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UK Team Claims Breakthrough In Universal Cancer Test

gringer Re:Link to abstract (63 comments)

Right. I finally got around to writing an R function to do this, because this problem has cropped up a few times in the past year:

getPV <- function(prevalence, sensitivity, specificity){
        popnTrue <- prevalence;
        popnFalse <- (1-prevalence);
        popnTruePos <- popnTrue * sensitivity;
        popnFalsePos <- popnFalse * (1 - specificity);
        popnTrueNeg <- popnTrue * (1 - sensitivity);
        popnFalseNeg <- popnFalse * specificity;
        ppv <- popnTruePos / (popnTruePos + popnFalsePos);
        npv <- popnFalseNeg / (popnTrueNeg + popnFalseNeg);
        return(data.frame(prev = prevalence, sens = sensitivity,
                                            spec = specificity, ppv = ppv, npv = npv));
}

NCI tells me that 4% of the US population are cancer survivors, so I'll use that value for the population prevalence:


> prev <- 4 * 0.01;
> sensSpec <- rbind(c(94.8,54.7),c(81,78.7),c(62.1,94)) * 0.01;

> out.df <- NULL;
> for(i in seq_len(dim(sensSpec)[1])){
    out.df <- rbind(out.df,getPV(prev, sensSpec[i,1], sensSpec[i,2]));
  }
> out.df;
    prev sens spec ppv npv
1 0.04 0.948 0.547 0.08020305 0.9960546
2 0.04 0.810 0.787 0.13677812 0.9900409
3 0.04 0.621 0.940 0.30131004 0.9834779

So the best they can do for this test, according to the paper, is a 30% positive predictive value -- if this test comes up positive, there's a 30% chance that you actually have cancer (and that's allowing for 2% of "negative" results actually being cancer).

about three weeks ago
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UK Team Claims Breakthrough In Universal Cancer Test

gringer Re:Link to abstract (63 comments)

The actual paper is behind a paywall.

Yay for institute access. Their idea of "approach[ing] 100%" is a little bit loose:

Based on these calculations, the cutoffs for low (0.10), medium (0.25), and high (0.50) thresholds are 1.47 at a sensitivity of 94.8% and a specificity of 54.7%, 1.73 at a sensitivity of 81% and a specificity of 78.7%, and 1.99 at a sensitivity of 62.1% and a specificity of 94%, respectively

I have yet to do the calculations using population prevalence, but I'm going to guess that the positive predictive value of these tests are not particularly high.

about three weeks ago
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Popular Android Apps Full of Bugs: Researchers Blame Recycling of Code

gringer Re:All software is full of bugs (150 comments)

For that matter, all of everything constructed by human beings

You might not be terribly surprised to know that our genes (and the genomes of pretty much everything) are also full of bugs. We have a whole raft of deleterious genetic variants in our DNA that are just waiting for the perfect time to activate and say "hey, you know that life thing? I can make it worse." On top of that, we have a few viral genomes in our DNA (possibly some that are still active), and rely on bacteria and mitochondria to provide us with energy required to live.

In other words, defective objects are the rule, not the exception.

p.s. hmm... I've only just realised how much I miss that handy login form that SoylentNews has to deal with accidental AC posts.

about three weeks ago
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The First Person Ever To Die In a Tesla Is a Guy Who Stole One

gringer Tesla's response (443 comments)

We apologise for the inadequacies of our car at high speeds, and are investigating ways to make it even safer. We have designed a flexible partitioning system to take some of the energy from a "car split" incident, and will be implementing it in all new Tesla cars, and retrofitting it to all drivers who want it. Additionally, the car will require that the driver and all passengers are wearing seatbelts when the car is driving at speeds exceeding 70 mph.

about a month and a half ago
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Microsoft Opens 'Transparency Center' For Governments To Review Source Code

gringer Standards are meant to be broken (178 comments)

Microsoft notes that it worked with multiple international companies to secure its version of the standard.

Ah, yes. Once again, Microsoft has their own special idea about how to extend a standard. Said like a true Microsoft employee (or paraphrased by someone with a strong reporting bias -- it doesn't seem to be phrased in this way in the original Microsoft post about encryption and transparency).

about 1 month ago
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The New 501(c)(3) and the Future of Open Source In the US

gringer SoylentNews (228 comments)

SoylentNews has decided to avoid non-profit status due to the demands it puts on the organisation, so they're now trying to set up as a slightly more normal "we don't actually want to make money" benefit corporation.

about 1 month ago
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Nathan Myhrvold's Recipe For a Better Oven

gringer Re:How about just a good thermostat instead? (228 comments)

An induction cooktop with precise digital temperature control (SI) and a magnetic stirrer would also be great.

