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Inning-by-Inning | ||||||||||
Team | 1 | 2 | 3 | 4 | 5 | 6 | 7 | R | H | E |
KU | 0 | 0 | 0 | 0 | 0 | x | x | 0 | 1 | 2 |
OU | 2 | 2 | 1 | 4 | x | x | x | 9 | 10 | 0 |
Pitching | ||||||
W - Stevens (18-5) | 5.0 | 1 | 0 | 0 | 2 | 5 |
L - Kessler (17-8) | 2.0 | 3 | 4 | 2 | 2 | 2 |
Individual Leaders | ||||||
OU - Self | 3 | 2 | 3 | 4 | 0 | 1 |
KU - Stein | 2 | 0 | 1 | 0 | 0 | 0 |
Player of the Game |
Kady Self // So. // OF Self kept her red-hot hitting going and set the tone early in the Sooners' 9-0 win Friday night. On the second pitch of the game Self homered off the left field foul pole. One inning later, she hit a two-run single. Self finished 3-3 to tie a career high in hits, scored twice and drove in four runs. |
NORMAN, Okla. – Oklahoma and Kansas both entered Friday night's game undefeated in conference play, but the No. 22/15 Sooners (26-8, 5-0 Big 12) scored early and often en route to a 9-0, five-inning win over the Jayhawks (28-11, 3-1).
OU scored in every inning and pushed their season-best winning streak to eight games with the win. During the run, the team has outscored its opponents 59-5 with five run-rule victories.
It was Oklahoma's ninth win in the past 10 meetings with Kansas after OU's eight-game winning streak in the series was snapped in game two of a doubleheader last year in Lawrence.
The run-rule victory was the 14th posted by the Sooners this year. They have rattled off 83 straight run-rules since their last run-rule defeat. Of those 83 wins, 43 have come via shutout.
The Sooners couldn't have started much quicker than they did Friday night, needing just two pitches to take a 2-0 lead in the first.
Junior Georgia Casey was hit on the foot by the game's first pitch, and sophomore Kady Self pulled the next pitch she saw deep down the left field line. The ball hit off the foul pole to give Self her fifth home run of the season and fourth in the last five games.
"We knew we had to come out fast and kind of set a tone, and being that you're home and you have your home-field advantage you really try to do that," OU head coach Patty Gasso said. "With Georgia [Casey] getting on and Kady Self doing what she's doing these days, that really kind of started things up for us."
"It takes a lot of pressure off you, obviously," Oklahoma starter Kelsey Stevens said of pitching with an early lead. "I always feel pretty confident even if we haven't scored yet, that we're going to score, but especially when you get runs in the first inning, it really helps you as a pitcher."
OU doubled its lead in the second inning as Self came through again in the clutch.
Senior Destinee Martinez led off the frame by reaching on an error. Sophomore Leslie Miller followed with a single through the left side, and both players were sacrificed into scoring position on a bunt by junior Jessica Vest.
After a popup, Self stepped in and quickly got ahead in the count 3-0. KU starter Kelsey Kessler battled back to make it a full count, but Self drove in her third and fourth runs of the game as she hit a chopper up the middle.
That would be all for Kessler, who entered the game with a nation's best 207 strikeouts. She managed two punchouts in two innings of work, but she also gave up three hits, two walks and four runs, two of which were unearned.
For Self, it was just another game in the midst of her recent hot streak. In her past five games dating back to the series opener at Iowa State, she is 11-15 (.733) with four home runs, 11 RBI, 10 runs scored, a double, three walks and no strikeouts. Her slugging percentage in those games is 1.600, while her on-base percentage is .778.
Self's hitting streak is also at a career-best five games. She finished Friday night's game 3-3, her third 3-3 performance in the hitting streak, with two runs scored and four RBI.
"It's been really good," Self said of her recent performance. "It's been nice to see hard work pay off and to be able to help the team in any way I can."
Sophomore Whitney Ellis led off the third inning with a solo home run to center field to make it 5-0 for the Sooners. It was her seventh of the year to match Casey for second most on the team.
OU then put the run-rule into effect with a four-run fourth.
With one out, Self and junior Shelby Pendley hit back-to-back singles up the middle. Senior Brittany Williams followed with a three-run homer to the bleachers in left center on a full-count pitch. It was her fourth long-ball of the season.
The run support was more than enough for Stevens, who twirled her second straight shutout. A leadoff single in the second inning was all that KU could muster off of her as Stevens allowed just one hit with five strikeouts and two walks.
Stevens, who needed just 66 pitches to set down the Jayhawks Friday, has now thrown 18.1 consecutive scoreless innings over her last four appearances.
Oklahoma and Kansas wrap up the series Saturday with a doubleheader beginning at 2 p.m. The teams were supposed to play a single game Saturday and Sunday, but there is a threat of rain for Sunday.


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"The important thing is not so much that every child should be taught, as that every child should be given the wish to learn." - John Lubbock
Saturday, April 21, 2012
Trip to the Landfill
Today was the day! We finally took a tour of the county landfill. And it was one of the most interesting tours we've been on. Needless to say, M was so excited!
The free tour was organized by South Wake Solid Waste Management. After we got to the landfill, we were given a brief, but very informative presentation describing all the areas of the landfill (with areal photographs) and the layers it was composed of.
Then we all got into a big van and taken to the spot just a few yards away from the landfill's cell that is now being filled with garbage. Since it was Saturday, things were pretty slow. We saw only three or four garbage trucks pulling into the area and unloading. Consequently, there was only one compactor working. But that was just fine since even a not so busy landfill was a very happening place. But not very smelly at all.
Actually, that was one of the most surprising things of all. Even standing just across a road from all that trash, it didn't smell all that bad. Sure, there was an occasional whiff, but not much more than the smell from a dumpster behind a typical restaurant.
Another surprise was how clean the place was. I mean, sure, there was a whole lot of garbage in the cell, but driving all around the landfill we saw maybe just a couple of small pieces (plastic bags, actually), laying around, and there was a crew member walking towards them to pick them up and return to the proper area.
We were taken to all the interesting areas of the landfill, including the methane flare and the leachate tank. We also got to go to the very top of the old, sealed field. From 400 ft up, we had a nice 360 view of the entire facility as well as of the Shearon Harris nuclear power plant in the distance (what, you haven't gotten one in your neighborhood?!) It was almost a picnic-perfect spot, I'm telling you.
And then the tour was over and we returned back to the old transfer station shed. The last cool thing we got to see from the van was an area in which oyster shells are collected before being shipped to the coast. And then we got back to our car and headed home, but only after dropping off some old batteries at the household hazardous waste drop-off area.
If you live in Wake County, you can register for the next available tour (on Sept 10) - it's free and very interesting. You'll definitely think twice before throwing things away.
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subset: commoncrawl


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Switchel | |
Category | Beverage recipes |
Servings | 4 servings |
Time | ~10 minutes |
Difficulty |
Cookbook | Ingredients | Recipes | Cuisine of the United States | Beverages
Switchel, also known as Ginger Water or Haymaker's Punch, is a sweetened beverage made from ground ginger, apple cider vinegar, sugar or other sweeteners and water. It is a traditional drink on farms in the north eastern United States, where it was made to soothe the thirsts of farm workers as well as (allegedly) boost one's stamina. It is served chilled, but is often served warmed in the Winter months.
Recipe 1:
- 1 cup (about 240 ml) sugar
- 1 cup (about 240 ml) apple cider vinegar
- 1 tablespoon (15 ml) ground ginger
- 1 quart (1 liter) water
Recipe 2:
- 3/4 cup (about 180 ml) maple syrup
- 2/3 cup (about 160 ml) apple cider vinegar
- 1 heaping teaspoon (about 6 ml) ground ginger
- 1 gallon (about 3.75 liters) Water
- Dissolve sugar and ground ginger in the water.
- Stir in the apple cider vinegar
- Chill or serve over ice cubes. Shake well before serving.
Some traditional recipes have used maple syrup, honey and/or molasses, separately or in combination, as sweeteners. The ratio of sweetener and vinegar to water vary widely in traditional and modern recipes. A small amount of oatmeal is sometimes added to give the beverage more body and to add to the flavor.


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I was in Walmart yesterday just looking around at all of their Easter merchandise when I came upon these babies. Adorable marshmallows in ice cream, strawberry and cupcake shapes. Each bag only a dollar. That dollar price tag gets me every time.
I also found these Wilton baking cups. More than a dollar but what are ya gonna do? You have to have a cute container for those cute mallos. Am I right?I ended up liking the ice cream ones the best so I put them in a baking cup, added a pretty umbrella and there you have the perfect little mallow decoration and treat. mmmmm
I think it would also look cute at a baby shower. Shower- umbrella. see what I did there.
I'm thinking about adding the lace umbrella to my shop, what do you think?


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SW Virginia law blog
Southwest Virginia law blog.
Monday, January 19, 2004
Kaine says no on death penalty in Virginia
According to
this article
("Death penalty divides Kaine, Kilgore," 1/18/2004) in the Richmond paper, Lt. Governor Kaine opposes the death penalty, citing his religious beliefs.
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I guess someone at DavisCup.com understands my love for Jo-Wilfried Tsonga!
