Senataxin -- SETX

• Large 2677 amino acids
• Coiled-coil domain composed of helices
  
• Involved in DNA ds-break response
• Found in cytoplasm and nucleoplasm
  
• Binds nucleotides and ATP
• UvrD Helicase domain at C-term http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=127317
  
• Phosphoprotein (PTM -- post translational modification)
  
• No PDB structures yet
• Paralogs of UPF1 and IGHMBP2 proteins
• Homologs of yeast SEN1P, chimps, mouse SETX
• OMIM ( disease, Online Mendelian Inheritance in Men) -- ALS4 and AOA2 -- neurodegenerative disease that causes poor coordination with hands, eyes, limbs, speech.
  
• http://www.uniprot.org/uniprot/Q7Z333#section_comments

•  NP_055861 , Q7Z333

• http://www.genecards.org/cgi-bin/carddisp.pl?gene=Setx
• 1-Litre of Tears
• 3 isoforms
  

Doctor's Guide

Doctor's Guide
http://www.docguide.com/dgc.nsf/ge/Unregistered.User.545434?OpenDocument

〜始める (〜はじめる) (〜hajimeru)

Meaning: to begin/start VERB-ing

Example: I started reading yesterday.

本を読み始めた [ex #1180]
I started reading the book.

• 純 [じゅん]
  (adj-na,n) pure; innocent; chaste [K] [D]
• 医師 [いし]
  (n) doctor; physician [K] [D]
• 新 [しん]
  (n,n-suf,pref) new [K] [D]
• 主 [おも]
  (adj-na,n) chief; main; principal; important [K] [D]
• 主 [しゅ]
  (n) (one's) master; (our) lord [K] [D]
• 主 [ぬし]
  (n) owner; master; lover; god [K] [D]

Keynote with Jeffrey Veen - HighEdWeb 2008 Conference

http://ca.youtube.com/watch?v=AcZQSGxnP-Y

• Find a story in the data (using GoogleAnalytics for eg)
  
• Assign visual cues to each dimension of the data
• Remove everything that isn't telling a story
• Release control when publishing on the web (see CSS Zen Garden) --> interactivity
• Let users discover their own story, develop tools that lets user control their data
  
• Provide filters to enable clarity
• A word from entrepreneurs, "Everything I've built has come from the frustration that it didn't yet exist "
• New ideas come from your heart, not from your wallet
• When you start looking at a problem and it seems really simple with all these simple solutions, you don't really understand the complexity of the problem. And your solutions are way too over simplified, and they don't work. ... Then you get into the problem, and you see it's really complicated. And you come up with all these solutions. That's sort of the middle and most people stop, and the solutions tend to work for a while ... But the really great person will keep on going and find the key and underlying principle of the problem, and come up with a beautiful and elegant solution that works. -- Steve Jobs
• Find inspiration from the fossils and the users
  

Turns and loops

Turns

• serve to change the direction of the polypeptide chain, so if chain is going north, then a U-turn will change direction to south
  
• involves 4 residues, h-bond between carbonyl of residue i and amide of residue i+3
• type I is the most common
• turns are mostly found in the surface, so residues are usually charged and polar
• type I' and II' are mirror image conformations and are rare because of steric hindrance

Loops

• longer than turns, between 6 and 16 residues long
• term used to describe 2 stranded beta-sheet
  
• beta-hairpin (loop) like turns, generally polar, flexible and are often found in active sites, bin
  

Secondary structure - Beta sheets

• carbonyls alternate in direction
• side-chains alternate in direction (pleated, doubling the layers because CA alternates up and down the sheet)
  
• zig-zag
• phi: -135, psi: +135 (top-left or Rama plot)
• pitch: 7A tall, 2 residues per turn, 3.5A rise between residues
• 

• beta strands together form beta sheets via H-bonding between main-chain backbone carbonyls and amides
• vs. alpha helices, beta-sheets have H-bonds with different segments of peptide, 0.1A H-bond shorter, both are amphipathic
• left-hand twisted in terms of angle between strand crossings
• uninvolved strands on the edges can wrap around and be involved in H-bond with the other strand to form barrels
• Greek Key Motif (3214 or 4123 topology) (number in the order of translation, ie N-term is 1 and the C-term is the last number)
  

Types

• anti-parallel - strongest, H-bond perfectly 180 degrees horizontal, dipoles cancel with other strand, more solvent accessible, some bifuricate forming beta-bulge
  
• parallel - weaker, H-bond in an angle, dipole aligns with other strand, producing a net dipole on one side = unstable, usually burried, less twisted
  
• mixed - mixture of parallel and anti-parallel strands

Connection Types

• hairpin - When the backbone enters the same end of the sheet that it left.
• right-handed crossover - When the backbone enters the opposite end.
  

It's not the mistake, it's the recovery that counts.

Socrates' Way: Seven Master Keys to Using Your Mind to the Utmost

1. Know thyself
2. Ask great questions
3. Think for yourself
4. Challenge convention
5. Grow with friends
6. Speak the truth
7. Strengthen your soul
   

〜が (ga) (subject marker)

