Yes. First experienced TMJ pain as a teenager and almost overdosed on painkillers while trying to get rid of it at 3AM. Still recurrs about 2-3 times per year, but I've now learned to feel it coming on much earlier and start loading up on codiene in advance.
I had it a long time and was not sure the pain was localized in the jaw (was it the neck, shoulders, back?) or even the extent to which there was a physical lesion or it was how my brain was interpreting things.
My dentist told me I was grinding my teeth and prescribed a bite guard and within two weeks the pain got better but became very definitely focalized in the jaw and I noticed ‘popping’ as a symptom.
It has been about 1.5 years since the diagnosis. last summer I went through a phase of throwing a lot of random food into a pot and hitting it with an immersion blender, getting shakes from Burger King whenever I felt like it, etc. I lost almost 20 kg.
I have been eating more normally since, it doesn’t bother me very often.
What sort of bite guard did you use? I clench my teeth like there's no tomorrow and I've discovered over the years that any bite guard that doesn't completely cover every tooth (on either the lower or upper arch) will eventually result in a supra-eruption of the exposed tooth, with drastic consequences for my bite.
Just one from the drugstore which you put in boiling water and then bite down on. It costs about $20.
It covers all the teeth on the top, but not the bottom.
My dentist said he could make one if that didn’t work out, but it did.
I’ve seen sketchy looking web sites by dentists who claim they can make something uniquely effective but it doesn’t look any different from the one I use so I don’t believe it.
Interested outsider here; I work with a lot of HCLS research customers but don't have a biology-related background. Can you explain the problems with the Nanopore sequencer accuracy in more detail? Basically, I was wondering if I could get one for myself and sequence my own genome, then user the data to learn about life-sciences computing techniques. If I were to buy one of the USB-attachable devices and run it, is the data simply not viable for use in a genomics pipeline, or is it just that the results would be questionable? Also, if accuracy is an issue, what about just running the same sample N times and doing some error correction?
I guess there are limits to ensemble methods if the underlying accuracy doesn't increase. I don't work on gene sequencing algorithms but from what I understand of ML ensemble techniques, there are certain assumptions regarding the underlying independence of the errors. The errors for nanopore should be uniform but I am not sure. Any molecular biologist here care to comment?
I know that the error rate of the oxford nanopore sequencer depends on GC content (guanine/cytosine nucleotides), and that the Pacific Biosciences sequencer uses a polymerase that gets worn down during reading. So there is some non-uniformity in the chemistry.
The instruments do exactly as you say (run the sample N times), but this obviously comes at a cost. Also, keep in mind that sequencing needs to be very, very accurate to be useful. We share most of our DNA, and the small variations make up all the difference.
Yes, those are all relevant costs. There's also a tradeoff between accuracy and the number of reads (how many sequences you can observe), or how much data you can get out of the machine.
Tl;Dr: Nanopore data is historically lower quality than current gold-standard methods, but it is by no means "not viable" in a genomics pipeline. Their newer chemistry flowcells are competitive with current gold-standard (but I've not seen it with my own eyes in the lab yet due to limited release).
There are two components that drive sequencing error rate. 1) The chemistry behind the sequencing (for nanopore sequencing this is the "feeding DNA through a pore" bit) 2) the method to convert raw signal into DNA sequence (this is called "base calling").
The gold-standard in terms of error profile for sequencing is currently the Illumina short read platform. Illumina machines are really just microscopes (TIRF scopes for optics folks) that sequence DNA by visualizing incorporation of dye-labeled nucleotides into the sequenced molecule(s) (Imagine a really slow PCR [1]). Each base is labeled with a different color, then when a molecule has a match it makes a colored spot on the slide that the machine can read (see here for more info & details of newer chemistry that use fewer colors [2]). This whole process is mediated by DNA polymerase which itself has a very low error rate. Another important point is that DNA sequenced on the illumina platform (called a "library") tends to be from "amplified" template DNA, meaning the DNA will have been processed and potentially be missing chemical modifications on the bases that could be present in the organism. This works to Illumina's advantage, because when trying to answer the question of "what is the DNA sequence?" we want the ground-truth DNA, not the modification state.
In contrast, Nanopore sequencing works by feeding a long strand of DNA through a pore and measuring the change in electrical current through the pore (watch the cool video [3]). For the current set of nanopore flowcells, 8 bases of DNA sit in the pore at a time, meaning the current at each timestep is a product of 8 nucleotides in aggregate. This also means that the pore "sees" each base 8 times, but always in the context of an additional 7. In order to basecall from the raw signal, it's not as easy as saying "blue = A", instead, you have to deconvolve each base from a complex signal. As you might imagine, the folks at Oxford Nanopore & broader research community have turned to machine learning-based base callers to solve this problem, and they work quite well [4]. But they are not perfect.
