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Topics - Pingu

1
Science / Stephen Hawking thread
3
It's possible feature not a bug, but entering replies on Dave's mega thread is now impossibly slow (unless I write it in a separate text editor and paste it in).

I've also got about a yard of useless draft replies - could that be the problem?

If so, is there a way to delete them?

(Entering text on this thread and others is fine).
5
Science / 100% effective vaccine for Ebola announced!
http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(16)32621-6/fulltext

Quote
Background

rVSV-ZEBOV is a recombinant, replication competent vesicular stomatitis virus-based candidate vaccine expressing a surface glycoprotein of Zaire Ebolavirus. We tested the effect of rVSV-ZEBOV in preventing Ebola virus disease in contacts and contacts of contacts of recently confirmed cases in Guinea, west Africa.

Methods

We did an open-label, cluster-randomised ring vaccination trial (Ebola ça Suffit!) in the communities of Conakry and eight surrounding prefectures in the Basse-Guinée region of Guinea, and in Tomkolili and Bombali in Sierra Leone. We assessed the efficacy of a single intramuscular dose of rVSV-ZEBOV (2×107 plaque-forming units administered in the deltoid muscle) in the prevention of laboratory confirmed Ebola virus disease. After confirmation of a case of Ebola virus disease, we definitively enumerated on a list a ring (cluster) of all their contacts and contacts of contacts including named contacts and contacts of contacts who were absent at the time of the trial team visit. The list was archived, then we randomly assigned clusters (1:1) to either immediate vaccination or delayed vaccination (21 days later) of all eligible individuals (eg, those aged ≥18 years and not pregnant, breastfeeding, or severely ill). An independent statistician generated the assignment sequence using block randomisation with randomly varying blocks, stratified by location (urban vs rural) and size of rings (≤20 individuals vs >20 individuals). Ebola response teams and laboratory workers were unaware of assignments. After a recommendation by an independent data and safety monitoring board, randomisation was stopped and immediate vaccination was also offered to children aged 6-17 years and all identified rings. The prespecified primary outcome was a laboratory confirmed case of Ebola virus disease with onset 10 days or more from randomisation. The primary analysis compared the incidence of Ebola virus disease in eligible and vaccinated individuals assigned to immediate vaccination versus eligible contacts and contacts of contacts assigned to delayed vaccination. This trial is registered with the Pan African Clinical Trials Registry, number PACTR201503001057193.

Findings

In the randomised part of the trial we identified 4539 contacts and contacts of contacts in 51 clusters randomly assigned to immediate vaccination (of whom 3232 were eligible, 2151 consented, and 2119 were immediately vaccinated) and 4557 contacts and contacts of contacts in 47 clusters randomly assigned to delayed vaccination (of whom 3096 were eligible, 2539 consented, and 2041 were vaccinated 21 days after randomisation). No cases of Ebola virus disease occurred 10 days or more after randomisation among randomly assigned contacts and contacts of contacts vaccinated in immediate clusters versus 16 cases (7 clusters affected) among all eligible individuals in delayed clusters. Vaccine efficacy was 100% (95% CI 68·9-100·0, p=0·0045), and the calculated intraclass correlation coefficient was 0·035. Additionally, we defined 19 non-randomised clusters in which we enumerated 2745 contacts and contacts of contacts, 2006 of whom were eligible and 1677 were immediately vaccinated, including 194 children. The evidence from all 117 clusters showed that that no cases of Ebola virus disease occurred 10 days or more after randomisation among all immediately vaccinated contacts and contacts of contacts versus 23 cases (11 clusters affected) among all eligible contacts and contacts of contacts in delayed plus all eligible contacts and contacts of contacts never vaccinated in immediate clusters. The estimated vaccine efficacy here was 100% (95% CI 79·3-100·0, p=0·0033). 52% of contacts and contacts of contacts assigned to immediate vaccination and in non-randomised clusters received the vaccine immediately; vaccination protected both vaccinated and unvaccinated people in those clusters. 5837 individuals in total received the vaccine (5643 adults and 194 children), and all vaccinees were followed up for 84 days. 3149 (53·9%) of 5837 individuals reported at least one adverse event in the 14 days after vaccination; these were typically mild (87·5% of all 7211 adverse events). Headache (1832 [25·4%]), fatigue (1361 [18·9%]), and muscle pain (942 [13·1%]) were the most commonly reported adverse events in this period across all age groups. 80 serious adverse events were identified, of which two were judged to be related to vaccination (one febrile reaction and one anaphylaxis) and one possibly related (influenza-like illness); all three recovered without sequelae.