# バスが来るよ。 [basu gakuru yo.] [ex #670]
The bus * is coming!

# 台所にテレビがあります 。[daidokoro ni terebi ga arimasu ] [ex #674]
There is a television * in the kitchen.

# 熟 [つくづく]
(adj-na,adv) (uk) completely; really; thoroughly; deeply; severely; intently [K] [D]

# 円熟 [えんじゅく]
(n,vs) ripeness; mellowness; maturity; perfection [K] [D]

酒
sake

# 酸 [さん]
(n) acid [K] [D]

Non-covalent interactions

* C-C covalent bond requires 83 kcal/mol (~360 kJ/mol) to break
* 1 kcal/mol ~ 4 kJ/mol
* H-bond (O-H....N) is about 7 kcal/mol
* bond length is from H-donor to H-acceptor
* London forces, a special type of van der Waals attraction, is when two aromatics are on top of each other, induced dipoles
* charge-charge (electrostatic) strongest IN VACUUM F=kq1q2/r^2*e (Coulomb's Law) e = dielectric, in H2O, e ~ 80, interior of protein e ~ 2 (almost vacuum)
* dipole(mu) (permanent and induced), diff. in electronegativity, Molecules with no netchargebut with asymmetric distribution of charge (e.g. CO or H2O) –Polar (permanent dipole),
* peptide bond has dipole, eg H2O, vector toward q+, mu = qx q=charge, x=distance
* van der Waals (short range than charge-charge), very weak but plays important role in stability
* van der Waals (vdw) radii rv=R1+R2 H(1.2A), **C(1.7), N(1.5), O(1.4) (radii decrease because # protons increase but # orbitals stay the same)
* Lennard-Jones potential, e=(1/r)^12-(1/r)^6 balance between vdw attractions (1/r)^6 and repulsions (1/r)^12 http://en.wikipedia.org/wiki/Lennard-Jones_potential
* hydrogen bonds, between H-bond donor (O or N) and H-bond acceptor (O or N), strong and specific non-convalent interaction, 2.6-3.5A H-bond length, 180 degrees, straight H-bond is strongest, found in secondary structure, alpha-helices, at 2.55A, the h-bond is very strong and there's a low barrier hydrogen bond (LBHB)
* water, unique because of H-bonds, sphere of hydration enables salt to dissolve, water can steal hydrogen bonds from alpha-helices, breaking it
* hydrophobic interaction - lipids aggregate because it takes less energy to form a single cage than 2 separate water cages

Summary
* hydrophobic effect and van der Waal's forces
** weakest
** for stability of folded protein
** non-specific (doesn't matter what orientation is the water cage, as long as it helps minimize energy)

vs

* hydrogen bonding and electrostatic (charge-charge)
** strongest
** for single folded state formation, NOT stability of folded state
** highly specific

Maq

Convert FASTA to the standard FASTQ
Usage: fq_all2std.pl fa2std [-q 25]

de で

車で来ました。 [kuruma dekimashita. ] [ex #694]
(I) came by car.

ひとりで行きますか。[hitori deikimasu ka. ] [ex #695]
Are you going by youself?

desu - predicate
kare-wa sensei-desu (he is my teacher)

Post translational modifications (PTM)

Main chain modification
* Proteolytic cleavage
** Signal peptidase (preprotein): "molecular postal code", N(basic, +ve charged region), H(hydrophobic region), C(specificity region, has Ala-X-Ala consensus sequence in positions -3,-2,-1), eg secretion systems, in eukarytotes (co-translational translocation in ER) vs Post-Translational translocation in prokaryotes http://en.wikipedia.org/wiki/Secretory_pathway
** Zymogen (proprotein) eg trypsin digestive enzyme, from trypsinogen (inactive) to trypsin (active form)
** pre-pro peptide hormone: eg insulin, forms hexamer with Zn, signal is cleaved by signal peptidase and delivered to ER, then an intermediate (proprotein) form where it's needed to position the two chains in the correct place to form disulfide bonds, the intermediate peptide is cleaved by PC1 and PC2 endoprotease then digested by exoprotease to produce active form
** viral RNA - is used to make polyprotein (for viral coats) - protein that, after synthesis, is cleaved to produce several functionally distinct polypeptides.
** Inteins - intron-exon like at a protein level (has exteins too)
* N-terminal modifications
** Acetylation - added by Acetyl-Coa at N-term, blocks sequencing (for side-chains, it's Lys and Arg, because methyls CH3 are electron donating groups, so want to donate electrons to + charge groups)
** Myristylation - 14 carbon myristol(fatty acid) group, associate protein with membranes

Side chain modification
* glycosylation - proteins covalently linked with carbohydrate (for proteins bound to membrane)
** n-linked - N-linked (ND2 from Asn, N is single letter code for Asn) to sugar GlcNAc, occurs cotranslationally in ER, consensus Ans-X-Ser/Thr
** o-linked - O-linked (OG from Ser/Thr) to sugar GalNAc (both vowels, o, a, OH pointing same direction as CH2OH) and occurs post-translationally in Golgi (another vowel o)
* methylation - add methyl Lys or Arg
* phosphorylation - regulate activity, kinase phosphorylate proteins, groups with hydroxyl are phosphorylated: ser (happens 1000times)/thr(100times)/tyr(1time)
* sulfation - happens in Tyr, happens permanently, for stabilizing, NOT for regulatory modification, eg fibrinogen, donor is PAPS,
* prenylation/lipidation - adds 15 carbon farnesyl or 20 carbon geranylgeranyl group to Cys at carboxy terminus, consensus is CAAX (A is any aliphatic residue except Ala)
* hydroxylation - vitamin c-dependent modification - Pro and Lys hydroxylation (add OH), eg collagen
* carboxylation - vitamin k-dependent modification - Carboxylation of Glu (so two carbonyls), for blood clotting, chelating Ca2+ ions
* disulfide bond formation - oxidized 2 Cys residues in ER (oxidizing environment), in vivo, glutathione (glutamine+cysteine+glycine) (GSH) -> GSSG (glutatione disulfide) (oxidized form) -> these are the oxidizers
* citrullination (deimination) - neutralize arginine+ charge
* deamidation - replace amide of asparagine with carbonyl, changing it to aspartic acid

Summary:
http://en.wikipedia.org/wiki/Prenylation
Cysteine - Disulfide bond formation, Prenylation
N-termini - Acetylation, Myristorylation, Methylation
Aginine - Methylation, Citrullination (deamination) (NH to O)
C-term - Amidation
Asparagine - N-Glycosylation, deamiDation (Asparagine to Aspartic Acid and IsoAspartic Acid)
Ubiquitination - E1 activating, E2 conjugating, E3 ubiquitin protean ligase
Glutamate - Carboxylation (Vit K dependent)
Hydroxyl Groups (S/T) - Phosphorylation, O-linked Glycosylation
Tyrosine - Sulfation
Proline - Hydroxylation (Vit C dependent)
Lysine - Hydroxylation (Vit C dependent), Methylation

Secondary structure -- Alpha Helices

* Secondary structure -- protein folding brought by linking carbonyl and amide groups of the backbone together by means of hydrogen bonds

