text:
Alitalia's directors have approved the sale of a 25 percent stake to Air France-KLM for just over 320 million euros.
That came one day before the relaunch of Alitalia which has been merged with its smaller domestic rival Air One. A consortium of Italian investors, known as CAI, will have three quarters of the streamlined carrier. They said the fact that Air France-KLM's is taking a 25 percent stake will mean synergies of 720 million euros over the next three years. As the news came through, Alitalia workers demonstrated against how they are being treated in the reorganisation. One cabin crew member said those working on contracts have been left in limbo: "We're here to stress how precarious our position is, nobody has thought about us, we're like ghosts, without any value. After ten years of service we're being thrown away, just like that." The restive workforce, which has a history of wild-cat strikes, is just one of the problems facing the 'new' Alitalia. The investors believe they can restore the airline to operating profit by late next year. But it has made a net profit only once in the past nine years and is expected to record an operating loss of one billion euros for 2008. It also faces stepped up competition from Germany's Lufthansa which passed on taking a stake in Alitalia in favour of setting up Lufthansa Italia – flying from Milan to eight European capitals. In addition, European low-cost airlines have complained to the European Commission claiming Alitalia is continuing to receive million of euros of illegal state aid.


text:
The most casual-looking model in our Invert™ family, the Rotor provides the technical advantages of an Invert™ without the race day look. The adjustable hydrophilic nose pads allow you to fine-tune the fit to optimize airflow, stability and comfort.
The most casual-looking model in our Invert™ family, the Rotor provides the technical advantages of an Invert™ without the race day look. The adjustable hydrophilic nose pads allow you to fine-tune the fit to optimize airflow, stability and comfort.
Specs and Measurements
- Fit
- Medium-Large
- Weight
- 34 g
- Base Curve
- 6c
Fit GuideFind the best fit
antiFOG Rose
Finally, bike eyewear you can leave on your face.
Whether you're grinding through a tight, twisty climb or simply stopped at an intersection, fogged lenses are an inevitability for many of us when wearing sports eyewear. The RYDERS antiFOG lens is the ultimate solution to this all-to-common problem—and you don't have to take our word for it. See the growing list of published antiFOG reviews in our NEWS section.
- road
- trail
Lens Features
100% UV400 Protection
All of our lenses block 100% of UVA, UVB, and UVC rays and harmful, high energy light to 400nm. These rays are a leading cause of cataracts, skin cancer and wrinkles around the eyes—all great reasons to block them out.
Impact Resistant
All of our lenses are impact resistant, meaning they resist breaking up into dangerous little shards when impacted. If astronauts trust this material to keep their heads from exploding while on a 17,000 mph space walk, you'll have nothing to worry about on your adventures, no matter how fast you're going.
Optically Correct
All of our lenses are made by injecting molten polycarbonate into a mold that is specially formed to eliminate distortion. This process makes the lenses optically correct (also referred to as decentred), increasing long-term comfort and minimizing eye fatigue.
Scratch-Resistant Coating
We apply a scratch-resistant coating to all of our lenses. Though this process makes the surface of the lens considerably harder than the base lens material, it's impossible to make the lenses completely scratch proof (short of making them from diamonds) so please care for them properly as they may still scratch under certain conditions.
Frame Technology
Adjustable Nose Pads
Adjustable nose pads allow you to customize the fit of your eyewear for comfort and stability. This component is also used for fine-tuning the amount of airflow behind the lens to keep your face cool and combat fogging.
Grilamid TR90
A Swiss technology, this incredible thermoplastic is the material used in all of our sunglasses (with the exception of our metal frames). Its extreme flexibility, durability and light weight make it the perfect material for performance eyewear.
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subset: commoncrawl


text:
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Before you speak ask yourself if what you are going to say is true,
is kind, is necessary, is helpful.
If the answer is no, maybe what you are about to say should be left unsaid.
- Bernard Meltzer
A true friend is someone who
thinks that you are a good egg
even though he knows that
you are slightly cracked.
- Bernard Meltzer
When you forgive, you in no way change the past -
but you sure do change the future.
- Bernard Meltzer
If you have learned how to disagree without being disagreeable,
then you have discovered the secrete of getting along -
whether it be business,
family relations, or life itself.
- Bernard Meltzer
If you want to be original just try being yourself,
because God has never made two people exactly alike.
- Bernard Meltzer
Success is getting and achieving what you want.
Happiness is wanting and being content with what you get.
- Bernard Meltzer
Happiness is like a kiss.
You must share it to enjoy it.
- Bernard Meltzer
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We may give without loving, but we cannot love without giving.
- Bernard Meltzer
Use those talents you have.
You will make it.
You will give joy to the world.
Take this tip from nature: The woods would be a very
silent place if no birds sang except those who sang best.
- Bernard Meltzer
We must be willing to get rid of the life we've planned,
so as to have the life that is waiting for us.
The old skin has to be shed before the new one can come.
- Joseph Campbell
What lies behind us and what lies before us
are tiny matters compared to what lies within us.
- Ralph Waldo Emerson
There are only two or three human stories,
and they go on repeating themselves as fiercely
as if they had never happened before.
- Willa Cather
We all have our thorns. We, and Life, have our moments.
Life occurs before our morning coffee.
Life occurs in our bathrobe with our hair uncombed.
Bless and give thanks for All of Life - the bloom and the thorns.
- Jonathan Lockwood Huie
The golden age is before us, not behind us.
