The sequence read archives (such as the one hosted by NCBI) as a repository for this sequencing data, uses "compression by reference," a highly-efficient way to compress and store a lot of the data. The raw data that comes off these sequencers is often >99% homologous to the reference genome (such as human, etc), so the most efficient way to compress and store this data is only to record what is different between the sequence output and the reference genome.
How is this not just meaning no redundancy for the "same" digital object. Rather than host 1000 copies of the same file, Amazon minimizes redundancy and every cloud user who hosts the same file has access to the same block(s) of data.
The experiments in mice were performed at 12.5mg/kg, which would be (for the average 65-kg human) a shocking 812.5mg of Triclosan. If your standard amount of handsoap and toothpaste is 2ml that's like brushing your teeth with a 1/3 solution of triclosan and swallowing it.
Like most of the research in PNAS this was not subjected to the high level of peer review expected in most scholarly journals and this paper got through without regard to its relevance and real-world significance.
At a high enough dose, caffeine causes cancer in lab animals. But not at the doses even Slashdotters consume.
While your statement is correct the cancer risk is minimal.
A typical xray is about 1-10 mrem. You get about 5 mrem of radiation dose from just an airplane ride. If a child lives in a concrete apartment building he/she will receive 100 mrem just from the radiation the concrete gives off. Annual occupational exposure limits for radiation workers are 5000 mrem. A deadly dose of radiation is about 50,000 mrem.
For individual research units, the cost of maintaining the processing power and storage space for these types of projects can be cost-prohibitive. Cloud-based options offer distributed computing power and low-cost storage that is often a more economical solution that paying for the equipment in house, especially when genomic projects can come in spurts rather than a continuous stream.
Disclaimer: I work with large amounts of genomic data and use both in-house and cloud-based analysis tools.
Just call it what it is -- the internal version can be 1.0.0.3 or whatever, but the version on the box and in all literature can be Version 2009 (or the year of release). That was popular about 8 years ago...and still works too!
This research is far from novel. The technique of growing tumor-derived breast epithelial cells was championed by both John Brugge at Harvard and Mina Bissell at Berkeley. The authors of this BBC article should have done a little research before; this work has not only been published (it is several years old) but it is a truly accepted model for DCIS among cancer researchers.
Reference: -Morphogenesis and oncogenesis of MCF-10A mammary epithelial acini grown in three-dimensional basement membrane cultures. Debnath J, Muthuswamy SK, Brugge JS. Methods, 2003 -Phenotypic reversion or death of cancer cells by altering signaling pathways in three-dimensional contexts. Wang F, Hansen RK, Radisky D, Yoneda T, Barcellos-Hoff MH, Petersen OW, Turley EA, Bissell MJ. J Natl Cancer Inst, 2002
Considering this is for calling selected BUSINESSES only, I have no problem with this. In many states, it is ILLEGAL for businesses to have caller ID. For those that do not, this is a way one can call a business (to reply to an advertisement) anonymously, without providing a name. I find this a good, pro-consumer approach.
At least in the biomedical sciences, the major alternative for academia is the not-for-profit research institute. The majority of these are run like academic labs, with PI's, post-docs, and staff researchers (and techs), but the funding for these labs is through collaboration with large pharma and biotech firms. That nearly eliminates the need for grant writing, and in these environments, creativity and ingenuity are still respected.
Considering that the most potent viruses are "RNA viruses" and that biology students are taught that "the RNA universe" preceeded the "the DNA universe" (basically meaning that on Earth, organisms used RNA before DNA evolved) then the theory that viruses promoted evolution (possibly as a way to combat the "RNA universe") holds water.
There have been significant roadblocks in the formation of genes. The first one, and most importantly, is that even if we could predict (and we currently cannot) what our desired protein or RNA would do, there is no guarantee that it would fold correctly. We could take elements of existing genes (motifs/domains) and fuse them together to interact with our proteins of interest, but when this has been tried in the past, the protein folds up on itself into a big gob of oil.
The second issue is that we are still many years from knowing whether we could just make this protein and have it work. In addition to folding, the addition of other modifications (like sugars, lipids, and other proteins) directly to our gene of interest, is a subtle change that highly regulates its activity. One may make a perfect protein only to find it functionally dead. We're just not there yet.
One could easily see the benefits to this technology: build a protein that stabilizes a tumor supressor, or construct a gene that confers highly specific affinity to degrade an over-active growth factor receptor (common in many cancers). But for the aforementioned reasons, scientists prefer to work with natural genes, constructing schematics of proteins and using only naturally-sourced DNA. Maybe in 20 years. Or 50. But not now.
