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Thursday, October 23, 2014

Cycling Under Attack! Things Are Tough All Over

So how much would you pay to run a cyclist down with your SUV in the Most Bike-Friendly City In America?  $1,500?  $1,000?  $500?  Well, if you act now, you can run down the annoying cyclist of your choice in New York City for the low, low price of $250.  That's only 5,306,250 Vietnamese Dong!

Of course, the cyclist did give the flat-brimmed fucktard the finger, so obviously he deserved to die:

According to Vaccaro and a witness affidavit [PDF], at around 5:00 p.m. on July 13, 2013, Michael (not his actual name) was riding his bike on Avenue B on the Lower East Side. Avenue B is a narrow two-way street with no bike lanes and parking on both sides. To avoid being doored, Michael was riding in the center of his lane. When a motorist approached Michael from behind, tailgating and honking, he responded by flipping the driver off.

Approaching the intersection of Avenue B and E. 13th Street, Michael slowed for a red light. According to the affidavit, the driver, still behind him, accelerated, striking the back of Michael’s bike and flipping him over the handlebars, causing him to hit his head on the ground. With Michael in the street bleeding from his face and head, the motorist swerved around him and attempted to drive off. A second motorist on the opposite side of the intersection tried to block the way, but the SUV driver went around the vehicle and left the scene.

Witnesses noted the SUV’s plate number, and the driver was identified by NYPD as 33-year-old Jose Henriquez, of Queens.

I'm not sure why the SUV driver attempted to escape, given the fact it's perfectly legal to mow down cyclists here in New York City.  Indeed, this turned out to be his fatal mistake, for the New York County District Attorney meted out justice in typical fashion and now he'll have to dip into his gold chain and body spray fund:

But on Monday afternoon, the assistant district attorney assigned to the case notified Vaccaro and Michael that, after consulting with her supervisor, Vance’s office offered to allow Henriquez to plead to leaving the scene of an accident with property damage. Henriquez accepted and was sentenced to a fine of $250.

Yep, $250 for what basically amounts to attempted murder.  That's not even a slap on the wrist--basically they just tickled his balls.  Then again, prosecutors are in a bind, since they have to make sure there's enough room in the prisons for all those low-level drug offenders.

This city should not be receiving accolades from cycling magazines.  We should be receiving sanctions from the United Nations.  Unfortunately that will never happen, since nobody benefits more from our motor-vehicular free-for-all than diplomats:

If you're ever riding in New York City and encounter a motor vehicle with diplomatic plates, my advice to you is to immediately take cover under the nearest parked car or subway grate until it passes, because a diplomat driver makes even the most maniacal cabbie look like a senior citizen on a Hoveround.

Meanwhile, down in the Land Frumunda, a reader informs me the guy running for Lord Mayor of Adelaide hates bikes with almost Rob Fordian passion, and to that end he proposed a 13 point "Car Friendly City Action Plan:"

First, he's going to get rid of the bike lanes:

“It’s insane giving a staggeringly small 0.8% of people
20% of the road space.”

The proliferation of cycling lanes is out of control.

Everyday 130,000 workers commute into the city, predominantly by car (91%), by public
transport (8%), and by bicycle, (a staggeringly small 0.8%).

Cycling lanes take up around 20% of effective roadway and numerous on-street car parks have
been removed to make them. How did we end up with so many cycling lanes in Adelaide where
there is clearly not the demand. The current Lord Mayor is driving this agenda at the expense of
easy car access to the city.

Wow, 20% of the roadway in Adelaide is set aside for bikes?  That has to be an exaggeration.  I don't think even Amsterdam has that many bike lanes.  Either way, for good measure he's also going to make sure you have to wear your helment at all times, because he knows this is the absolute best way to prevent the growth of cycling while simultaneously pretending to care about cyclists:

Finally, Mark Hamilton supports the helmet law and won’t allow it to be rolled back in the
future if he’s Lord Mayor.

Then, just in case you you decide "Fuck it, I'll just take the bus," he wants to get rid of bus lanes too:

“Just 8% of people use public transport.
This will not change for generations.
The rest must suffer inconvenience.”

He'll make a great Lord Vader.  I mean Lord Mayor.  If he fails to get elected, he should definitely move to Staten Island where residents would gladly make him their king.

Even in Portland, sub-Canada's erstwhile cycling nirvana, the situation continues to devolve, and recently some kind of AED (Artisanal Explosive Device) was discovered near Forest Park:

The Portland Police called in the bomb squad Saturday night to disarm an explosive device connected to a tripwire strung across a trail that leads into Forest Park.

According to a statement released this morning by the PPB, the tripwire was strung across Firelane 3, a wooded and overgrown old fire access road located east of NW Thompson Rd and accessible via Skyline Road from Thunder Crest Drive. Firelane 3 is open to bicycling and walking.

Here's the original report from The Oregonian, which tells the story of how the device was discovered:

But last Thursday the carefree walk from their Forest Heights home took a bizarre turn.

As they headed down toward the main trail, two men passed them. One was on a cellphone. Both men were sketchy and "were definitely not hikers,'' Colbach said. "It set off the hair on the back of my neck. They stuck out like a sore thumb."

Just before the couple entered the park with their Plott hound, Rhoda, Jennifer Colbach noticed a length of parachute cord stretched across the trail. They were headed toward Firelane No. 3 from the 4000 block of Northwest Thunder Crest Road off Northwest Skyline Boulevard.

"My wife said, 'Be careful here,' and she stepped over the cord," Mike Colbach said. "The dog stepped on it."

The line went slack and Jennifer Colbach noticed something move in the woods off to their right.

They continued on their walk and then went home. But the more Mike Colbach pondered the incident, the more it bugged him. So he went back Saturday.

What he found was chilling: The parachute cord was rigged to a three-quarter-inch-diameter pipe — open at one end, closed at the other — attached to a tree. There appeared to be a firing pin at the closed end. The cord was attached to a beer bottle that was supposed to swing down and strike the firing pin at the back of the device when the cord was tripped.

So they discovered the device on Thursday and didn't do anything about it Saturday?

The police might wanna take a look at these two is all I'm saying.

Lastly, Lance Armstrong may not be able to ride in George Hincapie's Gran Fondo after all:

Lance Armstrong may not, as previously reported, participate at the Gran Fondo Hincapie this weekend in South Carolina, due to the event’s sanctioning through USA Cycling.

Because of his lifetime ban, Armstrong is prohibited from participating in any event sanctioned by any signatory to the World Anti-Doping [WADA] Code.

What is at question is the status of the gran fondo, and how that lifetime ban applies.

Seems like time and money well spent on the part of USA Cycling.

shining trapezoid said...

Kenny said...

Jim Chapman said...

Third. Really!

blobby said...

dancesonpedals said...

Scranus today, Scranus tomorrow, SCRANUS FOREVER!!

JB said...

Guten morgen, Herr Rock Machine.

Top said...

Hey there

herzogone said...

Top ten.

crosspalms said...

Next we'll be game fodder in carnivals: "Knock over the cyclist, win a prize -- three shots for a dollar."

JB said...

The Bike Portland photographer guy still has a front derailleur? Get with the 1x revolution, bro-dog!

McFly said...

JB, Rode with a friend that has the 1 x 10 SCHRAMM yesterday.......and I quote him......."I really miss my granny gear!"

luiginine said...

samh said...

How do you do it, Snob? Day in and day incessantly hearing about the travesties of human transportation worldwide. Thank Lob you're so humorous because your subject matter is enough to make any rational person sick. Thanks for keeping your head up!

JB said...