- William Shakespeare
If you have no confidence in self,
you are twice defeated in the race of life.
With confidence, you have won even before you have started.
- Marcus Tullius Cicero
Look twice before you leap.
- Charlotte Bronte
Courage and perseverance have a magical talisman,
before which difficulties disappear and obstacles vanish into air.
- John Quincy Adams
It is darkest just before the dawn.
- Proverb
Strategy without tactics is the slowest route to victory.
Tactics without strategy is the noise before defeat.
- Sun Tzu
Who were you before you put yourself last.
- Mary Anne Radmacher
The challenge before us is to savor the unknown
and delight in the taste of possibility.
- Mary Anne Radmacher
We do not always see what is before our face -
sometimes we see what we hope to see,
or fear we will see.
- Jonathan Lockwood Huie
Doubt is the vestibule which we all must pass through
before we can enter the temple of truth.
- Osho
Never put passion before principle.
Even if win, you lose.
- Miyagi: character in the movie Karate Kid 2
How wonderful it is that nobody need wait a single moment
before starting to improve the world.
- Anne Frank
You have to expect things of yourself before you can do them.
- Michael Jordan
Cowards die many times before their deaths;
The valiant never taste of death but once.
- William Shakespeare
Children are born innocent.
Before they are domesticated they live in the moment,
love without fear, and don't even think about the opinions of others.
- don Miguel Ruiz
Habits age men before their time.
- Jonathan Lockwood Huie
Before we acquire great power
we must acquire wisdom to use it well.
- Ralph Waldo Emerson
Follow your bliss and doors will open
where there were no doors before.
- Joseph Campbell
When angry, count to ten before you speak.
If very angry, count to one hundred.
- Thomas Jefferson
Nurturing is not complex.
It's simply being tuned in to the thing or person before you
and offering small gestures toward what it needs at that time.
- Mary Anne Radmacher
The only place success comes before work is in the dictionary.
- Vince Lombardi
Anger is a killing thing:
it kills the man who angers,
for each rage leaves him less than he had been before -
it takes something from him.
- Louis L'Amour
Before you criticize a man,
walk a mile in his shoes.
- Anonymous
For the very first time the young are
seeing history being made
before it is censored by their elders.
- Margaret Mead
Service which is rendered without joy
helps neither the servant nor the served.
But all other pleasures and possessions
pale into nothingness before service
which is rendered in a spirit of joy.
- Mohandas (Mahatma) Gandhi
All in the dark we grope along,
And if we go amiss
We learn at least which path is wrong,
And there is gain in this.
We do not always win the race
By only running right;
We have to tread the mountain's base
Before we reach its height.
- Ella Wheeler Wilcox
Before moving on, you have to clear away your cherished beliefs.
- Dick Raymond
Self-honor (self-respect) is in no way selfish.
Before I can give to others,
I must have something to give.
Only by first creating
my own self-esteem and happiness,
do I possess the resources to
contribute anything meaningful to others.
- Jonathan Lockwood Huie
My Mama always said you've got to put the past behind you
before you can move on.
- the movie Forrest Gump
Before the throne of the Almighty,
man will be judged not by his acts but by his intentions.
For God alone reads our hearts.
- Mohandas (Mahatma) Gandhi
That's what learning is, after all;
not whether we lose the game,
but how we lose and h
ow we've changed because of it
and what we take away from it
that we never had before,
to apply to other games.
Losing, in a curious way, is winning.
- Richard Bach
Before God we are all equally wise - and equally foolish.
- Albert Einstein
I like the silent church before the service begins,
better than any preaching.
- Ralph Waldo Emerson
The best time to make friends is before you need them.
- Ethel Barrymore
Before beginning a Hunt, it is wise to ask someone
what you are looking for before you begin looking for it.
- A. A. Milne (Winnie-The-Pooh)
We must be our own before we can be another's.
- Ralph Waldo Emerson
Naturally, every age thinks that all ages before it were prejudiced,
and today we think this more than ever, and are just as wrong
as all previous ages that thought so.
How often have we not seen the truth condemned!
It is sad but unfortunately true that man learns nothing from history.
- Carl Jung
Grace isn't just a little prayer
you say before receiving a meal.
It's a way to live.
- Jackie Windspear
From far beyond this life,
I hear the call.
From place beyond all place,
I feel the call.
From time before all time,
I know the call.
From one before all ones,
I am the call.
- Jonathan Lockwood Huie
I have three precious things which I hold fast and prize.
The first is gentleness;
the second is frugality;
the third is humility, which keeps me from putting myself before others.
Be gentle and you can be bold;
be frugal and you can be generous;
avoid putting yourself before others
and you can become a leader among men.
- Lao Tzu
Each day, I am healthier, younger,
stronger, more comfortable,
and more joyful than the day before.
- Jonathan Lockwood Huie
Man should forget his anger before he lies down to sleep.
- Mohandas (Mahatma) Gandhi
I did not wish to take a cabin passage,
but rather to go before the mast
and on the deck of the world,
for there I could best see
the moonlight amid the mountains.
I do not wish to go below now.
- Henry David Thoreau
True friendship is a plant of slow growth,
and must undergo and withstand the shocks of adversity
before it is entitled to the appellation.
- George Washington
As long as any adult thinks that he,
like the parents and teachers of old,
can become introspective,
invoking his own youth to understand
the youth before him,
he is lost.
- Margaret Mead
A friend is one before whom I can think aloud.