Types: alpha-helices, beta-sheets, turns and loops

Linus Pauling -- predicted right-handed alpha-helix and planar peptide groups

Why do alpha helices form?
- Solved by Linus Pauling, to neutralize the main-chain atom charges (NH and C=O) making hydrophobic cores possible through hydrogen bonding
- Formed by phi (X) and psi (Y) angles of -60 and -50 degrees (bottom left quadrant of Ramachandran plot)

Alpha-helix measurements
- 3.6 residues per turn (H-bond froms between n and residue n+4)
- 5.4A patch, so one full turn is 5.4A tall
- Therefore, each additional residue gives a rise of 1.5A per residue (5.4A/3.6residues)
- Mostly right-handed, thumb points in the direction of translation (N-termini to C-termini), finger curls in the helix curling direction

end of helices (N+) usually found on the surface of the proteins

side-chains in alpha-helices are outside and points downward looking like a christmas tree

**bad Proline, produces steric, no H in NH bond to donate, so interferes with H-bond pattern
solvents (h2O) also causes bends

preference for (aliphatic): ala, leu, glu, met
against (hydroxyl): pro, gly, ser, tyr

Locations
* surface helices: amphipathic (high hydrophobic moment, 50% hydrophobic 50% hydrophilic
* membrane helices: hydrophobic (low hydrophobic moment, all hydrophobic)
* soluble helices: hydrophilic (low hydrophobic moment, all hydrophilic)

helical wheel to help determine hydrophobic moment (50-50 hydrophobic, hydrophilic)

Non-common helices / variations:
- pi helix (n+5)(4.3-16) (short and stuby, more residues per turn)
- 3-10 helix (n+3) (3 residues = 10 atoms per turn)





groove - the through, bottom, A long narrow furrow or channel.
ridge - the one pointing up, A long narrow elevation on the ocean floor.
http://www.cryst.bbk.ac.uk/PPS2/course/section9/9_helhel.html

• i+4n ridge (more common) than i+3n (slightly more slanted) ridge

10 tips to learning Japanese

http://www.socyberty.com/Languages/10-Tricks-to-Help-You-Learn-Japanese.104734

1. Learn Hiragana and Katakana

2. Basic Words and Sentences (S-O-V) He apple eat
彼はリンゴを食べる vs of the English (S-V-O) He eats an apple.

* he かれ【彼】 NOUN
* eat たべる【食べる】 VERB
* apple リンゴ [りんご] OBJECT
* NOUN - wa (は) - OBJECT - wo (を) - VERB

3. Kanji

4. Complex Sentences
は marks the subject, に to, から from, とwith or and, が marks also the subject,

5. Reading
Read some comic and children books

6. Writing

7. Listening
Usually in Anime shows, they don't use the polite form, movies are recommended instead

8. Speaking
Use polite form when in doubt

9. Time to Get Friends

10. Culture

Learning Kanji

http://www.ajalt.org/kanmana/index_e.html

They have nice pictures to help you remember the kanji, like this set here
http://www.ajalt.org/kanmana/53-56/053me.html

eyes = me
ears = mimi
mouth = kuchi
self = ji (looks like a nose???)

The spreadsheet of sunshine: Who's hiring (updated)

The spreadsheet of sunshine: Who's hiring (updated)

http://news.cnet.com/8301-17939_109-10073394-2.html

Beginner Course 1 japanese-core-2000

http://www.iknow.co.jp/lists/19053-japanese-core-2000-step-1

sore - それ (picaSO's painting is there) that one
atarashi - あたらしい [ 新しい ] new
miru - みる　 [ 見る　] (to look at MIrror) see, look at
watashi - わたし　「私」 I
en - えん　「円」 circle (ENcircle)
ooi - おおい [多い」 lots of (lots of OO)
uchi (or ie) - うち　「家」 house, home
kore - これ this one (Kanada)
sensei - せんせい　「先生」 teacher
tomodachi - ともだち　「友達」 friend

shigoto - しごと　仕事 work,job
naru - なる　(New) become
hajimeru - はじめる　始める (women first) begin, start
suru - する (to make SOUp) to do to make
deru - でる　出る to go out, to leave (to DEpart)
tsukau - つかう　使う (angel USES wings - tsubasa) to use
tokoro - ところ　place
omou - おもう　思う　(my name oro?) think
motsu - もつ　持つ (Mine, Motsu, a hand pointing at ME) have, possess
jikan - じかん　時間 time, hour

kotoshi - ことし 【今年】 this year
shiru - しる 【知る】 (shi**t, I KNOW this one) know

20 Amino Acids

http://wbiomed.curtin.edu.au/teach/biochem/tutorials/aaquiz/index.html
http://www.tamu.edu/classes/eharris/410/Tutorials/Amino%20Acids%20tutorial%20.ppt

http://www.le.ac.uk/by/teach/biochemweb/tutorials/aminoacidstruct.html
Strictly speaking, aliphatic implies that the protein side chain contains only carbon or hydrogen atoms. eg Alanine but not Cysteine (because it contains a Sulfur)

A hydrophobic molecule is repelled by water; literally, hydrophobe means something with a fear of water. eg aromatics (6 carbon ring)? like Tyrosine, aliphatics (neutral), NOT histidine (charged+), usually neutral charged are hydrophobic and don't have OH group (non-polar) (except for Tyrosine), when in doubt, put hydrophilic
* neutral and non-polar
* aliphatics
Interestingly, exactly half (10) of the amino acids are hydrophobic.
Usually it goes, Polar Yes, Hydrophobic No (except Cys and Tyr which are both Polar Yes and Hydrophobic Yes so polar residues tend to be hydrophilic), Glycine is Polar No and Hydrophobic No

Hydrophobic Residues (10 amino acids):
* Cys and Met (all the thiol containing groups)
* all the aliphatics (ala, val, leu, ile)
* all ring containing (tyr, trp, pro, phe) except His because it has strong polarity?
For properties - the only trick I ever learned was FAMILY VW (family volkswagon) for the 8 hydrophobic amino acids: Phe, Ala, Met, Ile, Leu, Tyr, Val, and Trp.

