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Comment author: rseiter 05 April 2015 04:42:35PM 2 points [-]

Thanks for the explanation and tips! I used your procedure and ended up with the same 131MB file. Interestingly I did not need to remove the "--" entries. I have been exchanging email with BGI and they indicated files could have significantly different number of entries (but I am surprised at >3x!). Is there any chance your sequencing had greater than 4x coverage? My VCF file is queued up and should be available in a few months which should help clarify what I am seeing.

Comment author: VincentYu 07 April 2015 09:50:41AM 0 points [-]

Is there any chance your sequencing had greater than 4x coverage?

I don't know. How do I find out?

Comment author: VincentYu 07 April 2015 09:41:48AM 0 points [-]

There is the References & Resources for LessWrong (last updated in 2011), which has a good selection of older posts and other resources by subject.

Comment author: rseiter 30 March 2015 06:12:24PM 2 points [-]

I received a similar email and was able to download my genome file a few days ago. The file is 23andMe format output by Plink. It was text even though it had a .gz suffix. I had trouble uploading the file to Promethease, but was able to get it working by changing the header to one copied from an actual 23andMe file and removing the missing (--) SNPs. Unfortunately, despite being ~125MB (~5x the size of an example 23andMe file I have) my file is missing many of the 23andMe SNPs (7948 genotypes annotated in Promethease vs. 20k+ for the 23andMe example). I have an email in to BGI requesting additional information. For example, Promethease directly supports the dbSNPAnnotated.bz2 Complete Genomics file and I was hoping to get a copy of that file for my data.

Have you had any success analyzing your results? Would anyone be interested in starting a discussion group for analyzing our BGI results?

Comment author: VincentYu 04 April 2015 05:58:16AM *  2 points [-]

Are you sure you've downloaded your entire genome file? My uncompressed file is about 500 MB, and I got about 26000 annotations on Promethease. It seems like your file might have gotten truncated during the download.

Short step-by-step guide for those who want to get their genome annotated by Promethease:

  1. Use the 'Download All Files' link on the SpiderOak page to download your genome file.*
  2. Unzip then gunzip to get the raw text file genome.txt.
  3. Open the file in a text editor. Remove all the commented lines at beginning of the file except the last one (i.e., keep the line starting with # rsid; Promethease chokes if you don't) and save. This is required to get Promethease to recognize the file.
  4. (optional) Compress the edited file with zip, gzip, or bzip2 to save upload time and bandwidth.
  5. Upload to Promethease and follow the directions there.

* I advise against downloading the genome.txt.gz file directly because for some reason SpiderOak has Content-encoding: gzip in their HTTP response header, which means that browsers will transparently uncompress that file. This makes me uneasy because there is no checksum provided for the (somewhat large) plain text file, so we have little protection against corruption and truncation. In contrast, by using 'Download All Files' to download everything in a zip, the data's integrity will be automatically verified against CRC-32 checksums when we unzip and gunzip locally.

Comment author: Romashka 02 April 2015 11:31:20AM 0 points [-]

Can anybody send me this paywalled article? Rhizome Growth and Clone Development in Anemone nemorosa L. D. A. SHIRREFFS, A. D. BELL. Annals of Botany Vol. 54, No. 3 (September 1984), pp. 315-324 Thank you!

Comment author: VincentYu 03 April 2015 02:40:58AM 1 point [-]
Comment author: DataPacRat 20 March 2015 06:54:02AM 2 points [-]

Wrist computer: To Buy or Not To Buy

I'm considering whether or not to buy an Android phone in a wristwatch form-factor, and am hesitating on whether it's the best use of my money. Would anyone here care to offer their opinion?

One of my goals: Go camping and enjoy it. One of my constraints: A limited budget. I suspect that taking a watch-phone, such as an Omate Truesmart or one of its clones ( eg, http://www.dx.com/p/imacwear-m7-waterproof-android-4-2-dual-core-3g-smart-watch-phone-w-1-54-5-0mp-black-373360 ), and filling a 32 gigabyte SD card with offline maps, Wikipedia, and related materials would improve my camping experience. However, I could also purchase an iPhone-like Android phone of comparable stats for half the price, allowing me to also purchase, say, a Kelly kettle, which would also improve my camping experience. (I already have various other digital devices, but none with enough room for the maps etc. I already have solar panels to hang from my backpack and external batteries, to keep any such devices charged while in the field.)

I have some leeway in timing, to get whatever items I decide on before camping season starts, and I find myself having spent several days being indecisive about what options, if any, to pick. My thoughts keep bouncing between something like "Wrist-computers are cool and I want one" and "I've made poor electronics purchasing decisions in the past and regretted them".

How do you think I should redirect my thought processes?