- Ralph Waldo Emerson
A wise girl kisses but doesn't love,
listens but doesn't believe,
and leaves before she is left.
- Marilyn Monroe
I tried to remember how to exhale.
I had to look away before it came back to me.
- Bella, from Twilight saga by Stephenie Meyer
Praying is important when you wake up
at two o'clock in the morning
feeling sick from eating something dumb the day before.
- Charlie Brown in Charles M. Schulz' cartoon Peanuts
Sometimes I've believed as many as
six impossible things before breakfast.
- Lewis Carroll
Nothing is more beautiful than the loveliness
of the woods before sunrise.
- George Washington Carver
Do you not know that there comes a midnight hour
when every one has to throw off his mask?
Do you believe that life will always let itself be mocked?
Do you think you can slip away a little before midnight
in order to avoid this? Or are you not terrified by it?
I have seen men in real life who so long deceived others
that at last their true nature could not reveal itself;...
In every man there is something which to a certain degree
prevents him from becoming perfectly transparent to himself;
and this may be the case in so high a degree,
he may be so inexplicably woven into relationships of life
which extend far beyond himself that he almost cannot reveal himself.
But he who cannot reveal himself cannot love,
and he who cannot love is the most unhappy man of all.
- Soren Kierkegaard
In case you failed to notice,
in case you failed to see,
this is my heart,
bleeding before you,
this is me down on my knees.
- Jewel
Always speak the truth,
think before you speak,
and write it down afterwards.
- Lewis Carroll
Don't be dismayed by good-byes.
A farewell is necessary before you can meet again.
- Richard Bach
Before you can forgive others,
you must be a person whose forgiveness matters.
Before you can have gratitude for your life,
you must believe that your life has value.
Before your choices have value,
you must feel that you yourself have value.
Before you can dream a great dream for your future,
you have to believe that your future matters.
Before you can build positive habits of resolve and commitment,
before you can begin to live into the Japanese proverb,
"Fall seven times, stand up eight,"
you must believe that your life matters.
Before you can celebrate your life, you must Honor it.
And, before you can feel unity with,
and Honor toward, Spirit and all creation,
you must Honor yourself to feel worthy of that unity.
- Jonathan Lockwood Huie
I do not fear death.
I had been dead for billions and billions
of years before I was born,
and had not suffered the slightest inconvenience from it.
- Mark Twain
Perhaps one has to be very old before one learns
to be amused rather than shocked.
- Pearl S. Buck
Thank you for visiting: Before you speak ask yourself if what you are going to say is true, by Bernard Meltzer.
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text:
In literally the last 8 weeks or so I have been involved with starting a new business. It's over at Onix Central but for the purposes of this post it really could be just about any business.
What I wanted to write a little about is essentially in the face of all the doom and gloom in our midst just what great times we live in. And how fantastic it is that we are surrounded by so much empowering (and often free) technology that enables us to do so much with (quite frankly) so little. Just how democratic this makes capitalism is (for me) something that I hope will never lose it's shine.
I thought I would give a quick run through of some of the tools; applications and software that has enabled us to start a business from scratch; to develop our products; let people know about what we do; sell (although I use this term very advisedly – not sure anyone would call what we do 'selling' as such); communicate with both with our customers and between ourselves and deliver our products and services. Many of these tools will in fact be very familiar to almost any one reading this post.
So, a little about our setup. We run a software and publishing services business. Emma, my business partner is based in the Uk and I am based between the UK and Stockholm in Sweden. We have not met since we formed the business. Emma is on a PC and I am on Mac. I mention this as this again is one of the issues that in recent times has all but largely disappeared.
Without further ado and in no particular order:
1) Actually, I said in no particular order but number one with a bullet has to be Skype. Emma and I talk probably a good three or four times a day on Skype – for free. We also use this as our primary instant messenger client – largely because we have it open all the time anyway and also it tends on the whole to be the easiest and most reliable for sending small files between ourselves which is sometimes very helpful. It is also used to communicate with clients. And don't forget all for free. Yes, I know we take it for granted but let's repeat it and let it sink in for a moment – all for free. Free!
As well as being a free VOIP application (with video) it is also a very useful and affordable IP telephone system. Our client base already in this very short term separated by in some cases many thousands of miles. So, Skype gives us the opportunity to have a number in each of our client's countries that they can call for support or enquiries. A number that is local to them.
We can also call out to any phone (landline or mobile) anywhere in the world for flat affordable rates. Yesterday in the course of about 20 mins I rang someone on a cell phone in Singapore; made two calls to Oxford in the Uk and then a short call to Stockholm. All for the princely sum of about 35p! Contrast that with the traditional costs of the telecoms of even a couple of years or so ago. And, let's leave aside cell/mobile roaming charges even today.
It makes communication in our business wherever we are and irrespective of the location of our clients – easy and affordable (if not, often, effectively free).
2) To the real 'in no particular part of our list'. Drop Box. This is free (for up to 2gb and then you can pay $99 a year to upgrade to 50gb). It essentially gives you space on the internet which mirrors folders on your hard disk. You can also have shared folders – so for example, Emma and I have a folder called Onix Central which is mirrored across all our machines with Drop Box installed. Oh and it doesn't care if it is a Mac or a PC. For instance, I am mostly on a Mac laptop but use Windows Vista also on that same machine and work often on a 24″ iMac (for the fantastic screen real estate). Emma is on a Windows XP desktop and has a laptop also.