This doesn't seem so great...
on
Faster DNA Testing
·
· Score: 2, Informative
Many companies have produced faster thermocyclers. And indeed, the rate of heat cycling is a major factor in the time needed for a 30- or 35-cycle PCR. However, what this article omits are necessary wait periods to permit the annealing, elongation, and melting stages in typical PCR. Unless they have also re-engineered a DNA polymerase and can sufficiently prove that denaturation and annealing stages can be completed much faster, we're talking about maybe a 30 to 45 minute decrease in PCR. That's it. I've never seen anything less than 30-30-30 before, even in the smallest of genotyping markers.
The hard part about protein and molecule manipulation is getting in a pure form and obtaining the data about the molecule. For a single protein, it might not only take years to get the protein pure enough to work with, but once it is crystallized, you may get different versions of the data depending on crystallization conditions. For a given protein, you get at least two pieces of angle information for the phi and psi angles of the amide bond, plus any degree of rotation for the side chain. DNA can have any number of modifications detectable only by a good crystal, not to mention any proteins still attached to it.
Granted, this technology is nice if it gives researchers a tactile response to protein shapes. But I really can't see how it does more than some of the sophisticated graphical programs available now, especially considering molecules do not "fit" together in a simple jigsaw fashion in 3-D space (air) when you must consider that cellular water creates a shield of hydration that greatly influences molecular collisions, plus any electrostatic potentials not apparent in a handheld structure.
I'd like to mention that my own provider, RCN, encourages the use of NATs to distribute home cable-modem service to all of the computers in the household. Not only that, but they even offer IP address plans if you want external IP's for the computers. RCN will help fix a problem if there is an issue with the cable modem on an internal network, and even offer a paid home-network setup option that you can add onto a free basic installation to get your home network, Wi-Fi or otherwise, up, running, and secure.
I live in Austin where there is a good deal of student housing for the 100,000 college students that live here. Many, many, apartment complexes purchase high-bandwidth DSL or commercial Cable Modem connections (in excess of 2Mbit/sec) and then add about $20 to the standard rent they charged before installing the connection. These places set up routers and give everyone an internal IP address. One place I know does give real external IP's behind the firewall, but that is the exception. Either way, they are saving the tenant an average of about $20-30 per month by redistributing the connection, and the two prominent companies, Southwestern Bell and Time Warner, not only don't seem to care, but encourage this as use of their own commerical setups.
My favorite is USAIR's tactic
on
Window or Aisle?
·
· Score: 2, Interesting
As a consumer, my experience dealing with WorldCom was extremely negative and I have recommended against their services in an decision-making process I had a say in. They're billing and customer service departments DO NOT have it together. They stopped billing cell phone charges for 3 months and then put a massive 4-month conglomerate bill together and expect me to pay. Especially when I cancelled my service 1 month before the 3-month period in question. It was resolved with a nasty letter from my lawyer, but it should be an example of the awful work ethic these people have to let an error like that slip by. My advice: avoid WorldCom. If they can't treat customers right, sooner or later they'll be out of business.
I don't know what it's called. I think it was custom built. But the idea is to create some sort of low-level drive overlay that reinstates an image upon boot-up and triggers a reboot after logging out of the network. it's that simple. connecting the login to other pay services (such as printing) is additional to the schematic.
At my university, they use software that requires public access stations (to students & faculty) for the user to log in, and then a low-level hard-drive erase and rebuild from a second volume occurs (probably simply a mirror), which takes about 5 minutes and runs on PCs and Macs. Dunno the name of it, but it works quite well. I realize this is offtopic, but I'm replying to Chuck Milam, not the original post.
It would only work for a few genres
on
Immersive HDTV
·
· Score: 1
This idea I think would only work for television and movies of specific genres where one would WANT more viewing angles. In particular, porno, sports, and sci-fi.
I'm sorry, but there are games on that list that should not be there, such as Age of Empires 2. It just wasn't that revolutionary or remarkable. SimCity should have been higher on that list, and some games I expected to see (but didn't) were Super Mario Brothers (everyone, I am sure, knows the path to beat World 8 level 4), Mortal Kombat, and PacMan.