Polar if it has a charge or a free hanging NH, OH or SH that can do hydrogen bonding (but not Met) (11 amino acids):
* acids(-charged): asp, glu
* basic(+charged): lys, arg, his
* amides: asn, gln
* tyr (has OH) and cys (has free SH) (NOT Met because it has C-S-C)
* ser, thr (OH containing)

Mistakes when doing the quiz:
* hydrophobicity
* AspArtate not Aspertate
* Glutamate (E as in gluE) not Q
* Asparagine molecule is wrong, mixed with Glutamine (Gln, Q, Qlutamine) -- has CD (c-delta)
* Asparagine 1 letter code is N (asparagiNNNNNe) not A (A is alanine), neutral amide version of Asp
* Arginine 1 letter code is R (aRRRRginine) not N, basic
* Histidine, although a 5 carbon ring is still aromatic because of N lone pairs
* Proline is NOT aromatic

Group Names:
* Imidazole ring - His
* Pyrolidine ring - Pro
* Phenyl ring - Phe
* Phenol ring - Tyr
* Indole ring - Trp
* Guanidinium - Arg
* Ethyl - Ile

Atom naming
* alpha (A), beta (B), gamma (G), delta (D), epsilon (E), zeta (Z), eta (H)
* when picking 1 or 2, the precedence is S(16 heaviest), O(8), then N(7), then C(6)
* In proline, you count it in a circle
* In Trp, there's a point where you branch (CE2 - closer to NE1 and CE3) from a branch (branchpoint CD2)
* Asp (D) and amide sister (Asn N) only goes up to atom D
* Glu (E) and amide brother (Gln Q) only goes up to atom E
* Lys goes up to NZ (N-epsilon group), longest straight chain
* Arg is longer than Lys, goes up to NE-CZ-NH1 and NH2
* Only Thr and Ile branches early at atom B, like Thr, CB-OG1 and CG2 and Ile, CB-CG2 and CG1-CD1
* Met goes like CB-CG-SD-CE (Met has an E so it ends at E)


Dihedral Angles
* psi - CA-C bond (-60 degrees for right handed helix) (N-CA-C-N in N+1)
* phi - N-CA bond (-50 degrees for right handed helix) (C in N-1 - N-CA-C)
* omega - C-N bond (peptide bond, planar, 180 degrees, 1.33A in length)
* chi1 - CA-CB bond (4 atoms are N-CA-CB-CG)
note: Lys only has chi1, chi2, chi3 and chi4, NO chi5 (need 4 atoms) and Ala has no chi1
* Every angle needs 4 atoms, creating two planes
* In the Mage program, you hold look down the two atoms (so in psi, CA-C bonds are on top of each other), then a 90 degree psi angle will mean that N is 90 degrees away from N(n+1)
* rotamers are energetically staggered sidechain angle conformations

Amino Acid Covalent Bond Lengths. Peptide bond (C-N) is 1.33A long and has a partial double bond character due to the adjacent carbonyl.
ph, pKa, Henderson-Hasselbach Equation
http://www.le.ac.uk/by/teach/biochemweb/tutorials/hendhassel1.html
pH = pKa + log([a-]/[ha])

so if pKa > pH, equilibrium shifts to the left and you get more protonated ions than neutral
pKa = pH @ equilibrium

pI = pH = no charge = zwitterion NH3+ and COO- (normally at pH ~ 7)

explain why alanine has a +1 charge at pI=9.74 at neutral pH
pI=9.74=pH, so at this pH, there's the zwitterion form, no net charge, at pH=7, more acidic, then equilibrium shifts left, so we get protonation of nh2 to nh3+ (NOT coo- to cooh) and so we get a +1 net charge

Zwitterionic (net charge = 0) form in the middle
pka1 (coo-) on avg ~ 2
pka2 (nh3+) on avg ~ 9
pKa3 r-group

pI=(pka1+pka2)/2 for alanine, no charge, so (2+9)/2 ~ 5.5
but for aspartic acid, has a net charge, pkI=(pKa1+pKa3)=(2+4)/2 ~ 3
http://en.wikipedia.org/wiki/List_of_standard_amino_acids

Protonated His

ga が but

http://www.yookoso.com/

ちょっと　chotto a little
が　ga but
しずか　静か　shizuka quiet
わすれてました　[忘れてました]　wasuretemashita I forgot

悪いですがちょっと静かにしてください。[warui desu ga chotto shizuka ni shite kudasai] [ex #866]
Sorry but could you keep it a little quieter?

突然ですがボードゲーム告知をてっきり忘れてました。[totsuzen desu gabo-doge-mukokuchi wo tekkiri wasuretemashita.] [ex #865]
This is out of nowhere but I completely forgot about the BoardGame notice.

明日晴れるかどうかわからないが、もし晴れたら、私たちはピクニックへ行く。 [ex #4795]
I don't know if it will be fine tomorrow, but if it is fine we'll go on a picnic.

明日の11時に予約をしてありますが、時間を変更できますか。 [ex #4799]
I have an apointment at eleven tomorrow, but can I change the time?

毎日一生懸命に英語を勉強したが、あまり身につかなかった。 [ex #4802]
I studied English very hard every day, but I did not learn a lot.

樹 ju tree eg かじゅ　果樹　fruit tree
川　かわ　kawa - stream;river
火　ひ　hi - fire; heat hi get it?
震災　しんさい　shinsai - earthquake 災 sai - calamity/insurance

Obama Takes Oath Of Office

Obama Takes Oath Of Office

Barack Hussein Obama, 47 years old, has become the 44th President of the United States and the first of African descent.

countries

http://www.genkienglish.net/genkijapan/countriesinjapanese.htm

canada カナダ kanada
america アメリカ amerika
england イングランド ingurando
china 中国 chuugoku
korea 韓国 kankoku
japan 日本 nippon
australia オーストラリア o^sutoraria
new zealand ニュージーランド nyu^ji^rando

japanese numbers/time

http://www.genkienglish.net/genkijapan/learnjapanesenumbers.htm
いち ichi 1
に ni 2
さん san 3
し shi 4
ご go 5
ろく roku 6
なな nana (しち shichi) 7
はち hachi 8
きゅ kyu 9
じゆ jyu / zyu 10
じゅーいち　jyu-ichi 11

http://www.genkienglish.net/genkijapan/tellingthetimeinjapanese.htm
Once you've done the numbers, telling the time in Japanese is very simple. You just add "ji" to the number to get the "o'clock" part.

http://www.genkienglish.net/genkijapan/monthsoftheyearinjapanese.htm
Luckily, unlike in English where the "8th month", October, is actually the 10th month of the year, in Japanese they haven't had any Roman Emperors messing around with things so it's really, really simple, "1 month" or "ichi gatsu" is January, " ni gatsu" is February, right up to " jyu ni gatsu " which is December.