The photo:
By Paul Zimmer at DavisCup.com
The caption: "Desire adds to France's status as favourite"
And Tsonga understands my love for Davis Cup, though he doesn't understand Davis Cup Dodgers:
"For me it's difficult to understand all the people who don't play this competition," he said. "It's maybe the best competition in tennis. For me it's really important because you represent your country and you have to honour it."
Considering that Tsonga is coming into the tie seven pounds lighter, due not to zealous training but to a nasty gastro-intestinal illness, I'd say he's paying more than lip service to the storied competition. Of course, he's also benefiting from a home venue and a deep bench: Gael Monfils, Julien Benneteau and Michael Llodra will join him vs. Team Germany (led by Philipp Kohlschreiber) this weekend.
France also has a long and fruitful D-Cup history, having won the event nine times. And boy, do they know how to host a draw ceremony:
Photo from the Toulon Opera House. By Paul Zimmer at DavisCup.com
Here's the draw:
2010 Davis Cup World Group First Round: TEAM FRANCE VS. TEAM GERMANY
Played on indoor hard courts in Toulon, France
Gael Monfils (FRA) v Philipp Kohlschreiber (GER)
Jo-Wilfried Tsonga (FRA) v Benjamin Becker (GER)
Julien Benneteau/Michael Llodra (FRA) v Christopher Kas/Philipp Kohlschreiber (GER)
Jo-Wilfried Tsonga (FRA) v Philipp Kohlschreiber (GER)
Gael Monfils (FRA) v Benjamin Becker (GER)
And the required Men in Tracksuits photo:
Photo by Paul Zimmer, DavisCup.com
Go Jo!


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If you live in New York and have a nice bike, it can be a mixed blessing. It's great to have a bike you love and want to ride everywhere, but the downside is the seemingly large network of people who like to steal nice bikes and their parts. For that reason, a lot of people choose to store their bikes inside their apartments to prevent theft. Most of the racks on the market are more function than form, but it's been great to see designers start to tackle the world of indoor racks. This beautiful oak hanger by Woodstick is a perfect example. Each hanger is handmade in Europe and installs easily on three standard screws. I like that it's pretty enough to stand on its own when it's not holding a bike. If you've got to store bikes indoors, click here to check out this option in more detail and order online. xo, grace
I love the fashionable way of displaying a bike as a piece of art when not in use, and might I add that bikes are stolen from small "towns" like Chicago just like the big shots in NYC.
the trouble with something like this here in Glasgow (and the same goes in Edinburgh) is the old lathe and plaster walls aren't reliably strong enough to secure something like this on. The risk is you'd come home and find your bike, your nice bit of oak and a fair chunk of your wall in a dusty heap on the floor. Some people joke that there are walls in their flats held up only by the wallpaper-this is not as far from the truth as you might imagine!
Oh how I long for the easy to secure to 'studs' I hear New World folks talk about! Bit I wouldn't give up my tenement flat for anything :o)
Oh my! I don't like a lot of the products featured on design websites and magazines because I find them too artsy and not enough functional. But this scores on both counts! Now I first need the hangar and then a bike to hang in it!
Those bike racks are pretty sweet. Yeah I would say the same about DC…very aggressive bike-stealing community. Basically, if you have a bike in DC, it WILL get stolen at some point. So that's something to keep in mind when you're deciding how much you want to spend on one. And if you spend less on the bike, you could probably afford to spend more on a pretty bike rack like one of these. :)
For commuters… a whole wall of these in an office building would look pretty rad, just sayin'
It's gorgeous! Thank you for sharing it!
Love that you included this! I'll be living in an apartment soon and my boyfriend and I love to go biking often, however, I don't feel comfortable storing them outside. This is a great alternative! Thanks for sharing.
This is too cool!
Interesting Idea.
I would make a few of this this summer, but I will use a cheery wood because last summer my cherry tree just dry from the drought. Cherry wood is one of the hardest woods available.


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The Simpsons Arcade Game Gameplay
Posted: February 7, 2012
Check out this gameplay footage of the classic Simpsons Arcade Game, now available on Xbox Live and PSN. Please refrain from sticking quarters into your computer.
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This was made by the same people who made the Ninja Turtles arcade games. I'm downloading this for free on PSN+ right now.
Posted: February 7, 2012 4:55 PM
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Maxx GP (Windows)
missing cover art |
Critic Score
100 point score based on reviews from various critics. ...
User Score
5 point score based on user ratings. |
Maxx GP is a motorcycle racing game that features ten different courses and six bikes, each with their own different handling, speed and acceleration.When starting the game two tracks are available, and by winning the races the rest of them can be unlocked. You can choose from three modes: Practice Session, Qualifying Session and Race. In Practice Session you get the opportunity to learn all the twist and turns of the circuit. In the Qualifying session you have three laps in which to record the fastest lap time possible. At the end of the session the lap time achieved determines where you will be placed on the starting grid for the race. In the Race mode you race against five AI bikers over the specified number of laps (2 - 25 laps can be chosen). You need to finish first to unlock more circuits.
There are no Windows user screenshots for this game.
Promo Images
There are no promo images for this game
User Reviews
There are no reviews for this game.
Critic Reviews
There are no critic reviews for this game.
There are currently no topics for this game.
There is no trivia on file for this game.
3D Modelling:
Sound Effects:
Project Manager:
Quality Assurance:
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No Hidden Fees - No Credit Card Surcharges - Low Shipping Rates
Images shown may not be an exact representation of the actual product.You may contact us if you have questions about the exact specifications of this item.
A FIRST! Fully coated NiB-X AR 15 with a 16" match grade barrel, 1:7 twist, nitrided bore with a NiB-X barrel extension, NiB-X bolt carrier group and fire control group, NiB-X free float rails with adjustable Picatinny rails, NiB-X Muscle Comp compensator to reduce recoil, Headdown buttstock with cheek rest, low profile NiB-X gas block with nitrided gas tube and NiB-X buffer tube.
Optic/Sight ready. 2 mags (1 polymer and 1 NiB-X aluminum).
Shipped in custom Drago tactical bag.
This firearm (receiver) ships to your local gun dealer/gun store (FFL dealer). Use our easy 'FFL SEARCH' in the menu bar at the top of the page. They will gladly provide you with a copy of their license, and charge you a small transaction fee. No Sales Tax will be due (Except in Utah and Idaho).
Once we have a copy of their license, we can ship the gun to your local dealer, you then drop by their place, fill out the required paperwork/background check, and take the gun home. We can walk you thru the procedure and help you locate a qualified dealer- just call or email for more information.
Our customers generally find this process quite easy and we will help you thru each step.
Impact Guns is the gun shop for all your shooting needs. We offer a wide selection of firearms, including: handguns, shotguns, rifles, ammunition, rifle scopes and optics, as well as collectible machine guns and other NFA/Class 3 guns. Impact also services the needs of law enforcement and military with our wide variety of tactical weapons and accessories. Shop online through our 256-bit Secure Sockets Layer encrypted online gun store 24 hours a day!


text: John Williams will officially score Star Wars: Episode VIIRobbie Gonzalez7/27/13 1:20pmFiled to: star warsjohn williamsmusicscoreepisode viij.j. abramskathleen kennedy6612EditPromoteShare to KinjaToggle Conversation toolsGo to permalink Legendary film composer John Williams, the man behind the music for all six Star Wars films and master of the science fictional leitmotif, will return to score Star Wars: Episode VII! Here's what he has to say about his return to the Star Wars universe – including his thoughts on director J.J. Abrams. Advertisement Williams clearly hopes to feature past themes in his new score, though he admits he still hasn't seen Episode VII's script – but then, he says, that's part of his process:I always prefer not to read scripts, and even no to hear stories and look at cue cards and so on, and wait for the moment of discovery, with the audience, of the film itself. so I'm as surprised as they are, and I know where to put the surprise button, having not been prepared by a script.I'm waiting anxiously like the audience around the world to find out what the surprises are and discover what my continuing role is going to be.He also (perhaps unsurprisingly) gives a glowing endorsement to both Lucasfilms president Kathleen Kennedy and J.J. Abrams: Advertisement They are two people that I think are perfectly chosen to continue George Lucas' great odyssey. They're both young, they're both extremely gifted. Have tremendous energyI think the combination of their youth and their experience and their energy and gifts – if I'd been asked – I wasn't – but if I'd been asked by the various boards of directors: "Find me two people to take this project on to the next step," I would certainly have voted for them. We couldn't find better candidates for this opportunity.Williams' official return is fantastic news. Here's hoping they have the good sense to keep him onboard for Eps. VIII and IX. Read more at StarWars.com.Reply66 repliesLeave a reply


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this wiki
Pathways is a story in Clone Wars Adventures: Volume 8 about a lost battle droid.
Marching on a Republic stronghold on the planet Antamont,[1] a lone battle droid steps on a mine, blowing the line apart. Shockingly, that battle droid survives, his connection to the hive-mind severed. Realizing that he has a life of potential ahead of him, the droid flees, only to be spotted by a single grapple droid, who pursues him only to be knocked off a cliff, the battle droid falling shortly behind. Walking away from his crushed former-companion, the battle droid finds a secluded tree, where he sits down, his power source already depleted. He remains there for some years, only to be found later by a group of farmers, who decide to power him up and use him on the farm.