So, when we are working on software; documents or just about anything we simply save to the Drop Box and whether we are 70 or a thousand miles apart it makes little difference. There are no limits on file sizes – if it is a text file of a few k or a database of 400 mb all can be shared.
Anyway, almost certainly there are other options out there but for us this one does exactly what it says on the tin and really helps with pretty much every aspect of what we do.
3) A few years ago (2001 or so) when I founded a software business you could of course trade emails with people and even the odd phone call. But, at some point when you wanted to demo your software or service you often had to get on a plane/train/bus/get in your car and go see people. It would generally eat your day and eat your money. But, you did it because it was quite simply a cost of doing business. And, if people wanted training then you had little option but also to get on a plane and physically go somewhere. And again all these attendant costs had to come out of somewhere.
Roll forward to 2009. And with gotomeeting you can demo to people; train people or just collaborate on a project all over the internet. Oh, and for less each month than the amount you would have dropped in the airport bar waiting for your plane. Again, sure they are many other options available but for us gotomeeting seems to do all the things we need.
4) Youtube. Yes, I know I know in terms of quality and so on it is not great (although much better recently). But, so many of the other sites had a number of restrictions of one form or another that we ended up back here. What youtube does for use is enable us to share videos of demos of our software, post support tutorials, and of course get the myriad of free stuff that we provide to help publishers out to people in a way that just works. Oh, and is free. In time, we will probably develop our own solution but come on in 8 weeks – what do you want from us?
5) And lastly Google. When we very very first started and we needed an email address; to share documents; or just have a calendar Google did pretty much what we needed. We have since moved on and developed our own set of tools and of course have our own domain and so on. But, it was certainly helpful to start with. But, we do use one particular part of their service still every day and as we build our web presence it provides us with invaluable assistance in tweaking our content; tracking responses and just seeing who is interested in us and what we are about. Google Analytics – and again free.
Ok, well I could go and on. But, you get the idea. And hovering above all this of course is the internet without which none of this would be possible.
So, with the help of these tools what in these few weeks have we achieved? In that time we have:
- Built a suite of products and service
- Constructed and populated with content a website
- Written manuals and how to guides for all our software
- Produced buckets of videos to support our software
- Written mountains of free content for publishers to do much more for themselves
- Have 477 contacts within publishers with whom we have spoken/exchanged correspondence
- 72 open publisher enquiries from 7 countries
- 7 Actual customers
- And booked 31 meetings so far for the upcoming London Book Fair
In conclusion, as well as hopefully highlighting some useful tools what I really wanted to drive at was that really anyone can do just what we did. That we live in times; with these tools and all these options (often for free) that you can just have an idea and create your own business. So, if the traditional barriers of capital are removed and the technical requirements are greatly diminished surely this means that the focus is on ideas and the products and services that flow from that creativity. Surely, how it should be?
Oh, and the best bit? You get to be your own boss and if you lose your job it really is nobodies fault but your own. In short, your fate really is in your own hands. So, just get on with it.
Filed under: Business, Onix Central, Technology


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Airfare Speed – Evaluating Scheduled to Charter
Most of us desire cheap routes, dont we? Plus in virtually every case we could get an improved airfare price with a charter service than a standard flight.
The reason behind this is certainly prima-facie easy, here follows a contrast of both.
Scheduled Flight
Airfare price with a planned airline is nearly always more costly than a charter, primarily because they need fly the route regardless of how numerous individuals are on board. That is tied-up in contractual and worldwide agreements between certain nations and air companies.
Each agreement varies according to numerous aspects, however, the sheer number of flights daily or weekly at the contracted times must certanly be adhered to in order to keep agreements. Sometimes that is associated with a reciprocal arrangement. As an example, a Portuguese flight perhaps permitted to travel into Brazil 100 times each week supplying a Brazilian flight can travel into Portugal 100 times each week (there are some other elements too, however get the idea, dont you?)
Airfare price is usually higher then because partially they should preserve and average-out ticket rates to account fully for half-empty planes.
Charter Carriers.
Airfare rate with charter organizations is nearly constantly greatly discounted as they fly with a notably different purpose than scheduled carriers. Really, charter routes tend to be one-off, although a charter organization might have regular traveling spots they are able to usually cancel the flight (and often do) if they havent sold adequate seats.
The contractual plans with nation aviation authorities are basically diverse from scheduled carriers. In most cases they will just charter an airplane during peak periods or even to ferry passengers to hectic vacation resorts or one off events particularly an important sporting event.
The crux regarding inexpensive airfare price with charters is the fact that, including, they maybe jetting off with a 300 chair plane to someplace bright and hot. Completing the airplane is in fact the secret to inexpensive seats with charter businesses. (more about secrets later on).
So Lets imagine they will have 250 visitors booked, they'll then attempt to offer cheaply, the residual seating, therefore affording a cheap airfare rate for the likes of us that looking for a deal.
The secrets we pointed out are available to you personally in helpful information compiled by a former flight business resource who blows the lid off Airfare price. More over, he describes thoroughly what to do to ensure you won't ever pay complete airline price ever again


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From our bases in Llandysul, Cardiff, Bridgend and Holywell we offer a 24 hour locksmith service covering the whole of Wales. Including the counties of Chester, Denbighshire, Flintshire, Conwy, Gwynedd, Wrexham, Camarthenshire and Ceredigion, Cardiff, Swansea, Neath Port Talbot, Torfaen, Monmouthshire, Rhondda Cynon Taff and Bridgend.
We also do contract work for larger companies in Shrewsbury Telford and Bristol.