Yoroshiku onegaishimasu

Yoroshiku onegaishimasu is the king of all Japanese words

hiragana - ADDING THE "TEN TEN"

http://www.thejapanesepage.com/beginners/hiragana/combinations

* the 'K' row becomes 'G' (still the same good ole ka only with a ten-ten ; notice it is a harder sound)
ka か　->　ga　が

* the 'S' row becomes 'Z' (again harder sound)
sa さ　za ざ

* the 'T' row becomes 'D'
ta た　da だ

* the 'H' row becomes 'B' or 'P' ('B' is with a ten-ten (ex. ba) and 'P' is with a circle (ex. pa))
ha は　ba ば　pa ぱ

batch convert pictures

for i in `ls *.JPG *.jpg`; do convert -resize 50% $i resized_$i; done

hiragana - wa-n-o

http://www.thejapanesepage.com/beginners/hiragana/wa

わ　wa - It is a WAshing machine
かわいい　kawaii - cute
かわ　川　kawa - river
にわ　庭　niwa - garden

ん　n - It looks like a cursive "n"
きん　kin - gold
さん　san - 3

を　wo - looks like a guy jumping over someone's attack (the arc is a blade sweeping by). So "OH! The ninja's katana nearly hit him!"
ほんをよむ　honoyomu to read a book (book ほん　本　hon)

Organizational Development

Deming's message to Japan's chief executives: improving quality will reduce expenses while increasing productivity and market share.


http://en.wikipedia.org/wiki/W._Edwards_Deming


http://en.wikipedia.org/wiki/Organizational_development
As defined by Richard Beckhard, "Organization development" (OD) is a planned, top-down, organization-wide effort to increase the organization's effectiveness and health. OD is achieved through interventions in the organization's "processes," using behavioural science knowledge

The Frog and Prince -- book to read

Title	The frog and prince : secrets of positive networking to change your life / by Darcy Rezac with Judy Thomson and Gayle Hallgren.
Published	Vancouver : Frog and Prince Networking Corp., c2003.

1/ you have to kiss a lot of frogs to find a prince

Kiss more frogs: embrace it, enjoy it, give others a chance to meet and know you.

2/ discovering what you can do for someone else, eg introducing friends

3/ introduce yourself by name, always carry business cards and give them out. make it a habit.

if you don't have a job, you really need a business card (meishi in japanese).

the four E's - establish eye contact, extend your hand, exchange business cards, engage in conversation

when you receive a meishi, have a look at it first and say something admiring before filing it away

Three times Ribbit to help remember a person's name, use the person's name 3 times, say their name when you meet them, and find occasions to use it twice later

... and if you forget the name, ask it away ASAP or retreat for now, hope you remember it again, or ask someone else then return

4/ treat everyone as equals

Howard Schultz -- founder of Starbucks

Don't have a friend to bring to a party, then bring a guest to get to know them better

An agreeable companion on a journey is as good as a carriage

networking is an essential business skill, part of your job if you want to be successful, you can't get out of it so get into it

to attack the The Big Sweat, use enthusiasm or join Toastmasters (build confidence)

when you meet a snob, don't take it seriously, lighten up, move on, it's their problem not yours

a word about confidence, "you don't get what you want, you don't get what you deserve, you get what you get" you aren't Bill Gates or Julia Roberts, so don't beat yourself up for what you are not, you are who you are, if you treat people right, you'll be respected, liked and remembered.

5/ Give everyone permission to network, let them in to your network

6/ Learn the positive of asking questions and use it, step outside your comfort zone, Socrates was famous for it.
Put yourself in their place, if you presented something, you would want someone to ask a question about it later, shows their interested, before asking a question at a conference, introduce yourself and remember to speak up

Stanley Huang

http://www.youtube.com/watch?v=FCWgfjA9bhE
Stanley Huang's Night Is Almost Over .... Put me to sleep a bit, still better than the his other bam bam songs like this one
http://www.youtube.com/watch?v=Ytlh7zOVhBg
Who's your daddy?

I still like this one the best

The Atheist
http://www.youtube.com/watch?v=GlC7GEW8v9E
Looks like his MVs have a theme of spookiness/spiritual stuff.

hiragana ra-ri-ru-re-ro

http://www.thejapanesepage.com/beginners/hiragana/chapter_9

ら　ra - It looks like a RAttled # 5
から　kara - from
さら　sara - plate / dish
そら　空　sora - sky

り　ri - It looks like 2 arms REAching for something　(looks different in the image, no line in the middle ...)
とり　鳥 tori - bird

る　ru - It looks like a ROOt
くる　kuru - to come
さる　猿 saru　monkey
よる　夜　yoru night

れ　re - It is almost in the shape of a RAInbow
れい　rei - to bow
きれい　綺麗 kirei beautiful

ろ　ro - Think of a man in a boat ROWing
いろ　色　iro - color
しろい　白い　shiro - white
おもしろい　omoshiroi - interesting

hiragana ya-yu-yo

http://www.thejapanesepage.com/beginners/hiragana/chapter_8

や　ya - It looks like something a YAk stepped on
へや　部屋　heya - room
おや　親 oya - parents

ゆ　yu - If you look really close, you may see a Y, O, and U there
ゆき　雪　yuki snow
ふき　fuki winter
ゆめ　夢　yume dream

よ　yo - It looks like a fancy trick with a YO-YO
よい　good
つよい　強い tsuyoi strong

Note: These can form combinations
http://www.thejapanesepage.com/beginners/hiragana/Combinationstwo
Usually easy... BASE + a smaller ya, yu, or yo
kiya 気や　きや　!= kya 脚　= きゃ
shiyuu しゆう 雌雄　!= shuu しゅう　週

careful of sha (not sya), ja (not ya), cha (not chya)

hiragana - ma-mi-mu-me-mo

http://www.thejapanesepage.com/beginners/hiragana/chapter_7

ま　ma - Look MA! I caught a dragon-fly! [It looks like a dragonfly flying] (ma sideways)
いま　今　ima - now
うま　馬　uma - horse