Characters | Creatures | Droid models | Events | Locations |
Organizations and titles | Sentient species | Vehicles and vessels | Weapons and technology | Miscellanea |
Droid models
Organizations and titles
Vehicles and vessels
Weapons and technology
Notes and referencesEdit
- ↑ The Complete Star Wars Encyclopedia, Vol. I, p. 33 ("Antamont")


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AppRadio (SPH-DA01)
A Revolutionary Way to Use Apps in the Car
- Important Apple iOS 8 Notice
- Control compatible apps from the convenience of the industry's first capacitive, multi-touch display
- Compatible with iPhone® 4 and iPod Touch® 4th Gen
Suggested Price$399.99
Adding a New Touch to Your Connected Lifestyle
Pioneer's revolutionary, game-changing AppRadio™ is the first car stereo to revolutionize the driver's smartphone experience by bringing compatible iPhone® 4/4S apps to your dash. When connected to an iPhone 4/4S (or a 4th generation iPod touch) loaded with Pioneer's free AppRadio application, the AppRadio in-dash stereo provides the ultimate in-vehicle smartphone experience. Featuring the first ever in-dash, capacitive touchscreen, you can enjoy full on-screen access and control of your iPhone contacts, calendar, maps, and more with an intuitive interface, formatted and designed specifically for safer in-vehicle operation. Pioneer has teamed up with several app providers to offer compatibility with many of today's most popular in-vehicle apps, while also developing an expanding catalog of AppRadio compatible apps for future features and functions that can be easily and seamlessly added. AppRadio will even notify you when new compatible apps are released.
Your Dash Just Got Smarter
Simply download Pioneer's free AppRadio application and any other AppRadio-compatible apps to your iPhone 4/4S from the iTunes® App Store, connect it to the AppRadio stereo, and you're ready to experience your smartphone in an entirely new way.
Rethinking Connectivity
AppRadio allows you to bring many of the most used features from your iPhone such as browsing and searching your contact list and iPod music library, view important events and reminders in your calendar, access to your contact list, direct access to your iPhone maps app, Internet video streaming (with the car parked and parking brake engaged), and much more…. right from the driver's seat of your car.1
In addition to the revolutionary iPhone 4/4S connectivity, AppRadio features an AM/FM tuner with RDS, built-in Bluetooth® connectivity3 for hands-free calling, a rear view camera input and Pioneer's Easy EQ (EEQ) audio tuning that makes it quick and easy to tailor your audio experience.
AppRadioLIVE simplifies your drive by combining the information you need during your commute into a single, simple to use interface. It's YOUR digital lifestyle connected. It was specifically designed based on feedback from our current AppRadio customers and offers quick and easy access to personalized information needed in the in-vehicle environment including: Maps, Media, News and Calendar. AppRadioLIVE pulls content from many different sources and services which you likely already have an account with. All you have to do is download the FREE AppRadioLIVE app and sync your services. All you information saved on those accounts will be pulled into the AppRadioLIVE interface.
For more information, please visit www.pioneerappradiolive.com
- 800 x 480
- Capacitive
- 30-Pin Cable Included
Radio Tuner
- 24 Stations/6 Presets (18 FM/6 AM)
- Included
- MOSFET 50W x 4
- 12-Band Graphic
- External
- Push-Button
AppRadioLIVE simplifies your drive by combining the information you need during your commute into a single, simple to use interface, offering access to Maps, Media, News and Calendar.
Access your iPhone® or Android™ calendar. View important events and reminders. Functionality is bundled with the Pioneer AppRadio™ app.
Compatible with the AppRadio app for Android devices, CarKeyboard allows you to input text directly from the 7" capacitive touchscreen display of the AppRadio 2 (SPH-DA100).
CarMediaPlayer allows you to swipe, drag, and directly touch the desired artist, song, or album in your music library directly from the Pioneer touchscreen with Alphabet Search and Album View functions.
CommuteWX provides real-time weather information (current, forecast, en route). Weather conditions are featured in large, easy to read graphics in a streamlined user interface that's well suited for in-vehicle travel.
Access your contacts on your Android™ phone. Functionality is bundled with the Pioneer AppRadio® app.
DashCommand utilizes the built-in GPS & accelerometer sensors in the iPhone or compatible Android phone to provide advanced features such as the skid pad, race track, and inclinometer.
Pioneer's proprietary MIXTRAX app analyzes the music in your iTunes® library to create custom playlists for non-stop song mixes with added DJ effects.
MyPV is a free media app that allows you to select your favorite music PVs from a ranking of the world's popular music videos.
Parkopedia Parking for AppRadio
To date, Parkopedia has grown to cover over 25 million parking spaces in 28 countries around the world thanks to contributions from drivers like you.
View photos stored on your iPhone® or Android™ device. Access albums and camera rolls and even view a slideshow. Functionality is bundled with the Pioneer AppRadio™ app.
Saving Fuel
Saving Fuel monitors your acceleration, braking, cornering, and idling to gather an overall score for each trip. It scores your driving behavior and car health, as well as gives you tips to help you drive safely.
StreamS™ HiFi Radio
StreamS is a full-featured iPhone streaming audio player delivering thousands of tested, reliable, high quality hi-fi HE-AAC streams.
Tire Pressure Monitoring System (TPMS) app automatically monitors pressures and temperatures of tires in real-time.
Top Headlines
Top Headlines is an audible new headlines app. Listen to the most recent news updates from multiple sources.
Voice Directory
Voice Directory is a hands-free app that uses voice to search Yellow Pages' business listings in the US and call the phone number directly.
gMusic 2
Keep up to 20,000 of your favorite songs in the cloud without having to use any space on your iOS device.
NOTE: Do not use your Pioneer system if doing so will divert your attention in any way from the safe operation of your vehicle. Always observe safe driving rules and driving laws. In some states certain operations of devices while driving may be illegal. Where such regulations apply, they must be obeyed.
1Review instruction manual for safe operation of AppRadio. Do not use any feature of this product if it cannot be operated safely while driving. Prior to operating iPhone apps that are accessible from this unit, review all usage instructions, cautions, and warning messages that are provided by the App developer. When using navigation apps, stay alert and observe real world conditions first.
2Netflix and Hulu+ are paid subscription services not affiliated with Pioneer, and are not included. Visit www.netflix.com and www.hulu.com/plus for more information.
3Bluetooth functionality requires a compatible Bluetooth-enabled mobile phone. Certain Bluetooth features may not be supported by all compatible Bluetooth-enabled devices, and/or the functionality of such features may be limited in certain devices or by certain wireless carriers.
PIONEER and AppRadio are trademarks or registered trademarks of Pioneer Corporation.
Apple is a trademark of Apple Inc., registered in the U.S. and other countries.
IPOD, IPOD TOUCH, IPHONE, IPAD and iTUNES are trademarks of Apple Inc., registered in the U.S. and other jurisdictions.
GOOGLE and YouTube are registered trademarks of Google Inc.
DashCommand is a trademark of Palmer Performance Engineering, Inc.
StreamS HiFi is a trademark of Modulation Index, LLC.
AUPEO! Personal Radio is a trademark of AUPEO!
MotionX is a trademark of Fullpower-MotionX in the United States and other countries.
INRIX is a registered trademark of Inrix, Inc.
RDIO is a registered trademark of Rdio, Inc.
Pandora is a registered trademark of Pandora Media, Inc.
Netflix® is a registered trademark of Netflix, Inc.
Hulu and Hulu+ are registered trademarks of Hulu LLC.
BLUETOOTH is a registered trademark of Bluetooth SIG, Inc.


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Reader Comments (8)
Living in the moment is a good concept, and one worth contemplating. As a side thought to the same point think about this while living in the moment.
We can not control the past, It is gone.
We can not really control the future, we can not guarantee we will be here tomorrow.
What we all have equally is this moment in time. That is the only thing we can control, We can all control what we do right now.
We all have the same gift, this moment right now, so in that we are all equal. It is a great gift. I guess that is why we call it the PRESENT.
I love a brisk ride on a fine-handling road bike mostly for that very reason: it's the best kind of meditation there is.All my concerns melt away while I'm out there concentrating on my ride and on the scenery that flows by me. It's temporary, like transcendental meditation is, but if I string enough rides together day after day, it add up to a lot of serenity I wouldn't have otherwise.
For me, it's a getaway, and I have to do it solo, without any constraints, and without paying any attention to numbers... so, no groups, no computers.
Fantastic little piece, Dave. Great for the subtle bike advocacy but then the life messsage in general. I'm forwarding a copy (with a link of course!) to a number of friends.
I guess that's why commuting is not as much fun as a pointless ride.
I have a friend (about 40) who went through a divorce for the first time in his life. He is a cyclist of course. He told me that during that time of turmoil at home, he increased his time out riding a lot. It was his method of getting away from the unhappy camper at home. A sort of meditation/relaxation. I never knew what that is like, for I'm single and no where near his age. But I think I now now. You are right in saying that as the working class, none of us can afford to spend all our time riding bikes. But for the little moments we do have, it's important we go out riding in a pleasant state of mind. I do think of the future when I ride...but its hard to worry when you're riding. There's something about cycling that affords us this luxury...and maybe you're right...the brain has far better things to do when you're under some amount of cardiovascular stress :)
Dave I think you've hit on one of the primary reasons why people become addicted to cycling, or other sports. I read years ago that symphony conductors tend to be long lived and the article posited that this was because their chosen profession did not allow stray thoughts while practicing it. In effect they were meditating at work.