Comment author: VincentYu 21 March 2015 02:17:06PM 2 points [-]

Not directly answering your conundrum on wrist computers, but—I go trail running frequently (in Hong Kong), so I've thought a bit about wearable devices and safety. Here are some of my solutions and thoughts:

  • I use a forearm armband (example) to hold my phone in a position that allows me to use and see the touchscreen while running. I find this incredibly useful for checking a GPS map on the run while keeping both hands free for falls. I worry that the current generation of watches are nowhere near as capable as my phone.

  • I rely a lot on Strava's online route creation tool and phone app for navigation.

  • Digital personal locator beacons on the 406 MHz channel (example) are the current gold standard for distress signals.

  • Sharing your location through your phone (e.g., on Google+) can give some peace of mind to your family and friends.

  • An inactivity detector based on a phone's accelerometer might be a useful dead man switch for sending a distress SMS/email in the event of an accident that renders you incompetent. I haven't gotten around to setting this up on my phone, but here's an (untested) example of an app that might work.

  • In case of emergency, it might be useful to have a GPS app on your phone that can display your grid reference so that you can tell rescuers where to find you.

Comment author: DanArmak 02 February 2015 01:40:58PM 7 points [-]

I'm 30 years old and almost entirely unvaccinated.

I've always had poor health, I had lymphoma at age 27, type 1 Diabetes since age 13, all of which suggests poor immune system performance. And anecdotally, when I get sick with common cold etc, I seem to stay sick longer than other people. So I don't expect my body to be good at fighting off really dangerous disease.

Which vaccines should I get? Most resources either target or assume vaccination of children on a regular schedule.

Comment author: VincentYu 03 February 2015 03:53:09AM *  5 points [-]

I second gjm's suggestion to talk to a healthcare professional.

Every year, the CDC updates and publishes their recommended immunization schedule for adults (patient version), which doesn't assume childhood vaccination. Below, I've summarized the parts that are most relevant to you.

Vaccines recommended for adults aged 30 years:

Additional vaccines recommended for adults aged 30 years with diabetes:

Note that if you have a concurrent immunocompromising condition (e.g., lymphoma), then live vaccines should generally be avoided. This includes the varicella, MMR, and zoster vaccines. Again, your healthcare provider can tell you more.

Comment author: Username 25 January 2015 06:04:00PM 5 points [-]

I have (what I presume to be) massive social anxiety. I live near lots of communities of interest that probably contain lots of people I would like to meet and spend time with, but the psychological "activation energy" required to go to social events and not leave halfway though is huge, and so I usually end up just staying at home. I would prefer to be out meeting people and doing things, but when I actually try to do this, I get overcome by anxiety (or something resembling it), and I need to leave. Has anyone else had this problem, and if so, what techniques helped you overcome it? "Just practice" doesn't seem to be working--when I am able to muster up the willpower to go to social events (even very structured ones, which are much easier to deal with), it takes more and more willpower to stay there as the event goes on, and this doesn't seem to be changing.

Comment author: VincentYu 26 January 2015 01:22:36AM 0 points [-]

I recommend reading section 19 (on the management of social anxiety disorder) in the recent treatment guidelines from the British Association for Psychopharmacology (pp. 17–19). A sample:

19.1. Recognition and diagnosis

Social anxiety disorder is often not recognised in primary medical care (Weiller et al., 1996) but detection can be enhanced through the use of screening questionnaires in psychologically distressed primary care patients (Donker et al., 2010; Terluin et al., 2009). Social anxiety disorder is often misconstrued as mere ‘shyness’ but can be distinguished from shyness by the higher levels of personal distress, more severe symptoms and greater impairment (Burstein et al., 2011; Heiser et al., 2009). The generalised sub-type (where anxiety is associated with many situations) is associated with greater disability and higher comorbidity, but patients with the non-generalised subtype (where anxiety is focused on a limited number of situations) can be substantially impaired (Aderka et al., 2012; Wong et al., 2012). Social anxiety disorder is hard to distinguish from avoidant personality disorder, which may represent a more severe form of the same condition (Reich, 2009). Patients with social anxiety disorder often present with symptoms arising from comorbid conditions (especially depression), rather than with anxiety symptoms and avoidance of social and performance situations (Stein et al., 1999). There are strong, and possibly two-way, associations between social anxiety disorder and dependence on alcohol and cannabis (Buckner et al., 2008; Robinson et al., 2011).

19.2. Acute treatment

The findings of meta-analyses and randomised placebocontrolled treatment studies indicate that a range of approaches are efficacious in acute treatment (Blanco et al., 2013). CBT [cognitive behavioral therapy] is efficacious in adults (Hofmann and Smits, 2008) and children (James et al., 2005): cognitive therapy appears superior to exposure therapy (Ougrin, 2011), but the evidence for the efficacy of social skills training is less strong (Ponniah and Hollon, 2008). Antidepressant drugs with proven efficacy include most SSRIs (escitalopram, fluoxetine, fluvoxamine, paroxetine, sertraline), the SNRI venlafaxine, the MAOI phenelzine, and the RIMA moclobemide.