み　mi - It looks to ME like a 2 over a 4 (can you see it?)
かみ　神　kami - God

む　mu - It looks like an old film projector showing a MOvie (a u?)
さむい　寒い　samui - cold

め　me - It looks like a half closed eye (me means eye in Japanese) (looks like nu ぬ)
め　目　me - eyes
ひめ　姫　hime - princess
めいし　meishi - business card
あめ　雨　ame - rain or candy

も　mo - It looks like a man with a hat on taking a MOrning's rest (elephant nose MOing?)
もい　moi - heavy
もし　moshi - if
いも　芋　imo - potato

Structural Variations - SNPs on a larger scale

http://www.nature.com.proxy.lib.sfu.ca/nature/journal/v447/n7141/full/447161a.html

In its broadest sense, structural variation can be defined as all genomic changes that are not single base-pair substitutions6. Such variation includes insertions, deletions, inversions, duplications and translocations of DNA sequences, and encompasses copy-number differences (also known as copy-number variants, CNVs). During the past two years, several genome-wide surveys have described large-scale (>100 kb), intermediate-scale (500 bp–100 kb) and fine-scale (1–500 bp) structural variations in the human genome.

And these can have phenotypic effects that may lead to diseases due to improper dosage production like ...

colour blindness, rhesus blood group sensitivity, classical haemophilia and forms of beta- and alpha-thalassaemia

State Of Shock

State Of Shock - Best I Ever Had
Awsome music, nice video, the part in 2:52 where the rain were bouncing on top of the cymbals in slow mo was so cool.

State of Shock - "Money Honey"
Very distinctive intro :D
There's one female member, the guitarist, I thought she was some long hair dude till Money Honey

State Of Shock - Hearts That Bleed Official Video
MV's funny, girl's pretty hot too, looks like Lohan. Catchy chorus.

State Of Shock - If I Could
This one puts me to sleep a bit, even with the love scenes ...

State of Shock - Different Day
This one puts me to sleep too ...

Personality Tests

http://www.personalitypage.com
http://typelogic.com/isfj.html
http://www.humanmetrics.com/cgi-win/JTypes2.asp

Puzzle that fits

http://www.gather.com/viewArticle.jsp?articleId=281474977390430

A lot of pieces almost fit, and if you find a close fit and you are impatient, you may be tempted to try and force it in (perhaps like some of your relationships), but in the end you have to relent, because you know it isn't right-it doesn't fit. Now in your quest to finish the puzzle you aren't looking for the most beautiful puzzle piece, or the smartest puzzle piece, or even the puzzle piece with the best resume, you're looking for the piece that fits. And there is no way to find the piece that fits without looking at the puzzle (i.e., you).

hiragana ha-hi-fu-he-ho

http://www.thejapanesepage.com/beginners/hiragana/chapter_6

は　ha - It has two parts to make memorizing it HArd (looks like an H and a tiny wiggle a)
はい　hai - yes
はし　hashi - bridge or chopsticks
葉　ha - leaves

ひ　hi - It looks like HE has both hands raised
ひと　hito - person
日　hi - day

ふ　fu - looks like crying ... fu fu ...
ふね　船　fune - ship / boat
ひふ　皮膚　hifu - skin

へ he - looks like chomping shrimp (he2) / HEY it's an upside down 'V' (almost)
へた　下手　heta - not good or poor at
へいき　heiki - peaceful / calm

ほ　ho - HO OH! It is more complicated than は ha! (two lines, two-timer)
ほし hoshi - star
ほしい hoshii - want
ほね　骨　hone - bone

hiragana na-ni-nu-ne-no

http://www.thejapanesepage.com/beginners/hiragana/chapter_5

な　na - It looks like a rope all tangled in a kNOt
なつ　natsu - summer

に　ni - It looks like a person sitting on his kNEEs (as seen from above) (ni, sideways n, side i)
なに　nani - what
にし　nishi - west
あに　ani - brother

ぬ nu - looks like an "n" on top of a "u" (nu) (2 strokes)
いぬ　inu - dog
しぬ　shinu - die

ね ne - If you look carefully you will see a '1', '+' and a '2' but, NAY, no '3', looks like wa わ but with a squiggly -- for n's
ねつ　netsu - fever
あね ane - elder sister

の no - It's a circle! NO it's almost a circle...
の - This means 'apostraphe S' (possession)
この - kono - this

hiragana ta-chi-tsu-te-to

http://www.thejapanesepage.com/beginners/hiragana/chapter_4

た　ta - looks like a "ta"
たこ　tako octopus
うた uta song
けいたい keitai cellphone

ち　chi - It looks like a CHEAp version of the number 5
ちち　chi chi - father
くち　kuchi - mouth

つ　tsu - It looks like a wave from a TSUnami (tidal wave) ***
あつい　[熱い] atsui - hot
いつ　itsu - when?
Note: small つ　means a pause between syllables
http://www.thejapanesepage.com/beginners/hiragana/SmallTsu
ちょっと　chotto little　(cho == chi+yo combined http://www.thejapanesepage.com/beginners/hiragana/Combinationstwo)
ざっし　zasshi magazine

て　te - It looks like a TErrible seven (two strokes)
すてき　suteki - nice
手　te - hands

と to - It looks like someone's big TOE
そと　soto - outside
あと　ato - later

hiragana sa-shi-su-se-so

http://www.thejapanesepage.com/beginners/hiragana/chapter_3

さ　sa　- looks like き minus one line
さけ　sake

し　shi It looks like a woman's hair flowing in the wind (SHE)
おいしい　oishi - delicious

す　su looks like a noodle SOUp
すし　sushi

せ　se as in
せんせい　sensei

そ　so It looks SO abstract like PicaSO (one stroke only)
そこ　soko - there
うそ　uso - lie

Install a Print to PDF capability

http://timesync.gmu.edu/wordpress/?p=513

Install a Print to PDF capability.

I’m finding this very useful when I want to save a page I find while on the net (e.g., a Google Maps screen) and then have access to it later when I’m not in range of a wireless signal.