Same is very much true for cycling. On the mtn bike I find that if I am in my head too much the ride becomes unpleasurable. I fail to find the flow and in fact will more than likely take one or more bad spills.
The road bike within 10-15 minutes (usually following the first steep climb) always takes me to a place where it is just me, the road and the bike. I may be grunting to climb a hill, spurring myself to keep cadence but all of the "monkey chatter" has been left behind. Hard to dislike yourself when you're out riding for joy.
Same is true for me in the winter of freestyle nordic skiing. Ten minutes into it and its just me, the trail and the woods.
World would be a better place if more of us got out like this in some fashion every day.
Great post.
Riding a bike does put one in a different state of mind - the speed, the sensation, the effort involved. I commute almost daily, an hour each way, most of it on bike path - no cars or traffic. Even though I'm a music fan, have no desire to use an iPod while riding at all - though I see many riders doing so. The ride alone is enough for me.
As far as being completely "in the moment", that doesn't occur to me unless some speed or technical sections are involved - mountain biking usually.
When I was younger, used to ride dirt motorcycles quite a bit and raced motocross as well. I remember during races or practicing at race speeds - would be completely in the moment - no other thoughts in my head. A rare sensation.
Interesting stuff....
Great post!
Blood (& oxygen) delivery to the brain is not compromised during intense exercise, however. It receives a very steady flow of blood regardless of bodily movement.


text:
Sir Mervyn King, the Governor of the Bank of England, is likely to face two key lines of questioning over his own behaviour on the Barclays affair when he appears before the Treasury Select Committee today.
Firstly, MPs will want to know what he made of his deputy Paul Tucker's conversation with former Barclays chief executive Bob Diamond. The latter's note of this appeared to suggest that the Bank was instructing Barclays to falsely lower its submissions for setting Libor interest rates.
Mr Tucker, however, strenuously denied that he ever made such a suggestion to Mr Diamond. And Mr Diamond said he did not interpret the conversation that way, despite the note.
But his number two Jerry del Missier saw things differently, and passed what he saw as an instruction down to Barclays' money market desk.
Mr Tucker did not take his own note of the conversation with Mr Diamond, despite its importance. This left MPs aghast. The issue of note taking at the Bank is therefore also likely to come into focus.
The second issue MPs will want to hear about is what role Sir Mervyn played in the departures of Mr Diamond and Mr del Missier. Mr Diamond is on record as saying that the regulators' view on his position at the bank changed between the announcement of Barclays accepting fines of £290m as a result of Libor fixing and his departure days later. So what changed the Bank's view during that period?


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GRILLED TRI-TIP ROAST WITH TEQUILA MARINADE AND CHERRY TOMATO RELISH Recipe
lime juice, tequila, garlic, cumin, black pepper, green onion, +cilantro, +olive oil, +soy sauce, +lime, +oregano, +beef, +cherry tomato, +tomato, +balsamic vinegar, +green chilies
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Grilled Tri-Tip Roast With Tequila Marinade
Bon Appetite. June 2000. Note marination time. Make ahead!
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If you love garlic this is the dish for you. You'll be making this every week! It's easy to make too! Prep:10m
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The marinade from this is wonderful and produces very moist flavorful tenderloins, they can be grilled as well. Plan ahead they need to marinate for 24...
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Chicken With Peanut Sauce
This is a perfect dinner when cooking for two. It is very attractive and served on the bed of shredded Napa cabbage is a complete meal.
black pepper, garlic, green onion, cumin, lime juice, +chicken, +butter, +coriander, +cabbage, +peanut butter, +red pepper, +salt, +water
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Mill Valley, CAUSA
June 6, 2014
Co-founder and Chief Creative Officer of Survios
OC Virtual Reality Meetup is about bringing together the community of VR enthusiasts. What & Why? The Oculus Rift is an easy to use platform that allows you not only to experience VR but to create it as well. Everybody is welcome from designers, devs, entrepreneurs, and VR fans. Will be having demos, presentations and speakers. Share, Learn, Team Up Join Us!
OVR attend almost all our events, often bringing their latest hardware.
Leap Motion has donated several LEAP devices for our community to dev on
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Wednesday, 4 April 2012
Mimbalot Falls
It is located at Brgy. Buruun, Iligan City which is approximately 11km
drive from the city center.
i just love the scenic view of the huge stones..
One of the 23 waterfalls of Iligan City.
at the tree house while waiting for MR. OPERATOR
for the Cable car ride. :)
Iligan Paradise Resort boasts Iligan's most-accessible ziplines with multiple options
(superman, double harness, single harness), and cable car rides, given at a reasonable price.
We will eventually add quad bike rides, a swimming pool, and new methods for leisure.
at last~ we're ridin' after 15 mins. of waiting!
thanks to my boyfriend for makin' this day special <3
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Album: "RealBook2010/Songs In ONE Key"
Chapter: "RealBook 2010" (Another side)
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TOKYO--(BUSINESS WIRE)--RISO KAGAKU CORPORATION (TOKYO:6413)(President & C.E.O.: Akira Hayama) will conduct a worldwide successive launch of two high-end, high-speed digital duplicator series from May 2014.
The new products are RISO ME Series, a digital duplicator equipped with two drums, and RISO SE Series, a digital duplicator equipped with one drum.
RISO ME Series can print two colors in a single pass. The print setting can be switched between dual-color and mono-color printing with a single button press in accordance with customer needs.
RISO SE Series incorporates a high-speed print mode. This mode uses a technology for stable, high-speed transport to achieve print speed of up to 185 pages per minute (ppm), notching a new industry record for print speed for the first time in eight years.
RISO Digital Duplicators are renowned for delivering high-speed, high-volume printing with low running cost. Leveraging this advantage, these products are used in over 180 countries and regions for a wide array of applications, including handouts, educational materials, meeting documents and much more. With the launch of these two new series, RISO provide greater efficiency in high-volume printing.
Product Names and Specifications
RISO ME Series |
Model name | Print speed (Max.) | Paper sizes (Max.) | Printing image resolution | |||
RISO ME 9450 | 150ppm | Ledger, A3 | 600 dpi x 600dpi | |||
RISO ME 9350 | 150ppm | A3 | 600 dpi x 600dpi | |||
RISO ME 6350 | 150ppm | A3 | 300 dpi x 600dpi |
RISO SE Series |
Model name | Print speed (Max.) | Paper sizes (Max.) | Printing image resolution | |||
RISO SE 9480 | 185ppm | Ledger, A3 | 600 dpi x 600dpi | |||
RISO SE 9380 | 185ppm | A3 | 600 dpi x 600dpi | |||
Products handled may differ according to region. | ||||||
Features of RISO ME and SE Series
1) Processing dual-color and mono-color printing
RISO ME Series incorporates two equipped drums, enabling easy switching between dual-color and mono-color printing with the press of the Mode button according to the print task. Print speed of up to 150ppm*1 enables handling of a wide range of print jobs.
2) Print speeds up to 185ppm, the highest in the industry
At 185ppm*1, RISO SE Series boasts the highest print speed in the industry, enabling users to produce meeting documents, educational materials and other materials faster than ever before.
3) New RISO HG Master for high-resolution printing
To enable high-speed printing with finespun resolution, RISO focused on
ink permeability on paper to develop an innovative new master. RISO HG
Master* overlays a fine-filter layer over the existing
standard layer in the previous master. This two-layer structure improves
uniformity of ink transfer, enabling fine color gradations and finely
detailed reproduction.
* RISO HG Master is in compatible with RISO
ME 6 Series.
4) A4/Letter drum achieves high-efficiency printing (option)
For printing originals of size A4 or smaller, the newly added A4/Letter drum newly supports digital duplicators with two equipped drums. This drum uses consumables more efficiently than the A3-sized drum or Ledger-sized drum, minimizing running cost.
5) Eco Mode for reduced power consumption
Eco Mode function is available on RISO SE Series that enables printing with reduced power consumption. By turning down the brightness of the LCD panel and decreasing the printing pressure, Eco Mode reduces power consumption*2 during printing by 2% compared with normal operation.
6) Color universal design
The color scheme adopted in the parts, labels and other features of these Series are designed to be easy to distinguish and understand regardless of individual differences in sense of color. These printers are certified for color universal design by the Color Universal Design Organization, an NPO established in Japan.
7) Wide range of color variations
In addition to 21 basic colors of RISO INK E TYPE, a soybean-oil-based ink (soy ink), RISO offers a lineup of 50 custom colors, enabling a new level of color diversity and individual expression. According to customer preference, RISO can also create special order-made colors*3, for use in applications such as corporate color schemes.