McFly, I'm in Missurra (certainly no Colorado) and have a triple. I'm in the middle ring in downhill situations and in granny for the climbs. My big ring is essentially a bash guard.

If you've got the legs for it, though, good for you. You can shave an LB or so.

mikeweb said...

Anyone have Cy Vance's number? I want to see if I can pay $250 to take a giant shit on Jose's driver seat.

mikeweb said...

And on a related note, the only artisanal explosive device (AED) I've ever encountered was an Epic Burrito. It was on a time delay.

Bryan said...

Read everything, links included and still in the top 20? Cool! I thought about doing the Hincapie Fondo, but opted on an actual charity ride instead for a much lesser cost (still south cackalacky, though).

Bama Phred said...

Samh said it best but I read this and get so depressed. Scranus.

bieks! said...

What's a Plott hound? I guess in Portlandia the media have to infer the cost of your dog instead of listing the cost of your bike and/or your lack of helment. Well, Rhoda, glad you're okay, whatever you are. Guess I'll go Google it now.

DB said...

Mikeweb 10:42, early COD.

Snob, I was sure today's rant was going to be Thursday Styles Section of the NYT.

Freddy Murcks said...

Why is a grand fundo even sanctioned by USAC? That makes about as much sense as seeking official sanctioning for my morning masturbation ritual.

streepo said...

wouldn't that be " RobS FordSian passion"?

usac_loves_dopers said...

What is at question is the status of the gran fondo, and how that lifetime ban applies.

The only question for USA Cycling is, "how do we re-write the gran fondo release so it does not include the clause where the rider agrees to abide by the WADA rules and pretend it was that way all along?"

What a wretched lot of dopers running USAC. VeloNews is just playing along too. Sick, sick, sick.

ken e. said...

way too much articulation going on for this hour...

usac_loves_dopers said...

The UCI is trying to expand their worldwide dominance to all aspects of road bikeen Fredly activities.

Gran Fondos are a new thing in Canada's scranus, but bigger business in eye-taly and France.

The UCI wants their cut of the action that they have been missing and they are trying to get it through national federations like USAC.

Bama Phred said...

I can understand the lack of criminal prosecution and convictions in some of these cyclist, pedestrian, vehicle incidents. What I don't understand is the lack of reporting on the personal injury and property loss judgements that just have to be resulting from some of the more egregious accidents. Because confidentiality agreements?

JB said...

Lance Armstrong can't legally purchase bikecycle parts. My source says that he has resorted to buying from craigslist and wearing a fat suit or having Matthew McConaughey make the purchases.

Anonymous said...

Adelaide is so small that a few bike lanes probably do make up 20 percent of it's road use, that being said it's pretty dumb or decadent to be driving in a city that is so small you can cross it from end to end at a medium walking pace in under fifteen minutes.

PotbellyJoe said...

Snobi Wan,

Whats the fine if a bicyclist runs over a car? I promise you it's more than $250.

I think the key item missed in the NYPD's plea bargain is that cyclists are property according to them. I thought we had a war about people being property, but I was edumacated in the US, so i know nothing about history that doesn't include actors.

Unless of course he damaged other property in the act of fleeing and then he's only paying for that and the cyclist-murder is then free.

Vision Zero is awesome. Can't wait for Vision Negative 2 when they start to reanimate drivers who died the year before in accidents.

The nob from Aussie (the specific one in this article, as there are many who could fit this title) clearly missed the boat on distributive justice, i mean tax breaks only help corporations, but the rest of us still have to live with the government they buy for us.

Comment deleted said...

NYC cyclists are being advised by the NYPD to detach cleanly from their bicycles when hit from behind and to vault a safe distance away from said vehicle. This will avoid unnecessary property damage and inconvenience to the striking motorist.

Bicyclists are also warned not to get fleshy bits on motor vehicles which lawfully strike them.

Anonymous said...

The web.. pedia says "The Plott Hound is a large scent hound, originally bred for hunting boar."

What's in Lob's name is going on in the woods of Portland? Hunting down bores? I suppose in that case, the whole town should be on their toes.

Bryan said...

Snobi Won,
Someone posted this article on a bikecycle forum, and if you needed some good kickstarters to make fun of in the future, well, here ya go!

broken_computer_974597 said...

NYT really bolting those buzzwords together for that PR-disguised-as-news story.

a maker of samurai-inspired reflective capes that is run by a former Wallpaper editor.

In other words, a trust fund baby.

Bryan said...

the company selling reflective ballet slippers is also trying to make you walk in shit
Literally. Not even joking. And they are tryign to crowdsource the funding for it.

Anonymous said...

enough already, let the fucking guy do a fucking charity ride. he was doing what 99% of all pros were doing at the time, he was just better and more successful at it. If he were a pro football player he could beat his wife, his kid, take steroids, take other drugs, steal, make anti gay and racist comments, etc and maybe all of that together would result in a one year suspension or maybe not.

babble on said...

What. A. Day.

When I went to head out for my stoopid o'clock spin, there was a skunk on the welcome mat outside my door at five am, standing off against the cat, who was tethered there, hackles up like never before.

There was lightening and cold, cold rain as I spun my way through the park, though it did allow me to see the biggest coyote ever.

My yogurx exploded in my bag on the way to work and damaged one of my favourite pair of heels...

and now this. It's true. I don't want to believe it, but the evidence is clear. The whole world hates us cyclists, and why?! Because we have nicer bums than they do? Or is it because we don't have to mortgage our children's future for the price of a trip to the supermarket? Or is it because we are actually happy as we commute, instead of stressed, fat, and ugly?

sigh... well, at least I can turn to yesterday's post, and ponder ms Peta's lovely, ample attributes. Thank you for that, oh Snobi Wan. xo xo

ps. podium kisses, mr trapezoid. XX

Anonymous said...

I'm sure Travis Tygart just jizzed his Dockers over that news.

Anonymous said...

Way to encourage bad behavior there cy vance. So no fine or anything for intentionally hitting the guy, only for leaving the scene? I guess he could sue the little prick. Hopefully lady karma will dole out the appropriate punishment since our DA is too much of a little bitch to do so.

Anonymous said...

Did your pussy get stinky Babs?

babble on said...

Lol!! No, by the grace of God, whe still smells sweet, blessed be. :D

Bama Phred said...

Your cat is actually tied to the porch, like with a leash? I try to get mine to walk with a leash, it never ends well for anyone. And then it just sits down licking its paws as if to say, "You want some more of this?"

bad boy of the north said...

I guess USA Cycling will saction my daily rides.

Angry Beaver in Miramichi said...

Babs: The cat is "tethered" on the porch? Yikes; I hope Rob Ford doesn't find out, he loves a free meal.

bad boy from the north said...

oops!i meant"sanction".

Anonymous said...

vsk said ...
Dear Anonymous from the hour of 1:17,
I know Lady Karma, she carries an ice pick which she tells me is awesome easy for installing holes in steel belted radials (Sears Craftsman). She also works her upper body and forearms because then she can cause abrupt rear axle contact with windscreens when the time requires. She enlightened me about rebar.

I also know of Ms. Babble, who is just awesome at any speed.

Better days me hopes!!

All Gods People Gotta Have Guns said...

Gunfire in Canada? Sacrebleu! Hardly even a news story south of the border where the Glocks blaze away non stop.

babble on said...

Thanks, VSK! xx

Two things:
Cats murder songbirds at an alarming rate, and while she can still catch moths on a tether, she can't get the pretty birds.

Also, we lost a couple of furry pussies to cars (sound familiar?) and the boy couldn't take the loss of another. So she is tethered. Her lead is about fifteen feet long, and every day she begs for the harness because it is her only hope of freedom. Prolly helps that we put her in it right off the bat. She isn't a big fan of going for walks on it, but she does like the basket that attaches to the front of my bike, and she loves the cat specific backpack we have, too.