* sudo apt-get install cups-pdf
* point your browser to http://localhost:631/
* Add printer
* Doesn’t matter what you type in the next three blanks, hit continue
* On next page, choose “Virtual Printer (PDF)”
* On next page, choose Postscript
* On next page, select Color Postscript option that appears
* Click Add Printer
* Type root and your user password at the authentication prompt

artificial intelligence - AI

lec 1
forms of knowledge representation
1. formal logic - set of grammars and symbols
2. semantic networks
3. visual images

constraints for efficiency:
- geometry functions
- laws of physics

- modes ponens
- for all humans(x) -> mortals(s)
- human(x) - socrates
- socrates -> mortal

- metaphysics
- theories on physics
- heuristics - pieces of advice

Book
http://aima.cs.berkeley.edu/
Artificial Intelligence: A Modern Approach (2nd Edition), Stuart Russell, Peter Norvig,
Prentice Hall, 2002.

Zodiac signs

Ram/Sheep - Pig/Boar - Rabbit/Cat (4 years apart)

http://en.wikipedia.org/wiki/Chinese_astrology

Normal Distribution (aka Gaussian distribution)

The normal distribution, also called the Gaussian distribution, is an important family of continuous probability distributions, applicable in many fields. Each member of the family may be defined by two parameters, location and scale: the mean ("average", μ) and variance (standard deviation squared, σ2) respectively. The standard normal distribution is the normal distribution with a mean of zero and a variance of one (the red curves in the plots to the right). Carl Friedrich Gauss became associated with this set of distributions when he analyzed astronomical data using them,[1] and defined the equation of its probability density function. It is often called the bell curve because the graph of its probability density resembles a bell.

The importance of the normal distribution as a model of quantitative phenomena in the natural and behavioral sciences is due in part to the central limit theorem. Many measurements, ranging from psychological[2] to physical phenomena (in particular, thermal noise) can be approximated, to varying degrees, by the normal distribution. While the mechanisms underlying these phenomena are often unknown, the use of the normal model can be theoretically justified by assuming that many small, independent effects are additively contributing to each observation. The normal distribution is also important for its relationship to least-squares estimation, one of the simplest and oldest methods of statistical estimation.

Stochastic modelling (aka Monte Carlo) -- Introducing Randomness

http://en.wikipedia.org/wiki/Stochastic_modelling_(insurance)

Stochastic modelling

A stochastic model would be to set up a projection model which looks at a single policy, an entire portfolio or an entire company. But rather than setting investment returns according to their most likely estimate, for example, the model uses random variations to look at what investment conditions might be like.

Based on a set of random outcomes, the experience of the policy/portfolio/company is projected, and the outcome is noted. Then this is done again with a new set of random variables. In fact, this process is repeated thousands of times.

At the end, a distribution of outcomes is available which shows not only what the most likely estimate, but what ranges are reasonable too.

This is useful when a policy or fund provides a guarantee, e.g. a minimum investment return of 5% per annum. A deterministic simulation, with varying scenarios for future investment return, does not provide a good way of estimating the cost of providing this guarantee. This is because it does not allow for the volatility of investment returns in each future time period or the chance that an extreme event in a particular time period leads to an investment return less than the guarantee. Stochastic modelling builds volatility and variability (randomness) into the simulation and therefore provides a better representation of real life from more angles.

uni grad

こんにちは。
ko-nn-ni-chi-wa
Hello

大学を 卒業して、 いまは (imha) 会社に 通って　　　　　います　（imasu).
Univeristy to graduate, now company and through

2009年から あたらし (atarashi) く　日本語 (nihongo) の べんきょう(benkyou) を はじめました (hajimemashita).
From 2009 Newness 　　japanese study【勉強】 start/meet.


What's your name?
あなたの 名前 は 何 ですか?
anatano namae ha nan desuka?

ありがとう　(arigatou - thank you)

Cool stuff

Marily Monroe on Albert Einstein (helps if you blur/relax your eyes a bit, like in stereo images)

http://scienceblogs.com/neurophilosophy/2007/07/interpreting_hybrid_images.php



Invisibility Cloak using reflectin proteins from squids.

http://neurophilosophy.wordpress.com/2007/06/07/invisibility-cloak-materials-made-from-reflective-self-assembling-squid-proteins/
http://en.wikipedia.org/wiki/Reflectin

The researchers manufactured the cloak using "metamaterials" precisely arranged in a series of concentric circles that confer specific electromagnetic properties. Metamaterials are artificial composites that can be made to interact with electromagnetic waves in ways that natural materials cannot reproduce.

papers about genome structural variations

Some more links from my prof ...

1. http://www.nature.com/ng/journal/v39/n7s/abs/ng2093.html
This paper is a recent reviewing defining and unifying terms. It is a must read for a good understanding the emerging structural variations.

2. http://www.nature.com/doifinder/10.1038/447161a
This paper describes a new project supported by NHGRI focusing on identifying comprehensive structural variations in humans

3. http://www.nature.com/ng/journal/v38/n12/abs/ng1921.html
This paper reported many structural variations in humans by comparing two different human genomes (public and private).

4. De novo fragment assembly with short mate-paired reads: Does the read length matter?
http://genome.cshlp.org/content/early/2009/01/13/gr.079053.108.abstract

5. De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae
http://genome.cshlp.org/content/early/2009/01/13/gr.083311.108.abstract

genome assembly tools

List of tools provided by my prof

1. bowtie (http://bowtie-bio.sourceforge.net/)
This program maps sequence reads to a reference genome. It is a most recent program. It is very fast. It still does not address indels and paired-end reads.

2. Maq (http://maq.sourceforge.net/)
This program is more mature and address many different needs including mapping reads to a reference genome, constructing consensus sequences, identifying SNPs and indels. It also comes with many useful utility programs such as a reformating program.

3. SOAP (http://soap.genomics.org.cn/)
This program does similar jobs as Maq. It was used for assembling the first Asian genome (http://www.nature.com/nature/journal/v456/n7218/abs/nature07484.html). Some functions are coming.

4. velvet (http://www.ebi.ac.uk/~zerbino/velvet/)
This is a de novo reads assembler. It assembles sequences reads into long contigs without relying on a reference genome. It will be useful for closing some gaps and identifying genomic regions that are not present in the reference sequence.