Note: For more information on product specifications and other details,
please visit our website at
(ME Series)
(SE Series)
*1. | In high-speed mode. | |
*2. | Actual value as measured based on the measurement standards stipulated in Japan's Law on Promoting Green Purchasing. | |
*3. | Order-made colors may not be available in soy-oil-based inks | |
About RISO: RISO KAGAKU CORPORATION (RISO) is the leading manufacturer and distributer of high-speed inkjet printers and digital duplicators. RISO strives to create fundamentally unique products in paper-based communication through an approach that emphasizes productivity, cost containment, and versatility. Every product we manufacture delivers these benefits in a balance that offers the ideal solution to our customers. RISO products are used in over 180 countries and regions worldwide in various settings that include companies, schools, governments and public agencies.


text:
Dead Air by Iain Banks. I bought an import copy of this from Glen Cook at Readercon– to the best of my knowledge, it's not available in the US yet (save through amazon.co.uk).
This is one of those books where it's awfully tempting to describe it by analogies to other books. You might call it Crow Road 2: Electric Boogaloo, or "Iain Banks writes High Fidelity" or even "Wonder Boys by Iain Banks." It's got elements of all those things, wrapped up with characteristically Banksian wit and black humor.
The book tells the story of Ken Nott (nee McNutt), a Scottish shock-jock DJ in London, who's sort of bumbling along through a life of outrageous publicity stunts, mixed with lots of recreational drugs and casual sex. He eventually starts up a torrid and extremely secret affair with the wife of a brutal gangster, which kicks off a series of increasingly messy escapades that culminates in him finally getting his shit together (sort of).
Parts of this book are strongly reminiscent of each of the works cited above. The illicit affair subplot is somewhat reminiscent of Wonder Boys, both in the way her husband can wreck the narrator, and also the way Ken's serial idiocy brings things to a head. The other sexual relationships in the book have a very High Fidelity sort of feel to them, in their desperate immaturity. And the book is very much like The Crow Road in that it bumbles along episodically for a while, until the last third, where you can imagine the author saying "Shit! I need to wrap this up!", stubbing out a joint, and banging out the ending in a rush. It all wraps up very abruptly, with some of the trademark Banks ultraviolence, but the ending is, on balance, a happy one.
That's the good part. Unfortunately, Ken's shock-jock job provide a platform for a large number of DJ rants– indeed, the sheer bulk of DJ material occasionally makes it seem like that's the primary reason the book was written. Given Ken's position and inclinations, these bits consist largely of extended rants about political matters, from a very leftist position (UK leftist, that is– not the sort of mealy-mouthed centrism that gets tagged "radical" in the US).
On several occasions, I've half-seriously wished for a liberal equivalent of Rush Limbaugh, or the talk-radio ranter of your choice. Ken's rants provide a nice demonstration of what (a mild version of) that sort of thing would be like, and it's not pretty. There are some entertaining rants, but the overall tone is a little too polemical, and as a whole, it didn't really work for me.
In some ways, it's nice to find that my aversion to excessive politicking in fiction isn't an inside/outside fandom problem— Banks's liberal ranting bugs me as much as Heinlein's libertarian ranting, and I agree with more of what Banks says. If you're not put off by that sort of thing, Dead Air is a very good book, but personally, I didn't like it as much as The Crow Road, which had a very similar plot, with fewer screeds.
(Originally posted to The Library of Babel.)
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Vince Beiser
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text: despite the fact that i was once a pastry chef and had to wake up every morning at like 5am, i have never ever been a morning person. but ever since we set our clocks back last week, i've actually been able to wake up "early." the sun is high up in the sky and if it's not overcast and gloomy, then it's pretty much guaranteed that i'll be out of bed and buzzing around before 8am. this is an incredible feat for a self-proclaimed night person like myself, and it's making my morning routine much easier for now. sometimes it's the little things.


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Journal Article
Simultaneous Infection with Three Different S. enteritidis Strains in a Nursing Home Resident
G. Scuderi, E. Filetici, M. Fantasia, S. Salmaso, G. Ferrari, A. Alessandrini and N. Binkin
European Journal of Epidemiology
Vol. 9, No. 4 (Jul., 1993), pp. 447-449
Published by: Springer
Stable URL: http://www.jstor.org/stable/3520506
Page Count: 3
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Topics: Plasmids, Bacteriophages, Bacteriophage typing, Infections, Nursing homes, Salmonella, Coinfection, Diarrhea, Epidemics, Epidemiology
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A culture taken from a nursing home resident as part of a S. enteritidis outbreak was found to have a mixed infection due to three different strains of S. enteritidis. One of the three strains belonged to phage type (PT) 4, one to PT6 and one reacted with phages but did not conform to any typing scheme (RDNC). All three strains had the 38.9 megadaltons (MDa) plasmid found in the isolates from the outbreak-related cases, in addition the PT6 and RDNC strains harboured a 69.9 MDa plasmid. The importance of phage typing and plasmid analysis for S. enteritidis strain characterization and their epidemiologic and bacterial significance are discussed.
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Snipes ft. KL & BC - Freakin' You
By Lucas G. | 4 years ago
Older, more seasoned DJBooth readers might recall a fond memory or two when they hear the latest feature from emcee Snipes. While video single Freakin' You is "new," the song's source material is based heavily on Jodeci's old-school ('95) baby-making jam of the same name. Snipes puts a refreshing spin on the R&B classic, contributing a few lite bar verses to KingPin Da' Composer's sample-based, twisting production. Joining the Memphis emcee are KL and BC, who share the spotlight, attempting to woo their ladies with a smooth southern styles. Freakin' You is a standout off Snipes' new album, Economic Development, available for purchase via the artist's Bandcamp.
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A full moon surprises me in Yellowstone National Park. They named the park correctly it appears.
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Related movies/dramas
Ladies, don't worry, it's in a movie! Our 22 year-old handsome actor takes on a role as a teen father in the new movie, 'Baby and I'.
High School student, Jun Soo (Jang Geun-seok) is a good-looking, stylish, and known to be a good fighter takes on a big challenge of his life. Being a father to baby boy WooRam! This will be a moving and funny movie of a troublemaker teen being changed through taking care of a child.
Jang Geun-seok has been filming this movie for the last 3 months. He has been seen taking care of the baby even when the cameras were off; feeding him and making him laugh with his cute dancing moves to the 'Tell Me' song.
This long awaited movie will be released by the end of this summer in August. Many viewers anticipate Jang Geun-seok's new movie, playing the role of a young hot teen dad!
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Female Singers Return for Summer
2008/06/24 (Source)
By Han Sang-hee
Staff Reporter
Summer is not just about the sizzling sun, cool beaches and ice cream; it's also about new styles, music and fashion.
Top Korean female singers are preparing for big comebacks this season and some are already making headlines with their new looks and music.
Expo on Traditional Korean Culture to be Held in Seoul
2008/06/24 (Source)
The Ministry of Culture, Sports and Tourism will hold the 2008 Han Style Expo for Korean traditional culture in Seoul.
This expo is an industrial event showing a variety of traditional Korean products and all kinds of information related to six categories of Korean traditional culture, dubbed "Ha,...More
Experts Discuss Digital Broadcasting Service
2008/06/24 (Source)
Two leading national organizations have held a forum to discuss ways to facilitate the launch of digital broadcasting services.
At the forum organized by the Korean Association for Broadcasting and Telecommunication Studies and the Korea Broadcasting Advertising Corporation, experts from various ,...More
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Volume 14 Supplement 1
Selected articles from the Eleventh Asia Pacific Bioinformatics Conference (APBC 2013): Genomics
A unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms
- Quan Chen1 and
- Fengzhu Sun1, 2Email author
© Chen and Sun; licensee BioMed Central Ltd. 2013
Published: 21 January 2013
Genome-wide association studies (GWAS) have identified many common polymorphisms associated with complex traits. However, these associated common variants explain only a small fraction of the phenotypic variances, leaving a substantial portion of genetic heritability unexplained. As a result, searches for "missing" heritability are drawing increasing attention, particularly for rare variant studies that often require a large sample size and, thus, extensive sequencing effort. Although the development of next generation sequencing (NGS) technologies has made it possible to sequence a large number of reads economically and efficiently, it is still often cost prohibitive to sequence thousands of individuals that are generally required for association studies. A more efficient and cost-effective design would involve pooling the genetic materials of multiple individuals together and then sequencing the pools, instead of the individuals. This pooled sequencing approach has improved the plausibility of association studies for rare variants, while, at the same time, posed a great challenge to the pooled sequencing data analysis, essentially because individual sample identity is lost, and NGS sequencing errors could be hard to distinguish from low frequency alleles.
A unified approach for estimating minor allele frequency, SNP calling and association studies based on pooled sequencing data using an expectation maximization (EM) algorithm is developed in this paper. This approach makes it possible to study the effects of minor allele frequency, sequencing error rate, number of pools, number of individuals in each pool, and the sequencing depth on the estimation accuracy of minor allele frequencies. We show that the naive method of estimating minor allele frequencies by taking the fraction of observed minor alleles can be significantly biased, especially for rare variants. In contrast, our EM approach can give an unbiased estimate of the minor allele frequency under all scenarios studied in this paper. A SNP calling approach, EM-SNP, for pooled sequencing data based on the EM algorithm is then developed and compared with another recent SNP calling method, SNVer. We show that EM-SNP outperforms SNVer in terms of the fraction of db-SNPs among the called SNPs, as well as transition/transversion (Ti/Tv) ratio. Finally, the EM approach is used to study the association between variants and type I diabetes.