We are an independent, local locksmith company offering good service and fair pricing.
Our prices are all advertised on our website; many of our competitors don't - or won't advertise their prices.
Ask yourself why others don't advertise their prices?!
Put the number in your mobile - because you never know when you'll find yourself locked out!


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Large Intestine
The large intestine, otherwise known as the colon, is the terminal part of the gastrointestinal tract, before excretion of the nutritional intake occurs. Its function is to absorb water from the indigestible food matter and to collect and eventually relieve the body of waste matter.
Here the sections of the colon will be discussed and at the end several pathological disorders will be mentioned.
The entire colon has three main characteristics, which are helpful when trying to distinguish it from the rest of the alimentary canal.
- The first feature is the teniae coli, which are three thickened longitudinal bands of muscle that span the length of the colon, with the exception of the appendix and the rectum.
- The second feature is called the haustra, which are the sacculations or bulging pouches formed by the contraction of the teniae coli.
- Lastly, the epiploic appendages which are fatty pouches situated along the part of the peritoneum known as the omentum.
The colon is divided into the cecum with its vermiform appendix, the ascending colon, the transverse colon, the descending colon, the sigmoid colon and the rectum and anal canal. It makes up part of the midgut and the hindgut and is both intraperitoneal and retroperitoneal. In the internal lining the plicae semilunaris are the areas of the mucosa that are raised.
Cecum and Vermiform Appendix
An intraperitoneal section that is around 7.5 cm in diameter and pouch-like in shape. It is bound to the abdominal wall via the cecal folds of the peritoneum and is a blind structure. It connects the ileum to the large intestine via an invagination known as the ileocecal valve.
The blood supply comes from the ileocolic artery and vein and the lymphatic drainage flows to the ileocolic nodes. The superior mesenteric plexus provides parasympathetic fibers from the vagus nerve and sympathetic fibers from the lower thoracic spinal cord segments.
The vermiform appendix is a small 6-10 cm tubular intraperitoneal structure that is blind and arises from the posteromedial side of the cecum. It is supplied by the appendicular artery that branches from the ileocolic artery.
Ascending Colon
A retroperitoneal section of the colon that is found on the right side of the posterior abdominal wall and stretches between the cecum and the liver. At the hepatic flexure which is the curvature just below the liver it turns left to form the next section.
It is supplied by the superior mesenteric vessels and their branches including the ileocolic artery and vein and the right colic artery and vein. The epicolic and paracolic nodes filter the lymph and the nervous supply comes from the superior mesenteric plexus.
Transverse Colon
The transverse colon is intraperitoneal, so within the peritoneum sheaths and it extends from the hepatic flexure to the splenic flexure. It is the largest of all the sections of the large intestine and it is the most mobile, although it is attached to the posterior abdominal wall via its own mesentery.
The superior mesenteric vessels provide it with the right colic artery and vein and the middle colic artery and vein. Innervation occurs via the superior and inferior mesenteric plexus and the lymphatic drainage goes to the middle colic nodes.
Descending Colon
The descending colon is retroperitoneal and can be found of the posterior left side of the abdominal wall, extending from the curvature next to the spleen to the sigmoid colon.
The inferior mesenteric artery and vein give the left colic artery and vein and also the superior sigmoid artery and veins as the vascular supply. Innervation occurs in the same way as the sigmoid colon.
Sigmoid Colon
This structure is intraperitoneal and suspended via the sigmoid mesocolon as an s-shaped loop whose length varies. It is the link between the descending colon and the rectum.
Its blood supply arrives via the branches of the inferior mesenteric artery and vein, which are known as the left colic artery and vein as well as the superior sigmoid artery and vein. The epicolic and paracolic lymph nodes drain the region, while the lumbar sympathetic trunk and the superior hypogastric plexus innervate it sympathetically. Parasympathetic fibers are contributed by the pelvic splanchnic nerves.
Rectum and Anal Canal
The rectum is intraperitoneal, but as it descends into the pelvic floor to the anal canal, it becomes retroperitoneal.
The rectum starts at the level of the 3rd sacral vertebra and is a 15 cm muscular tube which connects the colon to the anal canal, where it is fixed and continuous.
The anal canal arises from the lower end of the rectum at its ampulla and extends from the pelvic floor to the anus.
Clinical Aspects
There is an endless list of disorders that can directly or secondarily affect the large intestine and since this article's main focus is the macroanatomy of the organ, only a few common ailments shall be mentioned and briefly described.
Intestinal obstruction can affect the small or the large intestine. It occurs when an area of the bowels becomes twisted, blocked by food or stops working altogether. Symptoms include pain, vomiting, abdominal distension and constipation.
Colitis is the inflammation of the walls of the colon. It can be caused by a bacterial infection or by inflammatory bowel disease (IBS).
Diverticulosis occurs when certains areas of the colon's muscular wall become weak and the intestinal lining protrudes, forming little pouches, which can be subject to bleeding or inflammation.
Crohn's disease is an autoimmune inflammatory disease of the bowels which limits the ability of the alimentary canal to absorb nutrients.


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Te Kairanga Runholder Pinot Noir, Martinborough
The grapes for 'Runholder', a tribute to the original settlers, are grown on low-cropping vines, selective hand-picking, small batch fermentation and sensitive oak handling contribute to producing this rich, concentrated Pinot Noir. Traditional fermentation in small vats is employed with hand-plunging and gentle pressing off to release the flavour locked in the skins, movement of juice and wine around the winery is by gravity and the wine spends 15 months in French oak barrels, a quarter new. Initial aromas of black cherry, ripe plum and spice are backed by a velvety textured palate with subtle oak notes.
