such as progressive bone loss and muscle atrophy, will have to be found. Currently, there is no fully effective treatment for microgravity-induced bone loss, and counter measures against bone loss are a top space science priority."
For deeper reading try:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd= Retrieve&db=PubMed&list_uids=15852539&dopt=Citatio n -
Re:Off topic, but money talks ...Canadians are the among the shyest people on the planet...
Not according to a recent study that busts the myths of many national stereotypes: National Character Does Not Reflect Mean Personality Trait Levels in 49 Cultures.
...For example, Americans believe the typical American is very assertive, and Canadians believe the typical Canadian is submissive, but in fact Americans and Canadians have almost identical scores on measures of assertiveness, a little above the world average.
...I think Canadians may have higher levels of passive aggression, which on the outside *may* look like they are more shy about things. But I am not so sure that it is always so passive.
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Re:Research Purposes
For example, if I had the money, I would love to finance a study to see how effective relaxation techniques (TM, Yoga, other breathing exercises, exercise...) are in reducing anxiety.
Look at the research of Jon Kabat-Zinn. Here's an example. -
Re:More info regarding that study.
Yes, many studies are funded by interests central to the study, and it seems possible this may influence the study in some cases. I do not know anything about that study in particular beyond what I have provided. There are many other studies on PubMed showing similar results for caffeine, though. Using the query terms "caffeine anxiety", "caffeine stroop", "caffeine concentration", etc may help you find more of what you're looking for.
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Re:Who needs tests when we have Tom Cruise
Actually, exercise does increase the dopaminergic tone in the brain, the mechanism involved is a short-lived change in gene expression that upregulates calcium transport. It has also been shown to increase the number of dopamine receptors in animal models.
This is relevant because the common mechanism of effect behind SSRI-based antidepressants involves the sensitization of the dopaminergic system via increased serotonin levels. Some antidepressant medication actually has no direct interaction with sertonin at all.
This study shows an effectiveness of 50% of the use of exercise in relieving symptoms of depression, which is approximately that of antidepressant medication or cognitive behavioral therapy alone. Of course, it is likely the best results would come from a combination of all three.
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a small margin of errorI think it is important to remember that this was a math exercise not a serious study with predictive power. I remember several years ago people thought the human genome project was insane. They thought it would take hundreds of years to catalog our entire genome and cost some ludicrous numbers of trillions of dollars.
Then:
In 1999, the goal of producing a "working draft" seemed very far away, with less than 15 percent of the genome sequenced. If the accelerated goals had not already generated a sense of urgency in the consortium, a decision by the sequencing center leaders at a February meeting in Houston would. At the meeting, the leaders accepted Dr. Collins' challenge to ramp up their efforts to produce a "working draft" by spring of 2000. By January 2000, the centers were collectively producing 1,000 base pairs a second, 24 hours a day, seven days a week, and 2 billion of the human genome's 3 billion base pairs were sequenced by March. At a White House ceremony hosted by President Bill Clinton in June 2000, Dr. Collins and J. Craig Venter of Celera Genomics, which had carried out its own sequencing strategy, announced that the majority of the human genome had been sequenced. [from here
I tried to find the graph of speed over time because I have seen itseveral times. It shows the exponential increase in the speed of the project. Apparently there are many scientists that believe with techniques as they are now we could repeat the project in 2 years if we started over. The indexing of information could have a very similar timeline. Very slowly at first and then as technology and specific methodology develop off you go. So the truth is... this is a guess. I wouldn't put too much faith in it.
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it was a wolf
Here is an analysis of the DNA describing it as a wolf.
Here is an article in Audubon magazine titled, "How Tasmania's Marsupial Wolf Became Extinct."
So, I think you have no idea what you're anonymously talking about.
Seth -
Garlic, the geek's friend.> Not a cure, but... got garlic?
>
> One hundred forty-six volunteers were randomized to receive a placebo or an allicin-containing garlic supplement [ ... ] The active-treatment group had significantly fewer colds than the placebo groupAh, Garlic. Best vegetable ever. The antisocial geek's friend.
I prefer my garlic the old-fashioned way. One head of garlic (peel, squeeze through garlic press or otherwise grind it into mush), raw, whipped into one stick (1/4 lb) of butter. Spread over bread (cheese optional), toast, eat. Throw a teaspoon or two into a bowl of piping hot pasta (and grate some real Parmigiana Reggiano over it, none of that powdered cheese in a can crap). As a side dish, slug down a glass or two of red wine.
Take another head of garlic, peel it, and toss 3/4 of the cloves into a whole raw chicken. Slip the rest of the cloves between the skin and the meat. Roast tha mothaplucka. Good eatin' again.