The EM-based approach for the analysis of pooled sequencing data can accurately estimate minor allele frequencies, call SNPs, and find associations between variants and complex traits. This approach is especially useful for studies involving rare variants.
Finding genomic variants associated with complex traits is one of the most important problems in modern genomics. Genome-wide association studies (GWAS) based on common variants have been the dominant approach to achieve this objective [1]. However, the genomic variants identified in GWAS studies often explain only a small portion of the phenotypic variation related to heritable human diseases, a phenomenon known as "missing heritability" in genomics literature [2]. This missing heritability problem has led to increasingly skeptical views of the common disease-common variant (CD-CV) hypothesis which predicts that common disease-causing alleles, or variants, will be found in all human populations that manifest a given disease. On the other hand, interest in studies on rare variants with minor allele frequencies less than 1% is growing [3, 4].
Studies of rare variants are complicated by the low minor allele frequencies of rare variants. The development of next generation sequencing (NGS) technologies such as Illumina and Roche 454 has made it possible to sequence a large number of reads economically. Despite such important progress, sequencing a large number of individuals separately is still costly for most biological laboratories. One frequently adopted approach to reduce sequencing cost in the search of rare variants is pooled sequencing, where mixtures of genetic materials from several individuals are grouped together to form a pool for a single sequencing. While this design greatly lowers the sequencing cost, it also makes it hard to distinguish true genetic polymorphisms from sequencing errors, estimate minor allele frequencies at the polymorphic loci, and perform association studies on the rare variants.
Several research groups have used pooled sequencing to detect rare variants that are associated with complex traits such as retinitis pigmentosa, diabetes, cancer, and inflammatory bowel disease [5–8]. There are generally two types of pooling designs. One is pooling of tagged samples with each individual tagged by a unique short barcode. In this design, the genomic origins of the reads can be identified. However, barcoding many individuals and distinguishing these barcodes from each other can still be a challenging task. The second type of pooling is to mix the genetic materials from different individuals without tagging, and then generate reads from the mixture of genetic materials using NGS. With this design, the identities of the individuals from whom the reads originate cannot be identified. In this paper, we concentrate on the second type of pooling design.
Several groups have developed SNP calling methods based on pooled sequencing data [7, 9–12]. Out et al.[7] modeled the number of sequencing errors as a Poisson random variable and identified SNPs by comparing the number of minor alleles within the reads with the Poisson distribution. For rare variants with minor allele frequencies similar to or lower than the sequencing error rate, this approach could miss many true variants if the pool size is relatively large. Druley et al.[9] developed a SNP identification method, SNPSeeker, that can be applied to large pools by using control sequences without SNPs. In many studies, control sequences may not be available, making this approach impractical. Also, the program can only be used to analyze Illumina data. Bansal et al.[10] developed a method called CRISP to identify rare variants by comparing the minor allele frequencies across multiple pools using contingency tables. It was shown that CRISP outperforms SNPSeeker in terms of accuracy, but CRISP is more computationally demanding. Altmann et al.[13] improved the computational speed of CRISP and identified SNPs as the variants with different minor allele frequencies across at least two pools. Wei et al.[11] developed a statistical tool, called SNVer, for variant identification. For each pool, SNVer first defined a p-value by testing the hypothesis that the minor allele frequency is above a given threshold and then combined the p-values for individual pools to give an overall p-value using Simes methods as in [12]. This algorithm makes it possible to rank the observed variants so that the top ranked ones are more likely to be true SNPs. However, the algorithm needs a pre-specified sequencing error rate which can be difficult to do because the sequencing error rates can be position dependent. In the above studies, the investigators are mainly concerned with the detection of SNPs; they do not aim to estimate minor allele frequencies.
In order to estimate minor allele frequencies in pooling studies, several groups developed statistical models for the sampling of individuals and the sampling of reads from the individuals in the pools [14, 15]. These studies assumed a pre-defined constant sequencing error rate across different loci. However, sequencing error rates can vary for different loci depending on the nucleotide contents of the surrounding genomic regions. The effects of mis-specifying the sequencing error rate on minor allele frequency estimation, SNP detection and power of association studies are not clear. Using similar models, Lee et al. [16] studied an optimal design in pooling studies. This involved the number of individuals in each pool and the number of pools. Recently, Chen et al.[17] considered more complex issues such as uneven sampling of individuals, different coverage of the minor and major alleles due to either PCR amplification or reads mapping, and reads quality scores.
In this paper, we develop new methods for estimating minor allele frequencies, SNP detection, and association studies using pooled sequencing data based on the models in [14–16]. In contrast to methods developed in previous studies, we do not assume that the sequencing error rate is constant. Instead, we estimate the sequencing error rate for each position together with the minor allele frequency based on the minor and major allele counts for all the pools using an expectation-maximization (EM) algorithm. We show that the naive estimation of the allele frequency by the fraction of minor alleles in the reads can be significantly inflated, especially for rare variants, while the EM approach can give an unbiased estimate of the minor allele frequency in all situations we studied. The estimation accuracy of the EM algorithm increases with the number of reads and the number of pools, but decreases with the number of chromosomes in each pool. Based on the allele frequency estimation, we develop a SNP calling method, EM-SNP, and an association test using likelihood ratio statistics. The likelihood ratio statistic used in EM-SNP is then used to rank candidate polymorphic loci to determine if they are true polymorphisms. Using a real re-sequencing dataset, we show that, for rare variants with minor allele frequencies lower than 1%, the fraction of dbSNPs (http://www.ncbi.nlm.nih.gov/projects/SNP/) among the SNPs called by EM-SNP is higher than that of SNVer. Similarly, the transition/transversion ratio of rare variants called by EM-SNP is higher than that of SNVer. These observations show that EM-SNP outperforms SNVer at calling rare variants with minor allele frequencies less than 1%.
Materials and methods
Assume that a total of G pools of individuals are sequenced and each pool contains K/ 2 individuals (K chromosomes). For each pool g, a total of n g reads are mapped to this locus, with reads carrying the major allele and reads carrying the minor allele. Thus .
Given the above likelihood expression and the data , our objectives are as follows
Find the maximum likelihood estimate of (f, α, β).
Determine whether an observed variant is a true SNP or not, i.e. SNP calling.
Find the variants associated with a phenotype of interest.
Computational methods
An expectation-maximization (EM) approach for allele frequency estimation
Based on the likelihood function, an approximate solution to the maximum likelihood estimation of the parameters can be obtained using the EM algorithm. We consider the following missing data:
C g : the number of chromosomes carrying the minor allele in the g-th pool;
I gi : the true underlying allele state (major (0) or minor (1)) of read i in the g-th pool;
r gi : the observed allele state (major (0) and minor (1)) of the i-th read in the g-th pool.
Note the expectation E(t)is taken when the parameters are at Θ(t).
where all the parameters in the equations are of the values taken at the t-th step.
From Equations 3 and 4, we are able to obtain the recursive formula for f.
Similarly, we can derive the formulas for E(t)(T10|Data), E(t)(T01|Data) and E(t)(T00|Data), and the recursive formulas for α and β can be derived from them.
SNP identification using EM
Due to sequencing errors, the observed variants may contain a significant amount of false positives, i.e. loci that are not truly polymorphic. Thus, before testing for associations with phenotypes, we need to determine the true polymorphic sites. This step is especially important in the case of rare variants since the sequencing error rates for NGS could be close to or even higher than the minor allele frequencies.
where lf is the maximum log-likelihood of the observed data for both the cases and the controls. Note that the null hypothesis f = 0 is on the boundary of the region of the parameters of interest. Therefore, the asymptotic distribution of Λ is when the number of pools is large according to [18], where I0 is the point mass at 0 and , i = 1, 2 are the chi-square distributions with i degrees of freedom. When the number of pools is relatively small, simulation approaches for the null distribution of Λ are needed to obtain the asymptotic distribution.
to test each hypothesis, where and are the maximum log-likelihood of the data for the cases and controls, respectively. Because the null hypothesis f i = 0 is on the boundary of parameter region f i > 0, the statistic Λ i has an asymptotic distribution when the number of pools is large according to [18]. We refer to the above method for SNP identification as EM-SNP.
Testing for associations between a SNP and a phenotype in case-control studies
This statistic has an asymptotic chi-square distribution with 1 degree of freedom.
Simulation studies
We use simulations to evaluate our approaches for allele frequency estimation, SNP detection and test for association. A large range of parameter space is considered to see how different parameters affect the performance of our methods. These parameters include minor allele frequency (f), sequencing error rate (α), the number of chromosomes in each pool (K), the number of pools (G) and the relative risk for a disease (λ).