19.4. Comparative efficacy of pharmacological, psychological and combination treatments

Pharmacological and psychological treatments, when delivered singly, have broadly similar efficacy in acute treatment (Canton et al., 2012). However, acute treatment with cognitive therapy (group or individual) is associated with a reduced risk of symptomatic relapse at follow-up (Canton et al., 2012). It is unlikely that the combination of pharmacological with psychological treatments is associated with greater overall efficacy than with either treatment, when given alone, as only one in four studies of the relative efficacy of combination treatment found evidence for superior efficacy (Blanco et al., 2010). The findings of small randomised placebo-controlled studies suggest that the efficacy of psychological treatment may be enhanced through prior administration of d-cycloserine (Guastella et al., 2008; Hofmann et al., 2006) or cannabidiol (Bergamaschi et al., 2011).

From a patient perspective, the guidelines suggest that each of the following four approaches should be similarly effective for the treatment of social anxiety as long as the care provider is adequately trained and up-to-date with current best practice:

  • Pharmacotherapy
    • given by a psychiatrist.
    • given by a primary care physician.
  • Psychotherapy
    • with a therapist.
    • in a group setting.
Comment author: RowanE 19 January 2015 01:27:06PM 4 points [-]

How long do the effects of caffeine tolerance, where when you're not on caffeine you're below baseline and caffeine just brings you back to normal, last? If I took tolerance breaks inbetween stretches of caffeine use, could I be better off on average than if I simply avoided it entirely?

Comment author: VincentYu 20 January 2015 03:58:38AM *  6 points [-]

where when you're not on caffeine you're below baseline and caffeine just brings you back to normal

This is a hypothesized explanation for the acute performance-enhancing effects of caffeine that fits well with the Algernon argument, but it is not a conclusive result of the literature. For instance, the following recent review disputes that.

Einöther SJL, Giesbrecht T (2013). Caffeine as an attention enhancer: reviewing existing assumptions. Psychopharmacology, 225:251–74.

Abstract (emphasis mine):

Rationale: Despite the large number of studies on the behavioural effects of caffeine, an unequivocal conclusion had not been reached. In this review, we seek to disentangle a number of questions.

Objective: Whereas there is a general consensus that caffeine can improve performance on simple tasks, it is not clear whether complex tasks are also affected, or if caffeine affects performance of the three attention networks (alerting, orienting and executive control). Other questions being raised in this review are whether effects are more pronounced for higher levels of caffeine, are influenced by habitual caffeine use and whether there [sic] effects are due to withdrawal reversal.

Method: Literature review of double-blind placebo controlled studies that assessed acute effects of caffeine on attention tasks in healthy adult volunteers.

Results: Caffeine improves performance on simple and complex attention tasks, and affects the alerting, and executive control networks. Furthermore, there is inconclusive evidence on dose-related performance effects of caffeine, or the influence of habitual caffeine consumption on the performance effects of caffeine. Finally, caffeine’s effects cannot be attributed to withdrawal reversal.

Conclusions: Evidence shows that caffeine has clear beneficial effects on attention, and that the effects are even more widespread than previously assumed.

The authors' conclusions:

  • Caffeine improves performance on both simple and complex attention tasks.
  • Caffeine improves alerting, executive control and potentially also orienting.
  • There is inconclusive evidence on dose-related performance effects of caffeine.
  • There is inconclusive evidence on the influence of habitual caffeine consumption on the performance effects of caffeine.
  • Caffeine’s effects cannot be attributed to withdrawal reversal.

Note the following conflict of interest:

The authors are employees of Unilever, which markets tea and tea-based beverages.

Comment author: ilzolende 19 January 2015 08:04:32AM 13 points [-]

Assuming you just want people throwing ideas at you:

Make it illegal to communicate in cleartext? Add mandatory cryptography classes to schools? Requiring everyone to register a public key and having a government key server? Not compensating identity theft victims and the like if they didn't use good security?

Comment author: VincentYu 19 January 2015 12:11:24PM 7 points [-]

Requiring everyone to register a public key

This is already the case in Estonia, where every citizen over the age of 14 has a government-issued ID card containing two X.509 RSA key pairs. TLS client authentication is widely deployed for Estonian web services such as internet banking.

(Due to ideological differences regarding the centralization of trust, I think it's unlikely that governments will adopt OpenPGP over X.509.)

Comment author: Mark_Friedenbach 11 January 2015 06:46:42AM 3 points [-]

Is this what you're seeing?


Comment author: VincentYu 14 January 2015 03:39:31AM 4 points [-]

The crappy resolution is due to the image host (postimage.org), which is downsizing some images served to some IPs (verified this through a few private VPNs).

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