(Whenever you roast a chicken, just throw another head of garlic into the oven next to the chicken. When the chicken's done, squeeze the now-mushy cooked garlic into a small jar. Dip a hunk of fresh artisan bread into the garlic mush, and then into some extra virgin olive oil. Yet more good eatin'!)
Some people think I eat too much garlic. Not true. Only once have I eaten so much garlic in a single sitting that I've been able to smell garlic on my farts for the next three days.
People at the office tend to avoid me. In fact, if I eat enough of the stuff (see above), even people whose noses are stuffed up with the flu tend to avoid me.
Haven't had a cold in two years. Funny how things works out. Must be the garlic.
Damn, I love garlic.
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Re:I would be much more interested...Not a cure, but... got garlic?
One hundred forty-six volunteers were randomized to receive a placebo or an allicin-containing garlic supplement, one capsule daily, over a 12-week period between November and February. They used a five-point scale to assess their health and recorded any common cold infections and symptoms in a daily diary. The active-treatment group had significantly fewer colds than the placebo group (24 vs 65, P
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Re:Oh, great.
What about raynauds Syndrome. My Own mother suffers from this and causes her fingers to go cold. She wouldn't be able to buy groceries in the winter if the scanner checked temperature. For about an hour after being outside in the cold she has "dead fingers" they get all white and look kinda like deflated baloons. It's gross. Here's some back ground info. http://www.niams.nih.gov/hi/topics/raynaud/ar125f
s .htm -
Re:Big deal.
Yes, here's the pubmed entry:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=P ubMed&cmd=search&term=Strigiphilus+garylarsoni -
Re:closed source?
I checked Pubmed http://www.ncbi.nlm.nih.gov/ for pertinent papers. One that I found using "Wells F" as the search term was: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd
= Retrieve&db=pubmed&dopt=Abstract&list_uids=1253724 4&query_hl=13 Dont know if that is the same guy, though. -
Re:closed source?
I checked Pubmed http://www.ncbi.nlm.nih.gov/ for pertinent papers. One that I found using "Wells F" as the search term was: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd
= Retrieve&db=pubmed&dopt=Abstract&list_uids=1253724 4&query_hl=13 Dont know if that is the same guy, though. -
Floppy mitral valve
Mitral valve prolapse, fortunately, is not deadly. But the usual treatment always has the potential danger of valve infection. I hope the new technique will help prevent that problem.
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Re:Benefit of the doubt
http://stemcells.nih.gov/info/faqs.asp#both
According to the National Institute of Health you merely have to follow accounting procedure to ensure funding doesn't get mixed up.... -
Re:Define enterprise
Enterprise:
From http://wordnet.princeton.edu/perl/webwn?s=enterpri se
1. a purposeful or industrious undertaking (especially one that requires effort or boldness); "he had doubts about the whole enterprise"
2. an organization created for business ventures; "a growing enterprise must have a bold leader"
There you go, a purposeful undertaking that requires effort. Now try to imagine something done in business that does not fit that criteria. Or, an organization created for business. Hmm... ok, in other words, a company.
From http://www.cit.nih.gov/dnst/handbook/Main/glossary .htm
In the computer industry, an enterprise is an organization that uses computers.
Ha! There you go. PLEASE people, when you see this word, like others here have said, they are trying to shovel a load of shit directly down your throat, through the esophagus, into the stomach (possibly interacting with the spleen and/or liver), through both sets of intestines, and directly out your ass before recycling it back to your mouth.
That's exactly what they're trying to do, it means their product doesn't have any features that can be described in human readable language, so they need to say "well OUR product is specifically designed for organizations that require effort and use computers".
Well congratu-freakin-lations, get a patent, quick. -
Re:Email vs. MarijuanaMarijuana isn't addictive.
American Psychiatric Association's DSM-IV doesn't require drug users to go through withdrawal in order to classify them as addicts. Instead, the criteria for what is called "drug dependence" looks how deeply people are immersed in drug use, for its negative consequences for their lives, and for its disturbances of their normal life functioning, including family, work, and health.
Marijuana does not modify the brain. It affects it yes, but once it's gone the brain
is the same
Although science is not absolutely conclusive on this, it is fairly clear that Marijuana usage does permanently modify the brain to some extent. Once it is gone, the brain may be similar, but it is definitely not the same. As people age, they normally lose neurons in the hippocampus, which decreases their ability to remember events. Chronic THC exposure may probably hastens the age-related loss of hippocampal neurons. In one series of studies, rats exposed to THC every day for 8 months (approximately 30 percent of their lifespan), when examined at 11 to 12 months of age, showed nerve cell loss equivalent to that of unexposed animals twice their age
Study