Last summer we took her with us to Hornby Island, and she figured that was just the cat's meow. Specially the couple of nights we spent in a tent - it was like the biggest box ever!

leroy said...

Well this is odd.

My dog sometimes introduces me as a plotz hound.

Weird, right?

LOLCAT said...

I can haz free time?

The Bitch You Call Life said...

babble on said...

Ha! So there is a partial solar eclipse starting in twelve minutes. Unfortunately, anyone looking up to see it from Vancouver will probably drown.

Herschel Raney said...

My cat has never tasted songbird. Though he dreams of it. And is dead excellent at taking skinks and bloodying them before I am on him. He is only allowed out when I am out. Presently the continuous fall of hickory nuts the size of bull testes has him nervous and skittish.

He has never met a skunk but a skunk on the porch is more likely trying to find the 'heavenly entry portal' of the kitty and not defensively spray it at this time of year. Guard your portals!

Comment deleted said...

If you run down an entire peloton, do you get a bulk discount, or is it $250 for *every* cyclist? If so, that hardly seems fair.

Neophyte said...

"If you run down an entire peloton, do you get a bulk discount, or is it $250 for *every* cyclist?"

OK a chance to test new skills. Here is a picture, a video and another video

bieks! said...

So, is the $250 fine this d-bag got more or less lenient than a hit & run charge? Because what he got charged with implies guilt of the latter. Or is it only hit and run in NYC when there's property damage so it's the same charge?

Spokey said...

Comment deleted @ 17:00

If you run down an entire peloton, do you get a bulk discount, or is it $250 for *every* cyclist? If so, that hardly seems fair.

and do you count axles? Unicycles at 1/2 price? recumbent trikes a 50% surcharge?

Dooth said...

Smiley Cyrus established a pretty shitty precedent. His dad worked for a pretty shitty president.

Fredder said...

That story is truly shocking! The DAs office web site has no way of leaving them a note so I posted a poor review on their FB page. Judging from the loud laughter I hear from the police car that just pulled up outside I can tell they were shaken.

recumbent conspiracy theorist said...

Wow! Ebola scare in NYC. NYPD guns down madman with a hatchet who attack officers. More of the usual drivers run down cyclists with no repercussions. Man I should shut off CNN and go reload some ammo or something.

Babble, please pet your kitty for me.

Anonymous said...

There WAS a civil case, settled for the usual "undisclosed sum".

But if I were pressing for criminal charges, and I sure as fuck would, I might pick a lawyer who's not a well publicized antagonist of the local law enforcement authorities, 'cause you know...

Anonymous said...

Mike web - I like the time delayed AED!

Dave said...

Babble - I've no objection to your cat management, but I must object to the misuse of the word murder for rhetorical purposes. Projecting human morality into animals is nonsensical. Example: a cowbird chick throws other eggs and chicks out of their nest to die. Hanging offense?

Predation is an essential component of the natural order, one of many which we have badly screwed up. Remember - only man is vile. Women, not so much, but still not exactly innocent. Cats? Innocent. Raging savages though they be.

Now let us bow our heads over these lovely bowls of spaghetti and apply the sacrament of the Parmesan.

Anonymous said...

Like your mother always told me - there is no such thing as a free blow job

Spokey said...

But cats kill for sport in addition to killing for food.

so Cats? Innocent.

I think not.

Spokey said...

The cat (that I do not own) that has lived here for over 20 years now (how long do these fuckers live anyway?) goes out all the time. Unfortunately he continues to come back despite the foxes, coyotes, and bears around here.

Bama Phred said...

The previous iteration of cat was a large orange tomcat. It's idea of fun was to catch whatever, wad it up in his mouth, run inside, and spit it out, very much alive and apparently uninjured. Then watch and participate in the hilarity as the large hairless food bringers tried to chase the whatever out of the house. Chipmunks, skinks, lizards, huge bugs, sparrows, robins, I can't remember it all. The coyotes got him, and I can feel for the boy. I still miss Steve the Cat like Lewis Grizzard missed Catfish the Lab. After losing so many to the coyotes, mine only go out when I do, and only in the middle of the day.

David Pearce said...

Dear Snob, and Snob-Hangers-On,

I, for one, am GLAD to see the guy running for Lord Mayor of Adelaide making a fist and walking on one of his planks to close all the dedicated bus lanes into Adelaide!

This is a very gutsy move, and it should be applauded by all, car-commuters and bus-commuters, and those sorry-ass 0.8% bicycle-commuters too.

I know that just published an online story, "A Look Back At The Brief Glory Days Of Port Authority Bus Terminal", and that the related link to the Port Authority,

Port Authority Bus Terminal History,

mentions how helpful the XBL, Exclusive Bus Lanes, were to speeding commuters from the New Jersey side into Manhattan, but this is obviously some terrible John Birch Communist Plot to fool us normals into believing that dedicated bus lanes help get to our destinations sooner.

Thank God, I, your humble guy running for Lord Mayor of Adelaide, knows what's going on here, and can put the kibosh on this commuter fiddle-fiddle before we achieve nirvana.

Anonymous said...

Adelaide woo. I live in that town and that guys is a fool. unfortunately alot of residents here are also fools and that type of stupidity is much loved around here. oh yeah and his figures couldn't be more wrong. vote yarwood. biek.

The fair to middling said...

Women, not so much, but still not exactly innocent.???

Well, batshit crazy counts as an innocence defence, so there's that.

semi serious cyclist said...

Sounds like Lance is going to have to pirate that Gran Fondo, scorch into the food stops and grap a few GU packets on the fly using his blazing speed to bedazzle them like the lone wolf on a downhill.

Shouldn't he be changing tires or something?

Adelbrainian expat said...

Live in Adelaide? Now that's an oxymoron.

There is ONE dedicated bike lane in Adelaide that doesn't actually go anywhere. It was built for Velo-City and opened in May 2014 - why the fuck they held a bike conference in helment law Australia is beyond me. I got a fucking $153 fine in fucking Adelaide for not wearing a foam hat and the fucking uppity turd in a uniform said the fine was for my own safety and threatened to let down my tyres. Luckily I don't live in Australia - oh excuse me - exist in Australia.

For comparison, the Lord Mayor of Sydney - Clover Moore - has built lots of bike lanes and Sydney is a real city - not like hicksville Adelaide where being a bogan in a V8 ute is something the general population aspire to.

benDE said...

Hate to kill it with the seriocity here but. . . Lets set up this fuckyou-finger-guy-gets-run-over-by-the-O.G. without the modes of transportation: Fuckyou finger guy fuckyou's the O.G. as they are both walking down the sidewalk. O.G. takes out a pipe and breaks fuckyou guy's face. What is the charge and sentence?

From here in peaceful Europe I have always heard the prosecution is tough on this in NYC (broken windows and all).

Anonymous said...

If you want to wear your jeans loose, then

Anonymous said...

So if brim-hat boy gets convicted it might cut off the financial means to collect on fuck-you-finger-biker guy's claims for injuries

As an example - a Texas law firm explains:

"Does Automobile Liability Insurance Cover Intentional Acts?

Scenario: A man gets angry because he believe you cut him off or wouldn’t let him in etc. He gets mad and intentionally rams your car. No worries, he has liability insurance, this is an auto collision and this is why we all are required to carry liability insurance right? Wrong.