- Type: Red
- Country: New Zealand
- Region: Wairarapa
- Vintage: 2017
- Producer: Te Kairanga
- Primary grape: Pinot Noir
- Bottle size: 75cl
- Code: 28208
- Expression:


text:
See also: IRC log
<Jonathan> ACTION: Jonathan to make sure parameters are added to the URI in the HTTP binding even when no whttp:location appears. [recorded in http://www.w3.org/2007/01/04-ws-desc-minutes.html#action01]
<plh> http://dev.w3.org/cvsweb/~checkout~/2002/ws/desc/test-suite/logging-messages/index.html
<Arthur> http://dev.w3.org/cvsweb/~checkout~/2002/ws/desc/test-suite/logging-messages/index.html
<plh> http://lists.w3.org/Archives/Public/www-ws-desc/2006Nov/0045.html
<Jonathan> http://lists.w3.org/Archives/Public/www-ws-desc/2006Dec/att-0059/20061214-ws-desc-minutes.html#action04
<scribe> Scribe: Roberto
Minutes approved
[Interop] ? 2006-11-30: [interop] John Kaputin to create a test case with "required=false". ? 2006-12-14: [interop] Jonathan to fix transferCodings - add control group [WG] ? 2006-09-21: Jonathan to check periodically that SPARQL has added schemaLocation. ? 2006-12-14: plh to come up with a more detailed proposal for CR112 if possible DONE [.5] 2006-12-21: Jonathan to reference the Versioning document in the WSDL Primer. DONE [.3] 2006-12-21: Jonathan to respond to Ashok Malhotra/WS-Policy on WSDL 1.1 component indicators. DONE [.4] 2006-12-21: Jonathan to raise new issue adding 4 new assertions as per Arthur's note. Current Editorial Action Items Note: Editorial AIs associated with LC issues recorded at [.2]. [.1] http://www.w3.org/2002/ws/desc/#actions [.2] http://www.w3.org/2002/ws/desc/5/cr-issues/actions_owner.html [.3] http://lists.w3.org/Archives/Public/www-ws-desc/2006Dec/0086.html [.4] http://lists.w3.org/Archives/Public/www-ws-desc/2006Dec/0085.html [.5] http://lists.w3.org/Archives/Public/www-ws-desc/2006Dec/0094.html
Jonathan: WG extended six
... from the implementor's call, there was no progress on the logging issue
... no visible progress on dashboard
... it will take ~2 wks to fix the logging issues and get testing done between WSO2 and Canon
... 19 issues still open
... at the pace we're at, it should take ~ 3wks to get the issue count to zero
for PR we also need to update the documents
Jonathan: for PR we also need to
update the documents
... still a few resolutions not incorporated
... another area: validator progress
... we got coverage of 50% of the assertions
... it shouldn't block us from moving forward to PR
... it could take a month to increase coverage
Arthur: do we have dates for these events?
Jonathan: no, extrapolating from current pace
Arthur: would like to see a schedule
Jonathan: would like to set up a
time to test each other's endpoints in the week of Jan
... looking for a 4-6 hour time window
... if we can do that by the end of January, it's going to take about 2 weeks to get to the Director's call
... it would go to the AC in two weeks, then the AC gets 4 weeks
... so ~10 weeks from the hand-off to REC
... so we are looking for Recommendation at the end of April
... may need to add a few weeks to address any issues, rewrite test cases, etc.
... e.g. issues with gzip transfer coding
... would like to send LC comments through the working group
... only substantial comment is (4) in http://lists.w3.org/Archives/Public/www-ws-desc/2007Jan/0011.html
... does anyone else plan on reading the document and send comments? deadline is next Friday
Paul: people can comment outside of the WG too
Jonathan: my comments were not
WSDL specific, really
... in WSDL we make special provisions for multiple inline schemas
... would like such a schema not to be flagged as violating any patterns
<scribe> ACTION: Paul to report back on which test cases in the WSDL test suite fail the basic patterns, with suggestions on how to address the issues [recorded in http://www.w3.org/2007/01/04-ws-desc-minutes.html#action02]
Jonathan: Policy last call comments by Charlton
Charlton: main issues are policy
intersection and security considerations
... also "policy expression (4)" is not editorial
Asir: how many comments are WSDL-related?
Charlton: 3
... "XML Element Attachment" (a note), already filed issues for two other ones
Jonathan: potential issue in the item under "Policy Expression (4)"
Charlton: theoretical interest in
defining an abstract policy for improved sharing
... analogy with interface/class relationship
Asir: policy doesn't deal with assertions
Charlton: placeholders for
... offers to write up some examples
Monica: idea from BPEL TC; it's a template with placeholders
Jonathan: it looks like a general
policy issue, not a policy one
... any other substantial issues we can look at today?
Charlton: no
<scribe> ACTION: Charlton to come up with a list of editorial comments and WSDL substantive issues [recorded in http://www.w3.org/2007/01/04-ws-desc-minutes.html#action03]
Philippe: it's still useful to let them know that there is interest from the group in an issue
<monica> +1
Jonathan: any news?