Deconvolving runs of the same base (e.g. "AAAAAAA") is difficult because without well-defined signal changes between bases, the caller has a hard time deciding how many bases it has seen, so a common error mode for nanopore sequencing is to create insertions/deletions at places in the genome with low nucleotide diversity. Another interesting reason is that most Nanopore library preps are often performed on unamplified DNA, and so in addition to normal A/T/G/C nucleotides, the template DNA can also contain bases with chemical modifications. For example, in bacteria, A's are often methylated, and in Humans, C can have all kinds of different modifications (5-methyl-cytosine, 5-hydroxymethyl-cytosine, etc. etc.) and each different modification affects the signal in the nanopore. Therefore, basecallers that weren't trained on modified bases will produce basecalling errors in the presence of base modifications.
For both Illumina and Nanopore basecallers, they assign a quality score to each base that indicates the probability that the basecaller produced an incorrect value. This is called a Q-score, which is defined as "Q = -10(log10(P-value))" (i.e. Q / 10 = the order of magnitude of the error probability) [5]. For example, a Q-score of 10 means an error rate of 1 in 10, but a Q-score of 50 means an error rate of 1 in 100,000. For Illumina sequencing, >95% of the reads have a Q-score > 30 (i.e. 1 in 1000 errors), while Nanopore reads tend to have lower average Q-scores (~Q20, i.e. 1 in 100 errors). For genetics, where 1 base difference can mean the difference between a severe disease allele vs a normal variant, 1 in 100 won't cut it.
The current gen Nanopore flowcell chemistry (R9.4.1) is what most people are talking about when they talk about Nanopore error rates, but they've just released a new pore type & made some basecaller upgrades that improve the accuracy to what they call "Q20+" and some claims of Q>30, and from the data I've seen, it's impressive, I just haven't got my hands on one yet to see for myself [6]. I think the comment saying "wait 5 years" is an overestimate, but if you want to genotype yourself today, I'd just pay someone for Illumina sequencing and process the fastq files yourself if you really want to do it as a learning exercise.
I've unintentionally written an essay, so I'll stop here, but real quick to your other point RE: rerunning the sample N times & using the repeats for error correction. This won't work the way you're thinking because a "sample" is actually a collection of DNA molecules that are sampled randomly by the sequencer. You have no way of knowing that the same read between runs was actually from the same molecule, so you can't error correct this way. Consequently, a totally different sequencing platform from Pacific Biosciences uses this strategy by doing some really cool chemistry, but I'll spare you the second essay (google "PacBio HiFi" or "circular consensus reads" if you're interested).
I for one am glad you wrote the essay, this was incredibly informative and filled in a bunch of blanks I had after reading what I could scratch together on the MinION product. I think I'm in a partial state of shock at how accessible this is becoming. Thank you!
Thanks - fascinating stuff. I'm now even more convinced I want to give it a try, but I think I'll play around with public data and tutorials before leaping into home sequencing.
You totally should, it's a lot of fun. I'd suggest trying to find some bacterial genome sequencing (like E. coli) done on nanopore if you're interested in those data. I don't have a link to any handy right now, otherwise I'd post here, but assembling bacterial genomes is shockingly easy these days and doesn't need near as many resources as doing a human genome, so it's great for learning (I love the assembler Flye [1] for this).
And RE: home sequencing, honestly the hardest part for a beginner will likely be the sample prep, since that takes some combination of wet lab experience and expensive equipment. I really wish molecular biology was as simple to get hacking on as writing software. The lag time between doing an experiment and getting a result is so much longer than waiting for things to compile, it just makes improving your skills take longer.
Exactly the same situation in the UK - snow is common but rarely persistent enough to justify the infrastructure investment to deal with it. Also, having an excuse to combine moaning about the weather with moaning about our inept government is basically enough to trigger a collective national orgasm.
Plenty of plows and gritters in Scotland (all with names like Lord Coldemort and Buzz Lightyear)
A fair number of plows in northern England too, the A66 across the Pennines is often blocked. Further south it’s typically just gritters spreading salt on the roads, but it’s rare to have the type of snow you need to shift.
We had heavy snow in the south east and northern france back in December 2010, my flight to the US was cancelled on the 22nd, I managed to get one from Paris to Newark for the 23rd, and had to drive from Bedfordshire to Paris. Felt like a massive blizzard driving though it, could barely see the tracks of the vehicle 800 yards ahead coming down through france.