Under the typical Texas automobile insurance policy, you lose the right to make a claim against a driver who intentionally hits you. There is a specific exclusion that says the insurance company is not obligated to pay a single dime if the insured intentionally causes the collision. It does not matter how much damage he does or who he hurts."

If I were FYFB I'd still want BHB to go to jail, but it does present an interesting financial problem.

Maybe he'll fall off a roof - karma

benDE said...

Adelaide . . .Adelaide . . . Adelaide.
Wasn't that a SecofState or VP or something under Nixon?

Anyway. Since my time here in Germany I have become obsessed with fact and accuracy to the point of being as fucking annoying as all the rest of 'em here. FACTS after my last hour on Google Earth following bike lanes around that unfair city.
--20% of the roads where bike lanes exist would be a stretch. Lets call it 10%.
-- bike lanes exist on no more than 8% of the roads.
--Therefore bike lanes take up a staggeringly small .8% of the city's roads.
-- lastly, how much room do you need man? If Hamilton ever visited Europe he was fall over dead from the injustice and misallocations. Grab some streetview and have a look for yourself

By his own calculations, Hamilton=idiot

benDE said...

Anon 4:07,

I will either charge you for plagiarism or congratulate both of us on some excellent interstellar thought channeling and ask in what hospital you were born to discover if we were separated at birth .

Please advise on how to proceed.

benDE said...

In the spirit of factual accuracy:

I had not zoomed in enough on the fair city I was only seeing the major roads. I was missing about 90% of the city streets.

New revised statistic bike lanes exist on a staggeringly small .08% of the city's streets.

This revision does show that the bicyclists are statistically underserved but does not change the overall annalysis:

Here is one of the 20% bike lanes totally fucking up the flow of that 6 lane thouroughfare.

Anonymous said...

Here is one of the 20% bike lanes where you will be totally fucked up if you ride in it. It's the bit of road in between the truck and the parked cars - yep right where car doors open - and if you cross the solid white line on your bike, Adelaide coppers will give you a ticket, but if you drive over the line in your car - then no problem.

Yep Hamilton = IDIOT.

ce said...
This comment has been removed by the author.
ce said...

Adelaide. Could be the name of an energy drink. One that sucks all the energy out of you and leaves you empty and lifeless.

The only rush hour they get in Adelaide is on Sunday morning, when all the old ladies are on their way to church.

ce said...

One more boring night in Adelaide

ce said...

The last time in Adelaide that a motorist and a cyclist where caught on film in close proximity to each other was back in 1966.

ce said...

I think I've found the perfect marketing slogan for the Adelaide energy removal drink: It's got that feeling!

ce said...

This is one of those games where you have to try and see if you can spot the difference

ce said...

What am saying? I've never been to Adelaide, I shouldn't be so critical.

No. Wait a minute! I think I did visit Adelaide once.

Or, did I? Ah, I don't know, I just can't remember.

Bama Phred said...

Is South Australia Down Unders' answer for Alabama? Alcohol, Ute driving Bogans, and football. All sounds familiar. And I'm guilty of all three.

On a bikeen note, I know, a real downer, I got my Dreck back yesterday after a warranty BB90 beefy bottom bracket issue. This is going to be kinda long.

BB90 shells have been known, for a long time, to not meet design specs in some instances due to manufacting issues with tolerance issues. I have one of those bikes. Mine is a Taiwan frame, I don't know if the Wisconsin frames had the same issue.

They reamed out the old bearing cup inserts. Laid down new carbon fiber to bring the shell to spec (that was the root cause of out of round condition) and bonded in new bearing cup inserts. It runs really smooth now, and it rides great. No complaints. Not making any promises on how long it will last, or something else goes wrong.

Dreck must have run out of warranty replacement frames, cause that's a lot of work for a mass produced frame that probably didn't cost $200 to produce. Even though they charge a lot more for a new frame.

Back to vehicular mayhem and scranus.

dancesonpedals said...

I'd a laid Adelaide, but too many people were watching

adelaide's lament

babble on said...

RCT - Done. Every day!
Dave - yes, it's true, but I am sure that the songbirds that don't get eaten because there's so much tasty catfood in the bowl don't see it the same way... and because of said food, I feel good restricting her right to kill with abandon.
Spokey - right?! The cat undoubtedly owns you.
BamaPhred - and after the skunk incident, I saw the biggest coyote I have EVER laid eyes on. I've seen a fair few of them over the years, but this one takes the cake. Lives by Lost Lagoon, and seems to take pleasure watching the cyclists sweat of a morning, cause I've seen him a few times now. First time I thought it was a wolf, it's so big, but that's impossible. And like the skunks and raccoons in this town, this coyote has absolutely no fear of humans.

meltyman said...

Damn. The Dulcie fund is stuck on $3,752 after one month, while the "Help James get to work safe" (suspected killer lookalike) GoFundMe campaign has raised $14,195 in just two days. Come on you stingy bastards, cough up some dough, you can manage ten bucks can'tya?

babble on said...

Wow. The US medical system can't seem to get this ebola thing right. It isn't rocket science. You would think that a DOCTOR who had spent time working in the hot zone and knew he ought to be quarantined until the risk was over would have known better than to go on public transit. Or bowling, fer fucksake.

And I'm sorry, but why the fuck did the CDC clear that second diagnosed nurse to fly on a commercial flight when she had a fever?!

It is hard to have conficence in the American medical system when such stupid stories keep coming out. I am so sorry, New York peeps. You should maybe come and visit Vancouver until this nonsense is over and done.

McFly said...

Bama, put Blue Loctite (242) on all mating surfaces. I.D. and O.D. of the bearings. The bearing journals and the crank spindle. Clean it with a powerful agent like Brakeleen prior to this sacrileious act.

Stealing that other guy's concept said...

If you like your fancy costume division you can keep your fancy costume devision.

YourRightItIsNotRocketScience said...

"Wow. The US medical system can't seem to get this ebola thing right. It isn't rocket science. You would think that a DOCTOR who had spent time working in the hot zone and knew he ought to be quarantined until the risk was over would have known better than to go on public transit. Or bowling,..."

People with Ebola are not infectious until 12+/- hours AFTER they develop a low grade fever. The doctor had been monitoring his temperature since leaving Africa and checked into the hospital as soon as he had a fever. He was NOT repeat NOT infectious at the bowling ally nor on public transport.

"...ought to be quarantined until the risk was over..."

People need to monitor their temperature after leaving the hot zone. They do not need to be quarantined until 12 hours+/- after they develop a fever.

"And I'm sorry, but why the fuck did the CDC clear that second diagnosed nurse to fly on a commercial flight when she had a fever?!

In America free citizens to not need to be cleared by the government before getting on an air plane.

The nurse in question flew to Cleveland and when she developed a fever their flew back to Dallas. Not no on on the plan caught anything from her.

"It is hard to have conficence (sp) in the American medical system..."

In American we have private doctors, nurses, hospitals, etc, and a few branches of various governments that deal with health. We do not have a monolithic "medical system" that is run as a single organization.

someotherkunt said...

Who knew Babblingons were such experts in world health - please go solve the crises with your brilliance.

Anonymous said...

Snob, this snob blog is about the sketchiest of the sketchy. I feel itchy.

dop said...

yourRightitsnot etc..

Yup. It's hard to catch. None of the family of that guy who died in Texas became infected. The 2 nurses who got sick taking care of him were literally knee-deep in his shit. galls me that the first (uninsured) patient in dallas was sent home with such a high fever.That aspect of our health care would benefit from the canadian experienced.

Comment deleted said...

I'm no cooler about FlatBrimDoucheBag's scot-free status after sleeping on it. Was this NOT assault with a deadly weapon?