<asir> Jonathan, I am signing off
Philippe: XMLP WG meets on Wednesdays
Jonathan: postpone the issue till next week
Youenn: issue with special
characters in parameters
... hard to parse the URI in that case
... possible solution escape these characters or just urlencode all parameter values
Philippe: currently we don't do
any escaping
... last time we discussed this, we decided not to do anything about it
Jonathan: is it a duplicate issue?
Philippe: duplicate of CR053
<plh> http://lists.w3.org/Archives/Public/www-ws-desc/2006Jul/att-0001/20060629-ws-desc-minutes.html#item06
Philippe: url escaping happens at the transport layer
Arthur: you can prevent "/"s by defining your own type
Jonathan: or use NMToken
Arthur: even if you encode a
slash, when the URL is decoded how do you reconstruct the
parameter values?
... we'd have to define a particular escaping
Jonathan: unclear when to encode things, except to prevent illegal characters
Arthur: encoding won't by itself
fix the problem
... are we going to have a primer example of constraining the schema type?
Jonathan: # could make the URL
invalid too
... 2 #s seem to be invalid
Tony: are there any security issues?
<plh> http://lists.w3.org/Archives/Public/www-ws-desc/2006Sep/0034
Philippe: nothing beyond what the URL spec already handles
<plh> "No percent-encoding mechanism, as
<plh> defined in section 2.1 of RFC 3986, is performed on the replacement
<plh> value. "
<pauld> notes this is a common issue, Microsoft Outlook Webmail constructs URIs from the subject line, which generates URIs you can't dereference with mails sent with '+' and '&' in the title
Jonathan: restricting schema types is a partial solution, won't work well for book titles with whitespaces
Philippe: whitespaces will get
encoded on the wire
... but there can be information loss
Jonathan: don't want to force
users to encode data themselves
... should we mandate or allow an escaping mechanism? what about precluding slashes (which we won't be escaped in any case)?
Arthur: no need to exclude anything, it can be done via a schema type
Jonathan: "The%20Bible" in user data would be bad
Arthur: distinction between what's legal in an URI and how URIs are transported
Jonathan: xs:anyURI allows more characters than the URL spec does
Arthur: even in ASCII, to parse a URL you have to know about the special characters
Jonathan: are spaces even an issue?
Arthur: some research needed
Jonathan: with slash, couldn't I
have a full URI in the data and the template contain just one
... http:location="{foo}"
<plh> [[ As a consequence, if
<plh> this IRI is an absolute IRI, the {address} property of the Endpoint
<plh> component is ignored. ]]
Jonathan: need to clarify if the
absolutization of the URI precedes or follows parameter
... the results can be different in the two cases (e.g. with .. in the parameter value)
... multiple issues
... if we allow slash characters, the resulting URLs may be ambiguous
... preference is not to outlaw this case
Arthur: we could require the serialization from XML to URI to be invertible
Jonathan: don't want to mandate
... e.g. the case of existing services which I'd like to describe
... it's the use cases of WSDL as a general HTTP description language
Arthur: we could define a more
constrained URI style
... leave the URI style as-is and define a new style which guarantees invertibility
Jonathan: it seems hard to define such a style in general terms
Arthur: we can do it in a fairly direct (but constraining) way
Youenn: it may be too complex
<scribe> ACTION: Jonathan to analyze CR117 further [recorded in http://www.w3.org/2007/01/04-ws-desc-minutes.html#action04]


text:
Ever since they sailed their clipper ships to China two centuries ago with cargoes of opium, foreign traders have brimmed with optimism about the potential of the vast China market. These days, however, on the first anniversary of the bloody suppression of the democracy movement, the flush of optimism is gone, along with much of the business.
While only a handful of American corporations have closed their doors and left China since the crackdown last June 4, and a few newcomers have set up shop, many companies say business is more difficult than ever, and in some cases slower than they had expected it would be.
For most traders with sales offices in China, business is in a deep slump.
''We feel that things just have to get better,'' said a foreign business executive in Beijing. ''But I can't say we're past the bottom of the cycle.''
Curbs on Imports and Credit
Executives say these hard times stem from the austerity program China began in the fall of 1988 and intensified last summer, with the Government clamping down on imports and on credit to local companies.
But beyond that, they say the violent crackdown last year and the mixed signals about economic liberalization since then have made it nearly impossible to assess China's political risk with any confidence.Continue reading the main story
Doing business in China has always been difficult, particularly because China's bureaucracy often requires myriad steps and approvals before any agreement can be signed. Collecting and confirming seemingly simple information, like the amount of a new tariff, can often lead a company through a maze of bureacratic red tape without a definitive answer.
Sales Have Decreased
Now China has tightened credit, cutting off funds to many Government entities and industrial enterprises that would otherwise purchase from American companies, and so sales of American products are down.
For many foreign companies, this year has been marked by other obstacles, further tainting the business climate. Some obstacles, like martial law, are being removed. But in the meantime China has recentralized its decision-making process, so that the central Government and not just the local authority must agree to certain investment and trade proposals. This has created a more difficult and confusing investment environment.
It is also unclear how long China's leaders will stall decisions on economic changes, especially in such areas as freeing prices and expanding stock ownership. Many foreign companies had pinned their hopes on a more market-oriented business environment in China. Now, greater uncertainty about the direction of economic policy and about political stability has led many companies to cancel or postpone plans for expansion in China.
Expansion Ruled Out
''We didn't set up any expansion plans before June 4,'' one executive said. ''But of course after June 4, we wouldn't even consider it.''
