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MLL2: errors explained
Today, I received an email from Sarah Ng with respect to the two discrepancies that I had
found last weekend in the
Supplementary Table 3 of the Exome sequencing identifies MLL2 mutations as a cause of Kabuki
syndrome paper. She explained that for kindred 25
the DNA mutation should have been "c.A13579T" (instead of "c.A13580T"),
which indeed results in "p.K4527X" as mentioned in the column "Predicted
Amino Acid Change". And with respect to kindred 50, she agreed that
there was a typo in the protein position and that it should have
read "p.P443HfsX487" (instead of "p.P442HfsX487"). I am totally
satisfied with the answer. I have update my MLL2
page accordingly. She thanked me for checking their results, but
it was only because I tried to understand the data (in order to use it
for web page), that I found these small discrepancies. I consider them
small, because from my own experience as a software engineer, I know
that these type errors are very easily made. And of course, they do
in no way diminish the discoveries as presented in the paper. Actually,
I should thank her for her contribution to finding the cause of
Kabuki Syndrome. Although the discovery will have no direct effect for
children who are affected by this mutation, it will benefit many
parents in future to get a clear diagnoses. Andy, our son, who did receive a clinical diagnoses of Kabuki
Syndrome, will also be tested for a defect in the MLL2 gene in the
coming months and we will know whether he has the defect or not.
I expect more discoveries to be made in the coming years.
Knot Nonogram (Part 3)
Last weekend, I studied the reason function of my nonogram solver. I needed paper and pen to understand what the various
things where doing. I added some comments to the code, so that the next
time, I will have less trouble understanding the code. During a biking
trip on Sunday, I came up with a way to fix the code, such that it
(probably) would be able to solve the Knot nonogram. Last Monday, I implemented the fix, and it did
work. This evening, I spend some time, to reduce my solver to the minimal
version that could solve the Knot nonogram. It appeared that I could remove
half of the reason function, the part that I had not yet studied, and it
would still solve it. I also made the program read the nonogram from its own source. The program
contains the Knot nonogram at the bottom of the file inside a multi-line
comment. The comment contains the export (using ID:16) from the Puzzle Export page of the Web
Paint-by-Number website by Jan Wolter.
Hardest Sudoku
Today, I heard about the hardest Sudoku puzzle created by
Arto Inkala.
Last year, I already wrote program to map Sudoku puzzles on Exact Cover problems. My Sodoku solver solved it within
a sixtieth of a second and it found one solution. It could not
do this with simple reducting, which means that you cannot solve
this Sudoku with simple elimination, but you need to make some
guess and see if it leads to a contradiction. I also wonder
what kind of measure has been used for determining that this
is the hardest Sudoku puzzle, and whether a solver for Exact Cover
problems could be used to define a hardness measure.
P versus NP still unresolved
The article Crowdsourcing peer review gives a good overview how
the claim by Vinay Deolalikar
that P doesn't equal NP was dissected. It contains some
very serious flaws and probably will be one of the many
failed attempts to resolve the P versus NP problem. For a more technical evaluation
see the wiki page Deolalikar P vs NP paper.
Labyrinth
A labyrinth
is a type of maze that consist of a single path without any
splits where you have to make a choice. Most traditional labyrinths
have one exit on the outside and have a path that leads to the
center. I wondered whether it would be possible to create an
interesting labyrinth with two exits. Today, I made the one shown
on the right. A larger version can be viewed as a PostScript file or as an PDF.
This labyrinth is rotational symmetric. Of course, I am already thinking about
the number of different labyrinth there are (within certain
constraints).
Diary 2011
This afternoon, I found the Moleskine Daily Diary/Planner 2011 (ISBN 9788862934015) at
bookshop Broekhuis for € 13.95.
At 16:56:48 I bought one. At home, I discovered that this is
the soft-cover edition. Last year I bought a hard-cover edition.
I use these diaries to record what I
did during the day.
Curly kail hotchpotch with tofu
Last Friday, I found some curly kail
and I bought one bag with freshly cut curly kail. Saturday, I
bought some fresh tofu, and today, I thought about combining them.
On some web site, I read about the idea to marinate the tofu. At
home I sliced half of the fresh dofu in small blocks and
added some light superior soy sauce. Then I peeled some
potatoes and boiled them together with the curly kail.
I chopped some garlic and two red unions. First I fried
the tofu and put them in a plate. Then I fried the garlic
and the unions, added the tofu and added some curry. I
smashed the potatoes with some milk. It tasted quite nice.
Even Li-Xia wanted a second plate.
Chestnuts
This morning, around 11:28, I picked up three chestnuts (picture)
from a tall chestnut tree on the Klokkenplas, a square in the center
of Enschede. The name of this square is translated in English "bell
pool", and received its name because it was the area where the bells
from the belltower of the church where placed when the city was hit
by a fire 1862. The largest of the three chestnuts has a crack.
Mitchell Heisman
Mitchell Heisman (1975 - September 18, 2010) was a 35 year old
Jewish-American
from Somerville,
Massachusetts
who published a 1,905 page-book entitled Suicide Note and then
committed suicide on the steps of Memorial Church of Harvard University in September 2010.
Heisman grew up in New Jersey and had a University at Albany bachelor's degree in psychology.
Before committing suicide at around 11 a.m. on September 18, 2010,
during services for Yom Kippur, the Jewish day of atonement, he published a 1,905 page
book entitled Suicide Note on the website suicidenote.info and emailed a link to the note to 400 of his
contacts (a mixture of friends, family, press and academia) about five
hours after his death. Suicide Note, in addition to being a
suicide note,
discusses sociobiology, transhumanism, history, religion, death, nihilism and other philosophical issues at some length, as well
as commenting on current events. The tone of the book is alternately
academic and sardonic.
- Man Found in Front of Church in Harvard Yard After Shooting Himself,
The Harvard Crimson. September 18, 2010.
- Man Dies After Shooting Himself in Harvard Yard,
The Harvard Crimson. September 20, 2010.
- Suicide Note Found Online, The Harvard Crimson. September 22, 2010.
- Somerville man left suicide note online before shooting himself to
death at Harvard, Wicked Local Somerville, Somerville Journal. September 22, 2010.
- Mitchell Heisman: suicide note, 1905 pages, blog the reference frame. September 22, 2010.
- Man Who Killed Self in Harvard Yard Leaves Massive, Online Suicide Note,
IvyGate. September 23, 2010.
- Man Who Killed Himself On Harvard's Campus Left 1,904-Page Note, The Huffington Post. September 24, 2010.
- Bizarre last writes for suicide man. New York Post. September 25, 2010.
The above text and links are based on a Wikipedia article, which was
considered for deletion, and probably will be deleted. I found it
interesting enough to archive. Today, I also started reading the book and I am keeping a log of my reading activities.
This months interesting links
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