Landed in a clear New York on the 23rd, but then went out for dinner opposite the hotel in Tribecca, possibly that night. The snow came down, and kept coming. First time I’d ever seen a snow plow in person, and the drifts the next morning with covering taxis. It was a different world to the 3-6” of heavy snow we were used to.
As a recent Mac adopter after spending 10 years as a Linux user, Homebrew is exactly what I need it to be.
Linux OS package managers are, almost by necessity, full of outdated packages which are not the versions I want to use for day-to-day CLI applications. Snaps, Flatpaks and AppImages all have their own downsides due to half-baked isolation goals and the associated usability compromises. Language-specific package managers are a mixed bag, but too narrow in scope when thinking about usage of tools rather than development based on libraries. Maybe Nix or the Arch AUR are a better option, but they come with a learning curve and/or stability compromise. I don't care how the packages are arranged on my Mac; the system is too locked down for me to really have the level of control I'd like anyway, so better to just accept the usability advantages and get on withy life.
> I don't care how the packages are arranged on my Mac; the system is too locked down for me to really have the level of control I'd like anyway, so better to just accept the usability advantages and get on with [my] life.
This is a valuable perspective. I wonder how much macOS primes users in general to value usability over other dimensions of good design.
(I also wonder how much better a time I'd have on macOS if I adopted this attitude.)
I think we'd all have a better time if Apple would let us run current versions of xnu with only Darwin without having to piece everything together to end up with a system than might work but just won't because xnu is proprietary. I think there are valid cases where Darwin can be a more attractive choice than Linux, but there's just no interest because xnu is unattainable, and the alternative is using a Hackintosh kernel with degrees of stability rather than it being straight up rock solid stability. I don't mind the requirement of Macintosh hardware, but that isn't good enough for Apple, you either take the whole system or nothing (or live vicariously dependent on a few intrepid kernel hackers).
In a cloud setting, I guess having user /home dirs on separate volumes from the root disk and having them relocatable is a reasonable analogue. The real issue is that much like the pen drive thing, absolutely no-one actually does this.
What place do these niche solutions have in the main project?
In the old days you would write a little script to set up the mapping for your USB drive, once it is plugged in. Linux provides the UID mapping feature, udev gives you a place hook your script, and you glue it together the way you want.
If your solution was particularly high quality it might get included as a package in the OS. Someone else might write a different solution that gets packaged alongside yours. Maybe they scratch the same itch in two different ways? Maybe theirs is just better?
Systemd on the other hand is judge, jury and package maintainer. What they decide upon is what gets included. They are the cathedral, where once there was a bazaar.
The key difference is that one of these things has the backing and approval of recognized governments who also control law enforcement, while the other is just some guys on the internet. I'm not so sure "finding a pre-existing bitcoin wallet I can claim, and doing so" is really any different than "generating hashes until the blockchain hands me a prize".
That's not an argument. In any case, more and more governments are now recognizing crypto as something real, and are coming onboard. E.g. most recently Dubai.
Looking through the comments, I can't imagine how else it could possibly be explained or clarified further. For this use case, it is assumed that the software producing the visuals has full control over the output. An orange dot that cannot be removed means that the software does not have full control over the output, which is unacceptable. It's that simple.
EDIT: As far as I know, the best long-term answer here is for apps that present visuals full screen to "capture" the external display for exclusive use using an API (https://developer.apple.com/documentation/coregraphics/14562...), but that's not super common right now.
Sounds like it's totally possible for the software to have full control over the output if it wants to, this only affects software that runs in a "standard" fullscreen mode without explicitly taking full control over the output.
Sounds like it's totally possible for the software to have full control
Yes, so you can go to the software vendor's "Ideas" or "Suggestions" page and ask for this, and post in forums asking people to upvote it, and hope the devs will do it. Not a great workaround. And sure, someone developed a script to get rid of this but no one is all that happy when Windows does something user-unfriendly that only a regedit hack will get rid of either.
Julia has some nice ideas but it is time for a do-over as a fully open language (ie without the commercial backer actively upselling in their mailing list), and with the "time to first plot" and package management problems addressed.
I just drew a vertical line, slightly off center to the left, almost perfectly straight, starting about x=0.1 and proceeding to x=0.95. I expected it would show as a digit 1. Page said it was a 6. Tried a 1 with a serif on top. Page said it was an 8. Added a serif on the bottom. Still an 8.
Heck, if you mouse over the area without drawing, the model is torn between 1, 9 and 3.
I just tried the demo sketch thing on the Gradio site and it wasn't able to correctly interpret a single digit I tried, even after 6 or 7 attempts with different values. Serious question - is this a spoof site? I find it hard to believe character recognition can be that bad, in a marketing demo no less.