Pooled data generation
In our simulations, we set α = β and choose four starting values of α = β = 0.05%, 0.1%, 0.5%, 1% corresponding to different sequencing error rates ranging from low to high. The sequencing error rate for current NGS technologies is around 1% and we expect that it will decrease as the technologies improve. Therefore, we also consider much lower sequencing error rate in our studies. For the allele frequency, we choose four values f = 0.1%, 0.5%, 1%, 5%. Loci with minor allele frequencies above 5% are considered to be common. We want to study if it is possible to estimate the minor allele frequency even if it is lower than the sequencing error rate. We let the read number n = 1000 and 3000, which is around the sequencing depth in [8]. To study the effect of the number of chromosomes, we let K = 50, 100, 200. The number of pools is set at G = 10, 20, 50.
Since the sequencing error rate can vary from locus to locus and from one pool to another, we generate 1000 α i (= β i , i = 1, · · ·, 1000) values from a normal distribution with mean equal to the starting values of α, and variance equal to 0.1 times the starting values. Finally, we generate 1000 pooled data sets with each combination of the five parameters (K, G, n, f, α) based on α i (= β i ), i = 1, ⋯, 1000.
Measuring the accuracy of the allele frequency estimation
- 1.In the i-th simulation, we use the EM algorithm derived above to estimate the parameters (f, α, β), denoted as . We also consider a naive estimate for the minor allele frequency as the fraction of observed minor alleles in the observed reads,(9)
- 2.
Repeat Step 1) for R = 1000 times.
- 3.Compute the mean squared error (MSE) of and from the true population minor allele frequency f,
- 4.Compute the MSE of and from the fraction of chromosomes carrying minor alleles ffrac = C/(KG) in the pools,
We use both MSE and Cg to compare the accuracy of the EM algorithm with the naive approach of estimating f by the fraction of reads carrying the minor allele.
Generating case-control data to study the power of SNP identification and association studies using EM
In order to evaluate the power of SNP identification using EM-SNP and test for association, we simulate case-control data as follows. When generating the control data, we assume that the minor allele frequency is f and that the locus is under Hardy-Weinberg equilibrium. When generating the genotypes of the case individuals, we assume that the penetrance (the probability an individual is affected) of the genotypes 00, 01 and 11 are g0 = 0.01, λg0, and λ2g0, respectively. In our simulations, we choose λ = 1.2, 2, and 4.
We can use the case or control samples separately or combine them for SNP detection as in the "SNP identification using EM" subsection. For example, we consider both the cases and controls jointly. The log-likelihood ratio statistic Λ (or Λ i if we use case or control samples separately) defined in equation 6 is used to test if an observed variant is a true polymorphic locus or not. For a given type I error γ (= 0.05 in our study), we claim that the variant is truly polymorphic if Λ >t γ , where t γ is the threshold corresponding to type I error γ. If the threshold can not be found theoretically, we can do parametric bootstrap to find the threshold. Firstly, assume that the variant site is not polymorphic, estimate the allele frequency and error rate using the maximum likelihood approach. Secondly, generate the reads data as in our model a large number of times (R = 1000), and obtain the empirical distribution of Λ. For a given type I error γ, we find the upper γ percentile t γ . Finally, the null hypothesis is rejected if the value of Λ is at least t γ . For a given relative risk λ, we repeat these steps 1000 times and the power is the fraction of times that the locus is called as polymorphic.
Similar approaches can be used to study the power of association studies using the pooling design. For details, see additional file 1.
A pooled sequencing data set related to type 1 diabetes [8]
We use our method to study the pooled sequencing data related to type 1 Diabetes dataset (T1D) in [8] and compare the results with current methods for SNP identifiction [11]. The data was generated using DNA samples of 480 T1D patients and 480 healthy controls, arranged in 20 DNA pools, with 48 patients/controls in each pool. Roche 454 sequencing was used to sequence 144 target regions that cover exons and splice sites of 10 candidate genes. We use MOSAIK (http://bioinformatics.bc.edu/marthlab/Mosaik) to map the reads to the human reference genome (hg19) with parameters -hs 15 -p 12 -mmp 0.05 -act 26 - mhp 100 -bw 51 as recommended in its documentation. MOSAIK is a widely used reference-guided assembler that hashes the whole reference genome and locate information in the hash table using a 'jump database' [19–21]. Then we use SAMtools (http://samtools.sourceforge.net/) [22] to pileup the reads onto the target regions. We also remove indels and keep loci that are covered by at least one read in each pool. Finally, we use ANNOVAR [23] to annotate the identified SNPs.
We first present our results on the effects of various parameters on the estimation accuracy of the minor allele frequency using the EM algorithm. We then present the results on the power of SNP detection and association studies. Finally, we present our results on the analysis of the data in [8] using the approaches in the "Materials and Methods" section.
The effects of minor allele frequency, sequencing error rate, number of individuals in the pools and number of pools on the accuracy of allele frequency estimation
Comparison of and in terms of mean squared error
α= 0.05% | α= 0.1% | α= 0.5% | α= 1% | |||||
MSE | Cg | MSE | Cg | MSE | Cg | MSE | Cg | |
f = 0.1% | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
f = 0.5% | 9 | 5 | 4 | 3 | 0 | 0 | 0 | 0 |
f = 1% | 13 | 10 | 9 | 7 | 0 | 0 | 0 | 0 |
f = 5% | 17 | 16 | 17 | 16 | 12 | 12 | 7 | 7 |
The relative errors of and in estimating minor allele frequency f
Comparison of and in terms of average relative error
α= 0.05% | α= 0.1% | α= 0.5% | α= 1% | |||||
f | | | | | | | | |
0.1% | 52.0 | 9.4 | 102.0 | 15.6 | 502.0 | 72.0 | 1000.0 | 146.0 |
0.5% | 10.3 | 4.0 | 20.2 | 4.9 | 99.5 | 13.3 | 199.0 | 26.5 |
1% | 5.0 | 3.3 | 10.0 | 3.7 | 49.2 | 5.7 | 98.3 | 9.5 |
5% | 1.0 | 5.4 | 1.9 | 6.0 | 9.1 | 6.7 | 18.1 | 6.3 |
Next we present our results for the effects of (K, G, n, f, α) on the estimation accuracy of minor allele frequency f using the EM algorithm. We note that the estimation of β = f(0| 1) is highly unreliable (data not shown). This phenomenon can be explained as follows. When minor allele frequency f is low, the expected number of chromosomes having the minor allele in each pool is also low. When the number of pools G is small, the estimation of β can be difficult with a small number of chromosomes carrying the minor allele. Thus, we do not show detailed results on the estimation of β. Despite the fact that β cannot be reliably estimated, the other two parameters f and α can be reliably estimated using the EM approach.
The effects of minor allele frequency f and sequencing error rate α on the estimation accuracy of
as an estimator of f or ffrac
α= 0.05% | α= 0.1% | α= 0.5% | α= 1% | |||||
f | MSE | Cg | MSE | Cg | MSE | Cg | MSE | Cg |
0.1% | 9.8e-7 | 4.3e-8 | 9.7e-7 | 1.2e-7 | 3.2e-6 | 2.8e-6 | 1.1e-5 | 1.1e-5 |
0.5% | 5.5e-6 | 1.9e-7 | 5.4e-6 | 1.9e-7 | 6.7e-6 | 1.5e-6 | 1.0e-5 | 5.8e-6 |
1% | 1.2e-5 | 8.6e-7 | 1.2e-5 | 9.6e-7 | 1.3e-5 | 2.3e-6 | 1.6e-5 | 5.6e-6 |
5% | 5.5e-5 | 1.3e-5 | 5.9e-5 | 1.7e-5 | 8.3e-5 | 4.3e-5 | 1.0e-4 | 7.0e-5 |
To reduce the effect of a few outliers of on the MSE and Cg calculation, we also modified the definitions of MSE and Cg by removing the top and bottom κ% of its values and recalculate the values of MSE and Cg. The results on the modified measures are presented in additional file 1 and the qualitative results on the performance of continue to hold.
We also studied the effects of (K, G, n) on the estimation accuracy of and the details of the simulation results are given in additional file 1. It was observed that the accuracy increases with G and n as expected. However, the accuracy decreases with the number of individuals K in each pool.
Results on the power of SNP calling using the likelihood ratio test
It can be seen from Figure 2 that at a type I error rate of 0.05, the power is consistently well above 0.9 in all scenarios demonstrated here except for the extremely rare variant case of f = 0.1%. The power tends to increase with the minor allele frequency or the number of pools, while it decreases with sequencing error rate or number of individuals in each pool. The power also increases with the number of reads in each pool. We observe that the power using the case samples is slightly higher than that using the control samples. This observation can be explained by the fact that the frequency of the minor allele in the cases is higher than that in the controls, resulting in higher power of SNP detection.
Results on the power of association studies using the likelihood ratio test
It can be seen from Figure 3 that at a type I error rate of 0.05, the power increases with λ and approaches 1 as λ goes up to 4, which happens in all scenarios demonstrated here except for the extremely rare variant scenario of f = 0.1%. The power increases with allele frequency, pool size or number of pools, while it seems robust with respect to changes in sequencing error rate.