A magnetic stirrer on a magnetic induction cooktop would be... interesting.

We have an induction coooktop with digital temperature control (in increments of 10 degrees). It seems to measure the temperature at the induction coil, rather than the temperature of the pot, so things can boil when it's set to 60C. Also, the PWM cycle of the cooktop (as with pretty much every other one I've seen) is far too long at about 0.5Hz (where I'd prefer a cycle of at least 10Hz, and ideally over 100Hz). Further, the power level can't be adjusted as much as I'd like -- I set it to 800W (or 130C, because that seems to be similar) and it's too cold for frying, but 900W (or 140C) is a little bit too hot.

Sure, I wouldn't change away from induction now that I have it, but I expect it'll be a while before we get a replacement cooktop, because I've become a whole lot more aware of the limitations (and possibilities) in the current technology.

about 1 month ago
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Harley-Davidson Unveils Their First Electric Motorcycle

gringer Tesla superchargers (345 comments)

And now that Tesla has freed up the patents for their superchargers, you'll be able to plug an electric bike into something that uses that connection and current (not necessarily the Tesla ones). Given that the motorcycle battery packs are much smaller than the car packs, I don't expect that a 2-minute charge to full would be out of the question.

That might almost be quicker than walking up to a cashier and paying money, and certainly would be quicker if you're not the first person in line.

about 2 months ago
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Google and Facebook Can Be Legally Intercepted, Says UK Spy Boss

gringer American citizens (104 comments)

And, of course, they can snoop on American citizens on google and facebook, as well as for all other communications in Great Britain because the Americans are foreigners.

When you have five eyes, and each eye is in a different country, it's quite easy to work around those pesky "no watching yourself" laws.

about 2 months ago
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545-Person Programming War Declares a Winner

gringer Re:Interdisciplinary crossover (57 comments)

It's extremely confusing to put it nicely.

I feel compelled to tell the world about a more confusing part of NCBI that I'm trying to navigate myself around at the moment: The Transcriptome Shotgun Assembly Sequence Database. Submitting sequences is... a little tricky. Here's a simplification of the process:

  1. Create a BioSample record for the organism that you're submitting data for
  2. Download a sample template tab-delimited file, and fill in arbitrary descriptions about your organism
  3. Upload the template file (using your web browser), and finish the remainder of the BioSample submission process
  4. wait for email confirmation of your BioSample record, after which it will have an "official" ID
  5. Create a BioProject record for your transcriptome assembly project, and link in the BioSample record (I don't think you need to wait for email confirmation to get an ID for that)
  6. Create a Sequence Read Archive (SRA) record for your transcriptome assembly project
  7. Create an experiment record (in the SRA record) for your transcriptome assembly project, one for each different method of sequencing that was used
  8. Get md5 sums of all the raw data files that will be uploaded to NCBI
  9. Create a run record (in the experiment record), and add in the file names and md5 sums of the raw data files
  10. Upload your files to the NCBI servers using an FTP client
  11. Wait for files to be transferred from the NCBI FTP server to the SRA server, after which the run record will get an official run ID
  12. Create a Transcriptome Shotgun Assembly (TSA) record for your transcriptome assembly project, and link in the BioProject and BioSample records, as well as the run IDs from the SRA record
  13. Use a web form to create a metadata file to download to your computer
  14. Use a custom NCBI program to merge the metadata file with your transcriptome assembly
  15. Upload the [large] merged file to NCBI using your web browser
  16. Wait for email confirmation, after which the TSA record will get an official ID

Congratulations, you are now the proud owner of a Transcriptome assembly ID, which you can insert into a single sentence in your research paper: "The transcriptome that was created for use in this study has been uploaded to NCBI (reference ID: GAAA00000000)."

about 2 months ago
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545-Person Programming War Declares a Winner

gringer Re:$5.74 == Wow hardware resources have become che (57 comments)

$10,000 barely gets you ONE modern well-equipped 20 core server system

I get 4x16 core AMD Opteron 6366HE on a Dell PowerEdge m915 for $5,578.70:

http://configure.us.dell.com/d...

So that's a bit less than $10,000 for 100 cores on a standard issue Dell machine. It's not completely crazy to expect you could increase that to 600 cores without too much extra cash laid down.

about 2 months ago
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545-Person Programming War Declares a Winner

gringer Re:Interdisciplinary crossover (57 comments)

You need to click on the "Elsevier Open Access" link from NCBI, which is a direct link to the article on the publisher's website (this location is where you click for all PubMed articles, as long as the publisher has provided access in that way). PubMed never displays complete articles.