Slashdot Mirror
The sequence read archives (such as the one hosted by NCBI) as a repository for this sequencing data, uses "compression by reference," a highly-efficient way to compress and store a lot of the data. The raw data that comes off these sequencers is often >99% homologous to the reference genome (such as human, etc), so the most efficient way to compress and store this data is only to record what is different between the sequence output and the reference genome.
How is this not just meaning no redundancy for the "same" digital object. Rather than host 1000 copies of the same file, Amazon minimizes redundancy and every cloud user who hosts the same file has access to the same block(s) of data.
how is this any different than the postal service, which charges senders and recipients do not receive anything except what is being sent?
The experiments in mice were performed at 12.5mg/kg, which would be (for the average 65-kg human) a shocking 812.5mg of Triclosan. If your standard amount of handsoap and toothpaste is 2ml that's like brushing your teeth with a 1/3 solution of triclosan and swallowing it.
Like most of the research in PNAS this was not subjected to the high level of peer review expected in most scholarly journals and this paper got through without regard to its relevance and real-world significance.
At a high enough dose, caffeine causes cancer in lab animals. But not at the doses even Slashdotters consume.
While your statement is correct the cancer risk is minimal.
A typical xray is about 1-10 mrem. You get about 5 mrem of radiation dose from just an airplane ride. If a child lives in a concrete apartment building he/she will receive 100 mrem just from the radiation the concrete gives off. Annual occupational exposure limits for radiation workers are 5000 mrem. A deadly dose of radiation is about 50,000 mrem.
For individual research units, the cost of maintaining the processing power and storage space for these types of projects can be cost-prohibitive. Cloud-based options offer distributed computing power and low-cost storage that is often a more economical solution that paying for the equipment in house, especially when genomic projects can come in spurts rather than a continuous stream.
Disclaimer: I work with large amounts of genomic data and use both in-house and cloud-based analysis tools.
Just call it what it is -- the internal version can be 1.0.0.3 or whatever, but the version on the box and in all literature can be Version 2009 (or the year of release). That was popular about 8 years ago...and still works too!
This research is far from novel. The technique of growing tumor-derived breast epithelial cells was championed by both John Brugge at Harvard and Mina Bissell at Berkeley. The authors of this BBC article should have done a little research before; this work has not only been published (it is several years old) but it is a truly accepted model for DCIS among cancer researchers.
Reference:
-Morphogenesis and oncogenesis of MCF-10A mammary epithelial acini grown in three-dimensional basement membrane cultures. Debnath J, Muthuswamy SK, Brugge JS. Methods, 2003
-Phenotypic reversion or death of cancer cells by altering signaling pathways in three-dimensional contexts. Wang F, Hansen RK, Radisky D, Yoneda T, Barcellos-Hoff MH, Petersen OW, Turley EA, Bissell MJ. J Natl Cancer Inst, 2002
Considering this is for calling selected BUSINESSES only, I have no problem with this. In many states, it is ILLEGAL for businesses to have caller ID. For those that do not, this is a way one can call a business (to reply to an advertisement) anonymously, without providing a name. I find this a good, pro-consumer approach.
At least in the biomedical sciences, the major alternative for academia is the not-for-profit research institute. The majority of these are run like academic labs, with PI's, post-docs, and staff researchers (and techs), but the funding for these labs is through collaboration with large pharma and biotech firms. That nearly eliminates the need for grant writing, and in these environments, creativity and ingenuity are still respected.
Well, I thought the bit with Burns looking and listening to his watch was pretty good.
Considering that the most potent viruses are "RNA viruses" and that biology students are taught that "the RNA universe" preceeded the "the DNA universe" (basically meaning that on Earth, organisms used RNA before DNA evolved) then the theory that viruses promoted evolution (possibly as a way to combat the "RNA universe") holds water.
There have been significant roadblocks in the formation of genes. The first one, and most importantly, is that even if we could predict (and we currently cannot) what our desired protein or RNA would do, there is no guarantee that it would fold correctly. We could take elements of existing genes (motifs/domains) and fuse them together to interact with our proteins of interest, but when this has been tried in the past, the protein folds up on itself into a big gob of oil.
The second issue is that we are still many years from knowing whether we could just make this protein and have it work. In addition to folding, the addition of other modifications (like sugars, lipids, and other proteins) directly to our gene of interest, is a subtle change that highly regulates its activity. One may make a perfect protein only to find it functionally dead. We're just not there yet.