Results on the analysis of the type 1 diabetes data in [8]
Allele frequency estimation and SNP calling in the control samples
We apply our approaches to analyze the pooled sequencing data in [8]. First, we conduct SNP calling using both our method EM-SNP and SNVer (parameter setting -bq 20 -a 0 -f 0 -p 1 -t 0) [11], a program that has been shown to outperform several other programs for SNP calling including CRISP, SAMtools, and GATK. Unlike many previous programs calling variants as SNPs or not, SNVer ranks variants according to their potential of being true SNPs using the p-value defined in the program. As a likelihood ratio test, EM-SNP can also rank the variants by the magnitude of the likelihood ratio. The estimated allele frequency spectrum of the top 100 called SNPs by either EM-SNP or SNVer is given in Figure S9 of the additional file 1. Note that 5 variants have dominant non-reference alleles and they are excluded from both lists for a fair comparison. In the SNVer list, we also exclude the variants that are removed in the preprocessing stage of EM-SNP. Both frequency spectrums of the variants called by EM-SNP and SNVer tend to concentrate on the lower frequency range.
Evaluation of the SNP calling results
In terms of the dbSNP ratio for the top 100 called variants, EM-SNP consistently outperforms SNVer under all allele frequency thresholds, and EM-SNP displays significant superiority especially for low frequency variants. In Table S7 of the additional file 1, we give an example of the dbSNP ratio among the top 100 SNP calls with fem ≤ 0.2% for the two methods. Using a total of 480 control samples, EM-SNP identifies variants with minor allele frequency less than 0.2% with a high dbSNP ratio, which serves as an evidence of its superior performance in rare variant scenarios. On the other hand, the upper left panel of Figure S10 in the additional file 1 shows that the relative performance of EM-SNP and SNVer based on dbSNP ratio depends on minor allele frequency. EM-SNP detects more rare variants and has higher dbSNP ratio at minor allele frequency less than 1%. Whereas this relative performance of EM-SNP and SNVer is reversed for minor allele frequency above 1%. Thus, EM-SNP is most useful in detecting rare variants.
Another criterion to evaluate SNP calls is the transition-transversion (Ti/Tv) ratio. It is well known that transitions are much more frequent than transversions in evolution, and the number of transitions over the number of transversions, referred to as Ti/Tv ratio, in known SNPs is expected to be between 2 and 4 [25]. Figure 4 shows that EM-SNP gives a consistently higher Ti/Tv ratio throughout the entire allele frequency range for both the whole set of called variants and the novel set. For the known variants, the Ti/Tv ratio trends of the two methods are similar to each other. Table S8 in the additional file 1 gives an example of the Ti/Tv ratio among the top 100 SNP calls with fEM < 0.2% by EM-SNP and SNVer. The effect of minor allele frequency on the relative performance of EM-SNP and SNVer in terms of Ti/Tv ratio is similar to that in terms of dbSNP ratio (Figure S10 in the additional file 1).
We also consider the top 150 ranked SNPs and the corresponding figures and tables are shown as Figure S11-S12 and Tables S7-S8 in the additional file 1. The qualitative conclusions are the same.
Identifying SNPs associated with type 1 diabetes
Association results
SNP | Gene | | n 0 | | n 1 | Fisher's p-value | EM p-value |
rs3184504 | SH2B3 | 0.52 | 499 | 0.41 | 394 | 1.9e-6 | 8.4e-7 |
rs7076103 | IL2RA | 0.19 | 178 | 0.10 | 93 | 4.5e-8 | 2.7e-7 |
rs2476601 | PTPN22 | 0.09 | 86 | 0.16 | 151 | 8.1e-6 | 9.2e-6 |
The SNP rs3184504 residing within gene SH2B3 has an EM p-value of 8.4e - 7. This SNP was also found to be associated with a preliminary p-value of 5e - 7 in the original study [8] and the corresponding gene was previously identified to be associated with T1D. The fractions of observed minor alleles in controls and cases in the original study were 53% and 41.5%, respectively, and our mapping results are consistent with the estimates. The EM estimated minor allele frequencies in the controls and cases are 52% and 41%, which are slightly smaller than the observed values since we took sequencing errors into account. The SNP rs7076103 within the gene IL2RA has a preliminary Fisher's p-value of 4.5e-8 and an EM p-value of 2.7e-07. This SNP was not reported to be associated with any phenotypes according to the catalog of GWAS studies (http://www.genome.gov/gwastudies/) to date. Nevertheless, other SNPs within the IL2RA gene were found to be associated with T1D by Cooper et al. [26] before the publication of [8] and by two other studies [27, 28] after the publication of [8] using different approaches. Barrett et al. [27] used genome-wide association studies giving a p-value of 1.0e-13 while Huang et al. [28] used imputation of the genotypes based on the 1000 genome projects yielding a p-value of 5e-9. These new studies support our significant result on the association of rs7076103 with T1D. The estimated minor allele frequencies in the controls and cases were 18.8% and 14.8% in [8] giving a p-value of 0.02 which is not significant after adjusting for multiple testing. This example shows that even for common polymorphisms, the EM approach can help to find likely associations that the naive approach can not. The SNP rs2476601 was found to be associated with T1D in several studies before the publication of [8] and was confirmed in a recent study in [29] that was published after the publication of [8]. All these studies support our results for the association of common polymorphisms with T1D.
For rare polymorphisms within the controls, we first use the naive approach described above to obtain a preliminary Fisher's p-value for every SNP. Due to the low minor allele frequencies of the rare variants, none of the p-values is smaller than 0.001. We did not pursue the association of individual variants with T1D further.
In this paper, we developed an EM algorithm based unified approach for minor allele frequency estimation, SNP calling and association studies, applicable to pooled sequencing data where genetic materials of multiple individuals are pooled together. This study differs from previous studies in that we estimate sequencing error rate for each position while previous studies generally assume a pre-specified sequencing error rate across all sequenced regions. Since sequencing error rate depends on the genomic context, it is essential that the sequencing error rate be estimated specifically for different loci. In a pooling design without tagging, the origin of the reads is not known, and it is impossible to obtain the individual genotypes from the pooled data. Therefore, we modelled the pooled sequencing data as a "missing value" problem and designed an EM algorithm to estimate the minor allele frequency and sequencing error rate.
We first studied the effects of minor allele frequency, sequencing error rate, number of pools, number of individuals in each pool, and the sequencing depth in each pool, on the estimation accuracy of the minor allele frequency. It was shown that the naive approach, which estimates the minor allele frequency by the fraction of observed minor alleles in the reads, can significantly over-estimate the true minor allele frequency, and that the effect is most severe for rare variants. The EM based algorithm, on the other hand, can estimate the minor allele frequency in a relatively unbiased manner. Although the variation of this estimation seems to be relatively large, a major part of the variation comes from the sampling of individuals from the population rather than the algorithm itself. We also show that the estimation accuracy of the EM algorithm increases with the number of pools and sequence depth as expected. However, the estimation accuracy decreases with the number of individuals in each pool, most likely because a more extensive pooling induces greater loss of information. Secondly, we used a likelihood ratio statistic based on the estimated parameters from EM to call SNPs. With the real data from [8], in terms of the dbSNP ratio, we showed that EM-SNP outperforms SNVer for rare variants with minor allele frequency less than 1%. We also showed that the transition/transversion ratio of the called SNPs for rare variants based on EM-SNP is higher than that of the called SNPs by SNVer. These two independent pieces of evidence demonstrate that EM-SNP is superior to SNVer in the discovery of rare variants. However, the extent of this advantage decreases as minor allele frequency increases due to the tradeoff between EM-SNP's bias adjustment for the estimation of minor allele frequencies and extra variation introduced in the EM algorithm. Finally, we applied our approach to reanalyze the case-control data from [8] and showed that we can find the associated common SNPs. Unfortunately we did not find any significantly associated rare variants. One possible explanation is that the power of finding rare variants associated with complex traits is generally low as a consequence of the low frequencies of minor alleles.
We made several simplifying assumptions in our study. First and foremost, we did not consider errors introduced by mapping the reads to the reference genome. The mapping of Roche 454 data still has many challenges, in particular, in regions around homopolymers, and further development of algorithms for mapping is needed. Secondly, although we assumed that the amount of genetic materials from each individual is the same for each pool, this assumption can be violated. To overcome this problem, one approach would assume that the fractions of genetic materials from individuals follow a Dirichlet distribution [17]. Thirdly, the called SNPs by EMSNP still have many false positives since the Ti/Tv ratio for the called novel SNPs is still low compared to the known SNPs. Further improvements in SNP calling are needed. Finally, the computational speed of the EM based approach can be relatively slow, and the method cannot be applied to whole genome association studies although this is not a problem for targeted sequencing studies as in [8]. These are the topics for future research.
Software can be downloaded from http://www-rcf.usc.edu/~fsun/Programs/EM-SNP/EM-SNP.html.
The publication costs for this article were funded by US NIH 1 U01 HL108634.
This article has been published as part of BMC Genomics Volume 14 Supplement 1, 2013: Selected articles from the Eleventh Asia Pacific Bioinformatics Conference (APBC 2013): Genomics. The full contents of the supplement are available online at http://www.biomedcentral.com/bmcgenomics/supplements/14/S1.
This research was supported by National Institutes of Health (P50HG002790 and 1 U01 HL108634). Q Chen was partially supported by the Viterbi Fellowship. F.S. is also supported by National Natural Science Foundation of China (60928007 and 60805010) and Tsinghua National Laboratory for Information Science and Technology (TNLIST) Cross-discipline Foundation.
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