5 BLAT (http://genome.ucsc.edu/FAQ/FAQblat)
This program is good for aligning highly similar sequences.

6. GBrowse (http://gmod.org/wiki/Gbrowse)
This software is very useful for displaying alignment and for identifying automatically sequence features.

Greetings

Good morning (add gozaimasu for polite)
お　早う（はよう）　ございます　ohayo gozaimasu　　（う　u after yo)


afternoon
konnichiwa こんいちは　(wa->ha)

です　(desu)

Good evening
こん　ばんわ　(konbanwa)

goodbye (polite)
さようなら　(sayonara but in romaji it's sayo-u-nara)

goodbye (casual)
じゃ　また　(ja mata)

see you tomorrow (casual)
また　明日 (あした）　mata ashita

mina-san (everyone)
みなさん

みなさん　こにちわ　たなか　はなこ　です
mina-san konichiwa tanaka hanako desu
hello everyone, I'm Hanako Tanaka.


http://www.genkienglish.net/genkijapan/japanesegreetings.htm
"O ya su mi na sa i" is "good night", but only just before you go to bed, so it's mainly used in families. If you leave work late at night you'll have to say "shi tsu re i shi ma su" - "Sorry for being rude and going home before you all"!

More Japanese

http://www.youtube.com/user/GenkiJapanNet

http://en.wikipedia.org/wiki/Japanese_language

Sentence structure
Japanese word order is classified as Subject Object Verb. However, unlike many Indo-European languages, Japanese sentences only require that verbs come last for intelligibility.[4] This is because the Japanese sentence elements are marked with particles that identify their grammatical functions.

The basic sentence structure is topic-comment. For example, Kochira-wa Tanaka-san desu (こちらは田中さんです). Kochira ("this") is the topic of the sentence, indicated by the particle -wa. The verb is desu, a copula, commonly translated as "to be" or "it is" (though there are other verbs that can be translated as "to be"). As a phrase, Tanaka-san desu is the comment. This sentence loosely translates to "As for this person, (it) is Mr./Mrs./Miss Tanaka."

Inflection and conjugation
Verbs are conjugated to show tenses, of which there are two: past and present, or non-past, which is used for the present and the future. For verbs that represent an ongoing process, the -te iru form indicates a continuous (or progressive) tense. For others that represent a change of state, the -te iru form indicates a perfect tense. For example, kite iru means "He has come (and is still here)", but tabete iru means "He is eating".

Questions (both with an interrogative pronoun and yes/no questions) have the same structure as affirmative sentences, but with intonation rising at the end. In the formal register, the question particle -ka is added. For example, Ii desu (いいです。) "It is OK" becomes Ii desu-ka (いいですか？) "Is it OK?". In a more informal tone sometimes the particle -no (の) is added instead to show a personal interest of the speaker: Dōshite konai-no? "Why aren't (you) coming?". Some simple queries are formed simply by mentioning the topic with an interrogative intonation to call for the hearer's attention: Kore-wa? "(What about) this?"; Namae-wa? (名前は？) "(What's your) name?".

Negatives are formed by inflecting the verb. For example, Pan-o taberu (パンを食べる。) "I will eat bread" or "I eat bread" becomes Pan-o tabenai (パンを食べない。) "I will not eat bread" or "I do not eat bread".

The verb "to do" (suru, polite form shimasu) is often used to make verbs from nouns (ryōri suru "to cook", benkyō suru "to study", etc.) and has been productive in creating modern slang words.


Politeness
Most nouns in the Japanese language may be made polite by the addition of o- or go- as a prefix. o- is generally used for words of native Japanese origin, whereas go- is affixed to words of Chinese derivation. In some cases, the prefix has become a fixed part of the word, and is included even in regular speech, such as gohan 'cooked rice; meal.' Such a construction often indicates deference to either the item's owner or to the object itself. For example, the word tomodachi 'friend,' would become o-tomodachi when referring to the friend of someone of higher status (though mothers often use this form to refer to their children's friends). On the other hand, a polite speaker may sometimes refer to mizu 'water' as o-mizu in order to show politeness.

where (do ko) are you from (ka ra)?
doko kara kimashita ka?
どこ から きましたか？

Some Katakana: sūpā (スーパー) supermarket

When learning Japanese in a college setting, students are usually first taught how to pronounce romaji. From that point, they are taught the two main syllabaries, with kanji usually being introduced in the second semester. Focus is usually first on polite (distal) speech, as students that might interact with native speakers would be expected to use. Casual speech and formal speech usually follow polite speech, as well as the usage of honorific.

Japanese Phrases

I'm Brown, nice to meet you.
watashi wa brown desu, hajime mashita (informally)
watashi wa brown to moshimasu, hajimete o-me ni kakarimasu (formally)

How do you do?
hajime mashite

pleased to meet you
dozo yoroshiku.

oh, is that so?
ah, so desu ka?

Yes
hai, sou desu.

I'm not japanese
watashiwa, nihonjin dewa arimasen
日本人ではありません。

Thanks
domo / arigatou

No
ie / arimasen (negative)

strawberry
ichigo

excuse me, but ...
shitsurei desu ga ...

what's that?
sore wa nan desu ka?

what's this?
kore wa nan desu ka?

newspaper しんぶん【新聞】 shinbun

sore wa doko no chizu desu ka?
where is that cheese from?

tokyo とうきょう【東京】

umbrella かさ【傘】 kasa

wife かない [家内] kanai

is this umbrella yours?
kore wa sensei no kasa desu ka?

yes, it is, thanks.
hai, watashi no desu, domo.

no, it isn't
ie, sore wa watashi no de wa arimasen.

Quotes, New Year

It's beeen awhile since I last blogged, so to start off the new year, we have these quotes


"Be greedy when people are in fear and be in fear when people are greedy" -- from my financial advisor

Natural selection and Jacques Monod (first saw this quote from the Beethoven Virus K-drama I think)

"Man at last knows that he is alone in the unfeeling immensity of the universe, out of which he emerged only by chance. Neither his destiny nor his duty have been written down. The kingdom above or the darkness below: it is for him to choose."

http://www.shellier.co.uk/grahamhellier.htm