One could easily see the benefits to this technology: build a protein that stabilizes a tumor supressor, or construct a gene that confers highly specific affinity to degrade an over-active growth factor receptor (common in many cancers). But for the aforementioned reasons, scientists prefer to work with natural genes, constructing schematics of proteins and using only naturally-sourced DNA. Maybe in 20 years. Or 50. But not now.
Many companies have produced faster thermocyclers. And indeed, the rate of heat cycling is a major factor in the time needed for a 30- or 35-cycle PCR. However, what this article omits are necessary wait periods to permit the annealing, elongation, and melting stages in typical PCR. Unless they have also re-engineered a DNA polymerase and can sufficiently prove that denaturation and annealing stages can be completed much faster, we're talking about maybe a 30 to 45 minute decrease in PCR. That's it. I've never seen anything less than 30-30-30 before, even in the smallest of genotyping markers.
The hard part about protein and molecule manipulation is getting in a pure form and obtaining the data about the molecule. For a single protein, it might not only take years to get the protein pure enough to work with, but once it is crystallized, you may get different versions of the data depending on crystallization conditions. For a given protein, you get at least two pieces of angle information for the phi and psi angles of the amide bond, plus any degree of rotation for the side chain. DNA can have any number of modifications detectable only by a good crystal, not to mention any proteins still attached to it.
Granted, this technology is nice if it gives researchers a tactile response to protein shapes. But I really can't see how it does more than some of the sophisticated graphical programs available now, especially considering molecules do not "fit" together in a simple jigsaw fashion in 3-D space (air) when you must consider that cellular water creates a shield of hydration that greatly influences molecular collisions, plus any electrostatic potentials not apparent in a handheld structure.
I'd like to mention that my own provider, RCN, encourages the use of NATs to distribute home cable-modem service to all of the computers in the household. Not only that, but they even offer IP address plans if you want external IP's for the computers. RCN will help fix a problem if there is an issue with the cable modem on an internal network, and even offer a paid home-network setup option that you can add onto a free basic installation to get your home network, Wi-Fi or otherwise, up, running, and secure.
I live in Austin where there is a good deal of student housing for the 100,000 college students that live here. Many, many, apartment complexes purchase high-bandwidth DSL or commercial Cable Modem connections (in excess of 2Mbit/sec) and then add about $20 to the standard rent they charged before installing the connection. These places set up routers and give everyone an internal IP address. One place I know does give real external IP's behind the firewall, but that is the exception. Either way, they are saving the tenant an average of about $20-30 per month by redistributing the connection, and the two prominent companies, Southwestern Bell and Time Warner, not only don't seem to care, but encourage this as use of their own commerical setups.
My favorite is how USAIR (US Airways) has already started advertising trips to space. You can either win a trip to space or redeem 10,000,000 frequent flier miles for one. I can't wait to see where this goes!
And according to my calculations, the 500 millionth results will be submitted by Sun Microsystems.
As a consumer, my experience dealing with WorldCom was extremely negative and I have recommended against their services in an decision-making process I had a say in. They're billing and customer service departments DO NOT have it together. They stopped billing cell phone charges for 3 months and then put a massive 4-month conglomerate bill together and expect me to pay. Especially when I cancelled my service 1 month before the 3-month period in question. It was resolved with a nasty letter from my lawyer, but it should be an example of the awful work ethic these people have to let an error like that slip by. My advice: avoid WorldCom. If they can't treat customers right, sooner or later they'll be out of business.
I don't know what it's called. I think it was custom built. But the idea is to create some sort of low-level drive overlay that reinstates an image upon boot-up and triggers a reboot after logging out of the network. it's that simple. connecting the login to other pay services (such as printing) is additional to the schematic.
At my university, they use software that requires public access stations (to students & faculty) for the user to log in, and then a low-level hard-drive erase and rebuild from a second volume occurs (probably simply a mirror), which takes about 5 minutes and runs on PCs and Macs. Dunno the name of it, but it works quite well. I realize this is offtopic, but I'm replying to Chuck Milam, not the original post.
This idea I think would only work for television and movies of specific genres where one would WANT more viewing angles. In particular, porno, sports, and sci-fi.
I'm sorry, but there are games on that list that should not be there, such as Age of Empires 2. It just wasn't that revolutionary or remarkable. SimCity should have been higher on that list, and some games I expected to see (but didn't) were Super Mario Brothers (everyone, I am sure, knows the path to beat World 8 level 4), Mortal Kombat, and PacMan.
Depending on their answer, slashdot, activewin, theregister, betanews, macworld, or the msnbc technology section!