After clicking through, there's a "Download PDF" link at the top left of the article, just under the green Science Direct header.

about 2 months ago
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Distant Stellar Explosion Helps Map Universe's Dark Ages

gringer Re:If you didn't ge the joke in TFS... (61 comments)

Since not everyone went to Sunday School, TFS is referencing Genesis chapter 1 verse 1.

I'd read you the verse proper, but since verse 2 hasn't been quoted yet, it's too dark to read...

You have an off-by-one error. Verses in the bible don't begin at zero.

about 4 months ago
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Why No One Trusts Facebook To Power the Future

gringer Re:Getting blocked? (218 comments)

Every day I'm more and more glad that I have never had an account, and never will.

I'm in the same boat, but I'm not deluding myself by thinking that Facebook doesn't have a shadow account for me -- this has been confirmed to have been done in the past. Facebook is probably aware that I exist, and they obtain some benefit from being able to identify me in photos or posts (for example) and tracking my actions.

about 5 months ago
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Free (Gratis) Version of Windows Could Be a Reality Soon

gringer Re:I could use it (392 comments)

The one I had written in 2003 would randomly change table margins when I add or select something. I mean freaking random where the only experience close is like designing a website in IE 6 where you do one thing and all the elements freak out and go apeshit.

So what makes you think this will look the same on the computers of all those people with Office who view your CV?

about 6 months ago
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Government To Require Vehicle-to-vehicle Communication

gringer LED communication (390 comments)

I'm okay with this as long as it is restricted to line-of-sight, in other words via LED or similar light transmission. That also removes some confusion issues, because if a car communicates "I'm stopping now", you know it's the car that you can see rather than the car 1km behind you that was hit by a stray radio amplification patch.

about 7 months ago
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Why Standard Deviation Should Be Retired From Scientific Use

gringer Re:Issues (312 comments)

Two different results from the same data points. Have I misunderstood something?

I believe it should be mean absolute deviation from the mean, rather than from the next value in the list (this wasn't particularly clear in the summary or the article). So you have three numbers, mean = (1 + 2 + 10) / 3 ~= 4.3333, MAD ~= (3.333 + 2.333 + 5.666) / 3 ~= 3.778

There's another MAD, the median absolute deviation from the median, so you have for this data set median = 2, MAD = median(1, 0, 8) = 1.

about 7 months ago

Submissions

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Dotcom MegaUpload case Gets More Complex

gringer gringer writes  |  about 2 years ago

gringer (252588) writes "The MegaUpload case against Kim Dotcom is proving to be a bit of a nightmare for the New Zealand government. Some information that was used as evidence against Dotcom was gathered illegally, and may not be able to be given to Kim or his lawyers for their defence in his extradition hearing. This is a continuation of an earlier hearing, where it was found that search and seizure operations carried out during the raid on Kim's residence were illegal."
Link to Original Source
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DNS flaw: it hits more than just the web

gringer gringer writes  |  about 6 years ago

gringer (252588) writes "Dan Kaminsky presented at the Black Hat conference in Las Vegas on Wednesday, and said that the DNS vulnerability he discovered is much more dangerous than most have appreciated. Besides hijacking web browsers, hackers might attack email services and spam filters, FTP, Rsync, BitTorrent, Telnet, SSH, as well as SSL services. Ultimately it's not a question of which systems can be attacked by exploiting the flaw, but rather which ones cannot. Then again, it could just be hype. For more information, see Kaminsky's power point presentation."
Link to Original Source
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"Silent" Mutations Heard by the Cancer Cel

gringer gringer writes  |  more than 6 years ago

gringer writes "Digging through a washington post article (found via digg), I came across this little surprising statement:

Earlier this year, however, a study in Science showed that these synonymous spellings can make a difference. That's because it can be harder to make a protein from the instruction with the unusual, but synonymous, spelling. The construction process takes longer, and the final protein folds up differently. It has a slightly different shape — and a different function.
Synonymous mutations are those that produce exactly the same string of amino acids for a gene, and so have been though to only be used as an "error robust" system, so that important proteins still function as usual in the presence of errors. This finding is a contradiction to that, where a "redundant" change in the DNA still affects the behaviour of the final product. In this case, the mutations are happening in a gene that contributes to the multi-drug resistant behaviour of cancer cells.

The abstract for the paper they seem to be referring to can be found here."

Link to Original Source

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