This is like the perpetrators of the Valentine's Day Massacre getting off with 400 counts of lead pollution.

Spokey said...

trying to sneak in

Spokey said...

for a nice

Spokey said...

centurion podi

Anonymous said...

I don't know but I've been told SCRANUS

Anonymous said...

if you like your scranus

dop said...

Him: scrambled eggs, sausage, bacon and scranus..there's not much scranus with that

Vikings: Scranus-scranus-scranus-scranus-scranus-scranus-scranus-scranus.SCRAAANUSSSSS!!!WONDERFUL SCRANUS!!

(by sure to clean and update your scranus filter)

dop said...

how do you like your scranus in the morning?

with a kiss

sorry...too many earworms today

Bama Phred said...

Damn, you're right McFly. I forgot about that. I will next time I take it apart. But there is like 0 wobble at the clock positions I checked and it turns like butter. Gee, like it was supposed to right out of the box. Nothing that a $1,000 worth of machining didn't cure. I hate CF now, but I'm kinda stuck with it.
Ms Babble, it's like we are in some kind of parallel universe thing. I rode up on a coyote on the road behind my house at 9:00 this morning. I saved my neighbors oblivious housecat from being breakfast. Wiley was not happy, the fucker. See, I told ya'll my bike was quiet now.

Anonymous said...

I thought bike commuting in the US was tough. WOW. At least our Mayor's here hide their hatred for bicycles, knowing full well it would make bad headlines given that mother's with young children might be upset (the mother's that don't ride bikes themselves).

Australia- the only place in the world I would wish to cycle less in than America. New Zealand as well.

Obat Herbal said...

Obat Herbal Kanker Payudara Ampuh
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Mark Anto said...
This comment has been removed by the author.
Mark Anto said...

$9 Million Fraud Judgment Against Antony Gordon In Federal Court
This fraud judgment has led to Antony Gordon’s Chapter Seven bankruptcy, which is a straight liquidation.
This (2:13-ap-01536-DS 1568931 Ontario Ltd., an Ontario (Canada Corporati v. Gordon et al) looks like a $9 million dollar fraud judgment in federal court against Rabbi Chanan (Antony) Gordon (an attorney, motivational speaker, and hedge fund manager).


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Large scale analysis of positional effects of single-base mismatches on microarray gene expression data

BioData Mining20103:2

DOI: 10.1186/1756-0381-3-2

Received: 11 November 2009

Accepted: 29 April 2010

Published: 29 April 2010

Affymetrix GeneChips utilize 25-mer oligonucleotides probes linked to a silica surface to detect targets in solution. Mismatches due to single nucleotide polymorphisms (SNPs) can affect the hybridization between probes and targets. Previous research has indicated that binding between probes and targets strongly depends on the positions of these mismatches. However, there has been substantial variability in the effect of mismatch type across studies.

By taking advantage of naturally occurring mismatches between rhesus macaque transcripts and human probes from the Affymetrix U133 Plus 2 GeneChip, we collected the largest 25-mer probes dataset with single-base mismatches at each of the 25 positions on the probe ever used in this type of analysis.

A mismatch at the center of a probe led to a greater loss in signal intensity than a mismatch at the ends of the probe, regardless of the mismatch type. There was a slight asymmetry between the ends of a probe: effects of mismatches at the 3' end of a probe were greater than those at the 5' end. A cross study comparison of the effect of mismatch types revealed that results were not in good agreement among different reports. However, if the mismatch types were consolidated to purine or pyrimidine mismatches, cross study conclusions could be generated.

The comprehensive assessment of the effects of single-base mismatches on microarrays provided in this report can be useful for improving future versions of microarray platform design and the corresponding data analysis algorithms.

High-density microarrays have revolutionized biomedical research by providing comprehensive profiling of DNA and RNA molecules extracted from normal and diseased cells and tissues [1]. The Affymetrix GeneChip is one of the most frequently used microarray platforms for gene expression and genotyping assays [1, 2]. For gene expression assays, each transcript is assessed by a set of 25-mer oligonucleotides probe pairs, a Perfect Match (PM) probe and a Mismatch (MM) probe; the difference between the PM probe signals and MM probe signals are used to estimate gene expression levels. In genotyping assays, PM/MM probe pairs are used to determine SNP calls. The MM probe is identical to the PM with the exception that there is a mismatch nucleotide at position 13, i.e., the center position of the probe Upon binding to the targeted molecule, the mismatch is expected to cause a disruption around position 13 and destabilize the binding. Consequently, a MM probe should yield less signals than the corresponding PM probe. MM probes were designed to measure nonspecific binding and background noise. However, the observed MM probe signals are sometimes substantially higher than the corresponding PM probe signals, which is unexpected from microarray design [3, 4]. Clearly, it is important to assess the effects of mismatches on probe signal intensity and the subsequent consequences in the interpretation of the microarray data. There have been several previous studies focused on the issue [511], which revealed that the hybridizations on microarrays are much more complicated than hybridization in solution. It was found that the mismatch effects may depend on the mismatch types, the positions on the probe, florescent labels and off-target hybridizations. The exact mechanisms remain unclear. Clearly, more data is necessary to understand the effects of mismatches on miocrarrays.

In this study, we hybridized rhesus macaque mRNA samples with arrays designed for the human genome (Human Genome U133 Plus 2 [Affymetrix, Inc., California]) and with arrays designed for the rhesus genome (Rhesus GeneChip [Affymetrix]). By comparing species differences in target sequences, we were able to examine the effects of a large number of mismatches (15,800) between target and probe on signal intensity. Moreover, the mismatch positions in our dataset are not limited to the center of the probes, which allowed us to perform the most in-depth analysis done to date of the effect of mismatches at each of the 25 probe positions.

Materials and methods

Microarray Data

Rhesus macaque RNA samples from five sources (immortalized fibroblast, cerebral cortex, pancreas, testes and thymus) were equally divided into two sets of aliquots. Samples from each of the five sources were labeled and hybridized with either two Rhesus Macaque Genome microarrays (Affymetrix) or two Affymetrix human genome microarrays (HGU133plus2.0) according to the manufacturer's instructions. Thus, a total of 10 rhesus and 10 human microarrays were processed. See Duan et al. 2007 for further details [12].

Affymetrix GeneChip Preprocessing

The .CEL files were exported and raw PM intensities were extracted for the 20 arrays. Quantile normalization was applied within two array replicates to control for variation in hybridizations (Figure 1). The raw data (20 .CEL files) have been uploaded to the GEO repository [13] (GEO accession no. GSE9531).
Figure 1

Probe-level log intensities for 10 HGU133 plus 2.0 Microarrays and 10 rhesus macaque Microarrays. Each tissue type was hybridized with two human and two rhesus GeneChips. The two upper plots were generated from raw data (before normalization) and the two lower plots were generated from data after quantile normalization was performed.

Identifying Single Base-Pair Mismatches between Human and Rhesus Probes

A five-step procedure was used to identify single base-pair mismatches between human and rhesus probes contained on their respective microarrays. Step 1: Rhesus macaque consensus sequences that corresponded to probesets from the HGU133plus2.0 GeneChip were obtained from Affymetrix. Step 2: All of the HGU133Plus2 probes in a given probeset were aligned with the corresponding rhesus consensus sequence using the GAP package in Accelrys GCG A GAPweight of 50 and a LENgthweight of 0.5 were used for the alignment. Scripts written in the Python programming language were used to submit alignments to GAP and parse the resulting output. Results from this step were stored in a relational database. Step 3: Probesets for which the probes did not align sequentially with the consensus sequence and those for which the alignment was incomplete were discarded. Step 4: 15,800 HGU133plus2.0 probes (from approximately 12,500 probesets) for which there was a single mismatch between the HGU133Plus2 probe and the rhesus consensus sequence in each of positions 1 to 25 were identified via database queries. These probes were used as MM probes in the MM to PM comparison that followed. Step 5: The matchprobes package in Bioconductor was used to search for the rhesus probe sequences that corresponded to the human probes identified in Step 4 [14]. The probes identified in this way were used as PM probes in the MM to PM comparison. The matchprobes package was also used to identify a set of 36,578 probes (from approximately 22,000 probesets) that were identical on the human and rhesus microarrays for use as controls.