Interpretation

The results add weight to the interim assessment that rVSV-ZEBOV offers substantial protection against Ebola virus disease, with no cases among vaccinated individuals from day 10 after vaccination in both randomised and non-randomised clusters.

Funding

WHO, UK Wellcome Trust, Médecins Sans Frontières, Norwegian Ministry of Foreign Affairs (through the Research Council of Norway's GLOBVAC programme), and the Canadian Government (through the Public Health Agency of Canada, Canadian Institutes of Health Research, International Development Research Centre and Department of Foreign Affairs, Trade and Development).
6
Science / Linear-circular correlations - help needed
Hey, what happened to the math forum?

Anyway this is science.

OK, so I have some EEG data from a study in which the participants did a reaction time task (doesn't matter what the task was for now).  So for each participant I have data from each trial of the task, including RT, and also the phase (and amplitude, but for now I'm just interested in phase) of their EEG alpha rhythm at the time when they saw the stimulus they had to react to.  What we are interested in is whether the alpha phase predicts RT.

So what I need is a linear-circular correlation coefficient.  If I plot RT against alpha phase (values in radians from -pi to pi), what I would expect, and what we do in fact see in some people, is that RT is minimal at some phase, and generally maximal at that phase plus pi.  But the phase offset i.e. the phase at which RT is minimal or maximal is not the same for each person.

However, if I knew the phase offset, and subtracted it from the actual phase i.e. centred the minimum or maximum RTs on zero, I could then simply get a linear correlation between absolute phase and RT. 

So I first fitted a quadratic to the phase by RT plot (RT on the vertical axis, phase on the horizontal) and computed the value of phase that corresponds to the minimum/maximum.  Then I essentially fold the plot at that point, i.e. subtract that phase from the actual phase data, and compute the pearson's correlation coefficient for each person between the absolute value of the centred phase at each trial and their RT.

I'm not interested in the sign of the correlation as it will depend on the phase offset anyway, so I'm also just adding pi to the phase offset if the correlation is negative, and calling the correlation positive.

I'm sure I'm reinventing the wheel here, as there are lots of horrible papers on linear-circular correlations and I can't make a lot of sense of them. One is here:

http://www.sciencedirect.com/science/article/pii/S016502701200101X

But is there something obviously wrong about what I just said?
7
Anyway, pianos don't use whole number ratios.
For years I've been meaning to ask you to explain tuning to me.

I know a fair bit about it already, but there's a huge amount I don't know, and I'm too lazy to research it.

Oh, you'd love it.  The first thing to know is that the Pythagorean comma isn't really a problem - it's very small when distributed amount 12 fifths.  The bigger problem is the syntonic comma, which is almost as big, and is the difference between a circle of only four fifths (e.g. from C to the E, a major third higher) and the "pure" major third given by the ratio 4:5.  In order to "purify" that third, you need to distribute all of it over just 4 fifths, and that means you are simultaneously OVER-compensating for the Pythagorean comma.  Which means that not only are your fifths too small (and much smaller than if you distributed the Pythagorean comma over 12 fifths), but you end up with a "wolf" at the end to make up the extra you've taken off.  Which you have to put somewhere where you hope you won't need it.

Systems in which you distribute the syntonic comma between four intervals of a fifth are called "quarter comma" mean tone. "Quarter comma" because you take 1/4 of a syntonic comma off each fifth, and "mean tone" because the resulting tones are the "mean" of the two "tones" given by the ratios of 9:8 and 10:9. The first is called the "major tone", and the second the "minor tone" (not a semitone, just a smaller "tone" than the "major tone".  Having all the tones the same size is convenient for Western music, but mean tone tunings have two sizes of semitone (because of the syntonic comma distribution". So on a fretted instrument, the frets are of alternating size (as well as decreasing over all as you go up the string of course).

I'll try to link a thing I wrote...
8
Technical Issues and Questions / Long threads
I was wondering what would happen when threads got long - and it looks like new replies don't show up on "New Posts" or "New Replies"

Is this fixable?
9
Now we are back on a big server?
10
Technical Issues and Questions / Multi-quote?
Is there a multi-quote facility that I am not seeing, and if not, could there be?