Statistical Analysis

The log-scaled ratios of PM and MM i signals, i.e., log2(PM/MMi) where i is the position of the single-base-pair mismatch, were used to represent the differences of the signal intensities between PM and MM i probes. In other words, log2(PM/MMi) represents the discrimination of PM and MM at the i th position [11]. For each tissue (or cell line), log2(PM/MMi) was calculated as the mean value from the two replicates. The average of log2(PM/MMi) over each tissue (or cell line) was obtained by applying a one-way ANOVA to each probe with the variables of Tissue (five levels, representing the five sources of RNA described in the "Microarray Data" section) and Chip (two levels, representing PM and MM i ).

To examine the effect of different types of mismatches at different mismatch positions, the estimates of log2(PM/MMi) from the last step were categorized according to mismatch type and mismatch position. Mismatch type was named so that the first letter denotes the base in PM and the second letter denotes the base in MM. The 25 mismatch positions were binned into 3 groups: the left group had mismatches in positions 1 to 8, denoted as the 5' end of a probe; the center group had mismatches in positions 9 to 17 and the right group had mismatches in positions 18 to 25, denoted as the 3' end of a probe. The statistical significance was assessed with Student's t-test.

We searched for pairs of probes that differed by a single nucleotide on the human U133Plus2 array and the rhesus macaque GeneChip. 15,800 such probe pairs were found. Table 1 shows the frequency of probes with mismatches at different positions. At least 500 probe pairs were found for each of the 25 positions. In general, there were fewer mismatch probes in the center positions than in the 5' and 3' ends. Position 13 had the fewest number of mismatch probes.
Table 1

Frequency of probe pairs for each mismatch position.

Single-base-pair mismatch position

Number of PM/MMi

The average difference between PM and MM depended on the position of the mismatch on the probe. Both the average and variability (represented by the interquantile range) of log2(PM/MMi) increased from both ends of the probes (positions 1 and 25) towards the center, and became relatively steady between positions 7 - 16 (Figure 2). The peak value of the average of log2(PM/MMi) was reached when i was equal to 12. For example, there was a 24% decrease in the value of PM/MM when the position changed from 12 to 1, and a 29% decrease in the value of PM/MM when the position changed from 12 to 25. In addition, we observed a strong linear association between the average and the variability of log2(PM/MMi)( R2 = 0.95) (Figure 3).
Figure 2

Distribution of log 2 (PM/MM i ) across 25 single-base-pair mismatch positions. The red dashed line represents the mean value of log2(PM/MMi) when there was no mismatch, i.e., the common PM probes from the HGU133plus2.0 GeneChip and the Rhesus macaque GeneChip.
Figure 3

Average of log 2 (PM/MM i ) versus the variability of log 2 (PM/MM i ) across 25 mismatch positions. The values of the median and the median absolute deviation (MAD) of log2(PM/MMi), representing the robust versions of the average and variability, were calculated for each mismatch position. The number inside the circle indicates the mismatch position. R- square measures the strength of the linear relationship between two variables.

Because the PM signals and MM signals were collected from different arrays, it is possible that the difference between the signals resulted in part from different hybridization conditions on the two types of array. To test this, we compared signals from probes that matched perfectly between the human array and the macaque array. As expected, the average differences were very small as compared to values obtained from log2(PM/MMi) across 25 probe positions (Figure 2). The p values from Student's t-tests comparing log2(PM/MMi) with the signal differences of identical probe pairs between human and monkey microarrays were extremely small (<10-6).

We found that mismatch type also had a strong effect on signal intensity. The greatest effects were observed with C → A (i.e., C on PM and A on MM; correspondingly G on target), G → A and C → G. The least effects were observed with A → C, A → G and A → T (Figure 4). In general, mismatching in a C-G base pair resulted in greater loss of intensity than when mismatching occurred in an A-T base pair.
Figure 4

Mean level of log 2 (PM/MM i ) for 3 groups of mismatch positions for each mismatch type. The x-axis denotes the 12 mismatch types. The first nucleotide represents the rhesus probe (PM) and the second nucletotide represents the human probe (MM).

To determine whether different types of nucleotide mismatches differ significantly across mismatch positions, the mean level of log2(PM/MM) was calculated and graphed for different categories according to mismatch type and mismatch position classification (Figure 4). Note that the subscript from MM i was removed because the mismatch positions were binned into groups. The signal intensity difference between PM and MM was represented by the average of log2(PM/MM). This difference was always greater for the center group (positions 9 - 17) than either the 5' end (positions 1 - 8) or the 3' end (positions 18 - 25). On average, the discrimination between PM and MM for the center group was 13% higher than for the 5' end group and 17% higher than for the 3' end group. In addition, the value of log2(PM/MM) in the 5' end was greater, with the exception of C-A, than the 3' end. The differences between the center group and the other two groups were statistically significant in most cases (Table 2). Only 3 out of 24 comparisons had p values larger than 0.05 (Table 3). However, there were 8 of 12 comparisons with p value larger than 0.05 when the 5' end was compared to the 3' end (Table 2).
Table 2

Student's t-tests between 3 groups of mismatch positions for each mismatch type.

Mismatch type

Center vs. 5'-end

Center vs. 3'-end

5'-end vs. 3'-end

*: p value ≥ 0.05

Table 3

Similarities across different studies in terms of the effect of mismatch type.

Spearman Correlation Coefficients, N = 12 (mismatch type) (Prob > |r| under H0: Rho = 0)

Current Study

Current study

Pearson Correlation Coefficients, N = 12 (mismatch type) (Prob > |r| under H0: Rho = 0)

Current study

Current study

3a: using Spearman's correlation coefficient; 3b: using Pearson's correlation coefficient. The statistics in bold indicate the correlation coefficient significantly different from the chance, i.e., p value ≤ 0.05; or marginally significantly different, i.e., 0.05 < p value < 0.07.

We took advantage of the differences between the human and the rhesus macaque genomes to evaluate the effects of mismatches between targets and probes on signal intensity in expression arrays using the largest dataset studied thus far. In a previous study, the positional effect of single base mismatches collected data from 935 pairs of perfect match and mismatch probes were examined [11]. Our study utilized data from 15,800 pairs of perfect match and mismatch probes.

Nonrandom Number of Mismatch Probes by Position

We expected to find approximately the same number of mismatches between human probes and rhesus sequences at all 25 mismatch positions. However, there was a general tendency for fewer mismatch probes at central positions than at the 5' and 3' ends. Interestingly, we found the fewest mismatches between human probes and monkey sequence at position 13. The explanation for this result is not obvious. One possibility is that the human probes were selected by Affymetrix to have fewer mismatches in central regions due to human SNPs. This preference for relatively conserved regions may have resulted in fewer probes with mismatches to rhesus sequence in this central region.

Mismatch Positional Effects

We found a mismatch at the center of a probe resulted in a greater loss in signal intensity than a mismatch at the ends of the probe. Various studies reported similar results [57, 11]. This may be due to the zippering effect, as discussed by Binder [15] and Deutsch et al [16]. The probability of "open" base-pairings may be minimal in the center of an oligonucleotide, on average, and thus the discriminating effect of the central bases may be maximal.

We also observed a slight asymmetry between the ends of a probe: the effects of mismatches at the 5' end of a probe were greater than those at the 3' end. This may be due to the fact that the probes on the Affymetrix microarrays are anchored to the silica surface at the 3' end of the probe. Thus, our result is consistent with Wick et al.'s finding that mismatches at the loose end are more discriminating than mismatches at the attached end.

Our results also suggested that the stronger the mismatch effect, the more variable the effect. In Figure 3, we showed that the value of log2(PM/MMi) is closely correlated with the median absolute deviation value of log2(PM/MMi). This may be because when the mismatch is strongly disruptive of the binding interaction on the probe, the adjacent nucleotides will have to accommodate the disruption. Thus, certain combinations of nucleotides may be more accommodating than others, leading to more variation in the free energy of binding for the more disruptive mismatch types.

Mismatch Type Effects

The role of the probe mismatch type on signal intensity has been previously investigated [6, 7, 911]. Among these studies, Wick et al's report (2006) and our analysis used the same statistic - log2(PM/MM) - to measure the discriminating ability of PM and MM. The biggest difference between our results and Wick et al's was the magnitude of PM/MM (Figure 5). On average, Wick et al's reported a 20-fold greater effect than was observed in the current study. This likely reflects the fact that the length of the probe was 18 oligonucleotides in Wick et al's report and 25 oligonucleotides in our study because different arrays were used in the two studies.
Figure 5

Comparison of log 2 (PM/MM i ) for each mismatch type between the current study and Wick et al. For each mismatch type, the first nucleotide represents the PM and the second nucleotide represents the MM.

We expanded the cross-study comparison of the effect of mismatch type [6] by including the current study (Figure 6). In addition, we quantified the similarities across different studies in terms of the effect of mismatch type (Table 3). We did not include the results of Sugimoto et al (2000) for two reasons: 1. their results were mainly summarized from the analyses of certain trinucleotide stabilities; 2. there was no C-C mismatch type in their study, which would result in a missing value for our comparison. There are several interesting results from this cross-study comparison.
Figure 6

Stability orders of 12 single-base mismatch types for hybridization in solution ( b ) and on microarrays ( a, c, d, e ). For a hybridization oligonucleotides duplex X/Y, X refers to probe and Y refers to target. For example, the microarray hybridization in our study is DNA/RNA, which means the probe is DNA and the target is RNA - cRNA used by an Affymetrix experiment. We refer to Naiser et al. (2008) for details. Specifically, both Wick et al (2006) and our study used log2(PM/MM) as the measure of discriminating ability, which has an opposite order compared to stability. Thus, the larger log2(PM/MM) value corresponds to the lower stability of duplex. Please note that there are two notations used under each study: the upper one is the notation that is commonly used- for consistency to that in Naiser et al (2008); the lower one is the notation indicating the base change from a perfect matched probe to a mismatched probe - primarily used in the current study. For example, C U in the common notation means the probe provides C and the target provides U for the mismatched base pair, while in the second notation it's A C indicating A is the base on the perfect matched probe and changes to C on the mismatched probe.

In general, the results from the different studies were only weakly similar (Figure 6, Table 3) in terms of mismatch type. However, there were some areas of agreement. For consistency, we used the same notation for mismatch type as that in Naiser et al (2008) for the illustration of this cross-study comparison (ours was listed as well, see Figure 3 for detail). Both Wick et al's study (2006) and our results placed the G-T mismatch type at a relatively higher position on the stability list- opposite to the discriminating ability list. Both Schwarz et al's study (2006) and our results placed the A-G mismatch type at the last position on the stability list. However, if the comparison is expanded to the group of purine/pyrimidine mismatches instead of individual mismatch types, our study agreed very well with Naiser et al's (2008). When a mismatch occurred to the C-G base pair, a greater loss in signal intensity was observed (Figure 6). However, each of our studies had an outlier, defined as a mismatch type whose real positions are different from expected according to the rules of Watson-Crick base-pairing. Specifically, positions 1 to 6 on the stability list should belong to the mismatch types whose mismatch occurs to the A-T base pair, and positions 7-12 should belong to the mismatch types whose mismatch occurs to the C-G base pair. Naiser et al (2008) reported an A-G mismatch values at a higher position - position 4 - on the stability list than expected, which should have been placed at positions larger than the 6th . Results from the current study indicated a A-A mismatch values at a lower position - position 9 - on the stability list than expected, which should have been placed at positions smaller or equal to the 6th. The difference between two studies may be due to the differences in the detailed hybridization conditions and the different microarray platforms used in the two studies --- Naiser et al (2008) designed their own technology for fabricating the chip of microarray while we used the standard Affymetrix GeneChip.

Because both Wick et al (2006) and our study used the same metric - log2(PM/MM) - to measure the discriminating ability - opposite to duplex stability. We want to further elaborate the comparison between two studies. Our results were in partial agreement with Wick et al. (Pearson's correlation: 0.47) (Figure 5). We found that, in general, samples with mismatches with probes where the sample is either an A or T had smaller decreases in signal intensity than when the sample contained a G or C which was mismatched with the probe as would be expected from Watson-Crick base-pairing. Wick et al. found that a sample with a C that mismatched the probe had a much greater decrease in signal intensity as compared to a sample with a G that mismatched the probe (the difference in the central region is about three-fold). In contrast, we found no major difference in the amount of the decrease in signal intensity when the mismatch was between a C in the sample or a G in the sample and the probe (they only differ by about 2% in the central region) (Figure 4). It is not clear what caused the discrepancies between our study and Wick et al.'s study. Wick et al.'s results are in good agreement with values of solution studies with nearest neighbor model [17]. However, it has been reported that the stacking free energies on Affymetrix arrays are different from that in solution [4, 18]. But there was also study showing a good agreement between the solution nearest-neighbor(NN) affinities and that on Affymetrix arrays [19]. Further experimentation might resolve these differences.

In general, it appears that mismatch type is more sensitive to different experimental methods than mismatch position. Microarrays produced in different ways may have different spatial features that complicate specific types of mismatched base pairing. This may be because mismatch type depends on many different experimental factors, e.g., solid substrate or solution, DNA or RNA (either probe or target) and the length of probe.

Practical Implementation of Our Analyses to Microarray Design

Our results may be useful for improving future versions of microarray platform design, especially those which involve the single-base mismatches such as the Affymetrix GeneChip. On the one hand, these results showed that mismatch position effect is relatively insensitive to experimental methods, which supports Affymetrix's decision to choose the 13th position when designing PM/MM probe pairs, (although our results showed that the position 12th may cause a slightly bigger loss of signal intensity in mismatches) (Figure 2 & 3). On the other hand, the results from different studies showed that mismatch type is more sensitive to experimental methods, implying that Affymetrix may improve the array's design by incorporating these results. For instance, Affymetrix typically uses a number of probe pairs to represent a probeset, e.g., 11 probe pairs for a gene on Human Genome U133 Plus 2.0 Array. Each probe pairs contains a mismatch probe which alters its 13th position compared to a perfect matched probe. These 11 mismatched bases may not necessarily be the same mismatch type. In fact, they very likely belong to different mismatch types. We found that when the experimental method changes, the effects of mismatch type may also change, indicating there may be some unpredictable uncertainty when summarizing the intensities of these 11 probe pairs. Our results may help Affymetrix minimize this type of uncertainty by incorporating the mismatch type effect when designing probe pairs. A simple resolution is to select the same mismatch type for all 11 probe pairs.

Correspondingly, our results may also be useful for improving array data processing algorithms, particularly those considering single base effects, such as GC-RMA [20] and PDNN [4].

We evaluated the effects of single-base mismatches on Affymetrix microarrays in a large dataset. We found that a mismatch at the center of a probe incurs a greater loss in signal intensity than the mismatches at the ends of the probe. There was a slight asymmetry between the ends of a probe: effects of mismatches at the 3' end of a probe were greater than those at the 5' end. These results were similar to previous research. The results from studies on mismatch type, including ours, were only weak correlated. Our study agreed very well with a recent study when the comparison was widened to the group effect of purine or pyrimidine mismatch type. Our results, together with that of previous studies, provide a comprehensive assessment of the effects of single-base mismatches on microarrays to date and may be useful for improving future versions of microarray platform design and the corresponding data analysis algorithms.

This project was supported by a grant from NIH [RR017444] to RBN and by NIH grant number P20 RR016469 from the INBRE Program of the National Center for Research Resources.

We thank the ONPRC microarray core for processing the microarrays. We also thank the reviewers of this manuscript for their helfpul suggestions.

Authors’ Affiliations

Center for Statistical Sciences, Brown University
College of Information Science & Technology, University of Nebraska at Omaha
Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University
Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center
Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center

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© Duan et al; licensee BioMed Central Ltd. 2010

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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KENNEDY, Joseph P. III, (1980 - )

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KENNEDY, Joseph P. III, (son of Joseph Patrick Kennedy, II, great-nephew of Edward Moore Kennedy and John Fitzgerald Kennedy, and great-great-grandson of John Francis Fitzgerald, first cousin once removed of Patrick Joseph Kennedy), a Representative from Massachusetts; born in Brighton, Suffolk County, Mass., October 4, 1980; B.S., Stanford University, Stanford, Calif., 2003; J.D., Harvard University, Cambridge, Mass., 2009; United States Peace Corps, 2004-2006; research analyst; Middlesex, Mass. county assistant district attorney, 2011-2012; elected as a Democrat to the One Hundred Thirteenth Congress and to the two succeeding Congresses (January 3, 2013-present).


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Japan’s Most Famous Rollercoasters

Spring is officially over in Japan with the first Monday of June settling into a start. This would mean the complicated weather of sunny and rainy days are about to commence. Before this confusing rollercoaster ride of sun and rain begins, here are a few actual rollercoasters in Japan worth taking a ride.

While its summer elsewhere, the rainy season is about to begin in the bigger parts of Asia of which include the country of Japan. June is relatively the start of heavy downpours which would be a big sign for travellers to opt other months for travel.

Yet, with June still settling in plus the sweet scent of Spring still fresh in the air, it’s a big risk to get out in the open. In an effort to enjoy the last days of Spring, heading out to the open is the best activity so far. When it comes to the open, nothing beats spending time at an amusement or theme park. Of course, in Japan the best parts of their theme parks are their crazy and not to mention awesome rollercoasters.

Here are rollercoaster rides that you should try out in Japan.

The Eejanaika

First up is the Eejanaika located at Fuji-Q Highland in Yamanashi, Japan. This rollercoaster was featured in Complex magazine’s best rollercoasters back in 2011. The Eejenaika has a height of 249 feet with a top speed of 78.3 mph. The ride starts off by pulling the cart backwards before the sudden 90 degrees drop vertically. Then, the ride throws around like a pendulum with a reverse, a flip, a corkscrew and a cracked out see-saw. This ride is definitely not for the faint-hearted.

The Dodonpa

Next up is Dodonpa also located at Fuji-Q Highland. The Dodonpa has a height of 52 meters with a top speed of 172 km/h. Like Eejanaika, the ride pulls you backwards before a vertical drop of 90 degrees. It’s not as exciting as the Eejanaika though.

The Fujiyama

Third is Fujiyama has been named “The King of Rollercoasters” with 4 Guinness World Records dating back to 1997. Fujiyama has a max speed of 130 km/h with a height of 79 meters.

The Takabisha

Last but not the least is Takabisha which has been named the “steepest drop in the world at 121 degrees.” This spine-tingling drop has been produced using the linear launch system with a vertical ascent and linear acceleration. It has a total speed of 100km/h.

Take advantage of the Spring weather before the rain showers start to pour and get a thrill of excitement from Japan’s most awesome rollercoasters.


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Synthesis Analysis of Regression Models with a Continuous Outcome Xiao-Hua Zhou 1,2, Nan Hu 2, Guizhou Hu3, and Martin Root3 1 HSR&D Center of Excellence, VA Puget Sound Health Care System, Seattle, WA 98101. 2 Department of Biostatistics, University of Washington, Seattle, WA 98195. 3 BioSignia, Inc., 1822 East NC Highway 54, Suite 350, Durham, NC 27713 To estimate the multivariate regression model from multiple individual studies, it would be challenging to obtain results if the input from individual studies only provide univariate or incomplete multivariate regression information. Samsa et al [1] proposed a simple method to combine coeﬃcients from univariate linear regression models into a multivariate linear regression model, a method known as synthesis analysis. However, the validity of this method relies on the normality assumption of the data, and it does not provide variance estimates. In this paper we propose a new synthesis method that improves on the existing synthesis method by eliminating the normality assumption, reducing bias, and allowing for the variance estimation of the estimated parameters.

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Best Law Firm Veteran, WYRemember, it’s also a great indication if the team you are talking to appears interested in your case. You’ll see this if they ask concerns about your situation and particular needs. If they don’t ask you any concerns, it’s ok to ask them if they have any concerns for you.

Lastly, a good thing to remember is that when you’re dealing with someone you wish to be involved with someone you trust and like. Personality, professionalism and trust are very important traits in a good Wyoming lawyer.

If you discover you do not have a great connection or chemistry with the law team in Veteran that you’ve been gotten in touch with, you can always change it up. It might not be wise to change your team in the middle of any legal proceedings, but if you haven’t begun yet it may be an alternative for you.

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Call 1 (844) 359-9813 Today To Connect With a Lawyer That Can Help You With Your Legal Needs!

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Looking for attorneys in another Wyoming city?

Check out these cities near 82243

  • Lawyer for Veterans in Green River, WY – 82935
  • Lawyer for Veterans in Burlington, WY – 82411
  • Lawyer for Veterans in Chugwater, WY – 82210
  • Lawyer for Veterans in Frontier, WY – 83121
  • Lawyer for Veterans in Big Piney, WY – 83113
  • Lawyer for Veterans in Midwest, WY – 82643
  • Lawyer for Veterans in Meriden, WY – 82081
  • Lawyer for Veterans in Torrington, WY – 82240
  • Lawyer for Veterans in Mountain View, WY – 82939
  • Lawyer for Veterans in Lance Creek, WY – 82222
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info [at] birdiesync.comE-mail Us Directly

My items on the desktop are not synchronized in real time while the mobile device is connected.

Presently BirdieSync doesn't offer a real time synchronization on PC side (although it does on mobile side). If modifications are done in Lightning after you have connected and synchronized your mobile device, you must then launch a new synchronization manually, before disconnecting your mobile. This limitation should be addressed in a next version. On XP you can choose a particular synchronization period in BirdieSync options (Tools/BirdieSync/Options/Synchronization/Synchronization frequency) On Vista, the mobile device is automatically synchronized every hour. You don't need to disconnect your mobile to manually relaunch the synchronization. On XP, you can click on the "Synchronize" icon of the ActiveSync window while on Vista, you can for instance select the "Sync all" command in the context menu of the Sync Center icon (the green one) in the task bar.