The freeze on lending by the World Bank has also meant that loans from foreign institutions are few and far between, and business for bankers has slowed so much that two of the four American bank representatives in Beijing have been reassigned outside China. For many foreign bankers who remain here, much of their time is absorbed with loan problems, primarily hotel loans that need to be renegotiated because the debtors have not been able to meet their obligations.
''I guess I was wrong because I thought things would have picked up,'' one foreign banker said. ''I've been disappointed too many times this year.''
Optimistic, but Restrained, Talk
Traders and corporate executives prospecting for lucrative investment possibilities have returned to China, and they fill the hotel coffee shops with optimistic, if restrained, talk of business. But the current economic recession in China has made prospects grim for new business and investment in the future.
''We're not seeing any new ideas in the pipeline,'' said John T. Frisbie, director of the United States-China Business Council in Beijing. ''For traders, it'll be lean business years unless there is a significant change in trade policy.''
In the first quarter of this year, American companies signed 65 investment contracts worth $48 million, according to statistics from China's Ministry of Foreign Economic Relations and Trade. The ministry has not publicized comparable quarterly figures for previous years, but other statistics show that the latest figure is far below the level in the past.
In the first six months of last year, for example, American corporations signed contracts worth $382 million. That was nearly three times the new investment for the same period in 1988. At the end of 1989, the total amount of American contracts for investment projects was about $4 billion, an increase of about 20 percent over the amount at the end of 1988.
Investing Smaller Amounts
Industry executives say there are isolated cases of American and Japanese companies that are considering large investment projects of about $100 million. But in general, companies are investing smaller amounts -an average of $700,000 in the first quarter - and negotiations on contracts sometimes have become more cumbersome and protracted during the last year.
''The Chinese are generally strapped for money, so negotiating is as hard as it ever was before, and they are trying to extract as many concessions as they can,'' said Timothy A. Steinert, an American lawyer in Beijing who helps negotiate some deals.
Mr. Steinert added that there seemed to be a rising number of commercial disputes, as American companies become more willing to go to arbitration instead of turning a blind eye to what they believe are contract violations. ''Problems that were swept under the rug before are now becoming conflicts,'' he said.
American Exports Down
United States trade statistics show that American exports to China had been on the rise, jumping 16 percent, to $5.7 billion, in 1989. The exports fell a percentage point during the first two months of 1990, to $876 million, compared with the same period a year ago.
Some companies say they expect the rest of the year to bring more business, and most companies in industries that China is strategically encouraging, including energy, telecommunications and transportation, say they are still closing sales. But most trade representatives say the last year has been a struggle, and they are cutting costs where they can to offset reductions in revenues.
The IBM China Corporation, for example, one of the most visible foreign companies in China, now has 100 employees in its office, compared with 127 a year ago. Many other companies have reduced their sales staffs and representatives. And most joint-venture hotels have cut down their expatriate staffing and electricity costs.
''The double whammy of economic retrenchment and political shock took the romance out of China,'' a Western diplomat said. ''It takes a lot of vision and staying power to remain here.''Continue reading the main story


text:
I love…
that he reads my mind and brings me kombucha. I'd been craving it all morning, and what do ya know, dlb shows up at my office with a bottle of Guava Goddess. love that guy. and kombucha. seriously, I'm totally hooked. our kombucha habit is an expensive one and I've tried to cut back, really. but it's so darn good.
I've been wanting to try making my own. has anyone made their own kombucha? if so, what were your experiences? I'd love to know.
{photos: left – these days in french life, right bogenswb}


text:
- Research article
- Open Access
High-throughput identification of interacting protein-protein binding sites
© Chung et al; licensee BioMed Central Ltd. 2007
- Received: 21 December 2006
- Accepted: 27 June 2007
- Published: 27 June 2007
With the advent of increasing sequence and structural data, a number of methods have been proposed to locate putative protein binding sites from protein surfaces. Therefore, methods that are able to identify whether these binding sites interact are needed.
We have developed a new method using a machine learning approach to detect if protein binding sites, once identified, interact with each other. The method exploits information relating to sequence and structural complementary across protein interfaces and has been tested on a non-redundant data set consisting of 584 homo-dimers and 198 hetero-dimers extracted from the PDB. Results indicate 87.4% of the interacting binding sites and 68.6% non-interacting binding sites were correctly identified. Furthermore, we built a pipeline that links this method to a modified version of our previously developed method that predicts the location of binding sites.
We have demonstrated that this high-throughput pipeline is capable of identifying binding sites for proteins, their interacting binding sites and, ultimately, their binding partners on a large scale.
- Support Vector Machine
- Protein Pair
- Accessible Surface Area
- Surface Residue
- Interface Residue
Protein-protein interactions are essential to most biological processes, for example, signal transduction, hormone-receptor binding and immunological recognition. These processes comprise complex cellular protein interaction networks that are becoming increasingly accessible in the post-genome era of high-throughput proteomics. Experimental methods such as mass spectrometry, phage display and yeast two hybrid have been developed to quickly identify interactions between proteins in various organisms [1–4]. Concurrently, computational approaches exploiting amino acid properties, genomic and evolutionary information [5–13] have been proposed to determine whether proteins interact or not (binary interactions). While both large scale experimental and computational methods are known to produce many false positive and false negative predictions, the combination of using several methods may provide more reliable results. The idea of using consensus results is not new and has been used in the meta-servers for structure prediction, generating consensus models according to the results of several prediction servers [14]. Here we provide a new approach to the computational prediction of interacting protein-protein binding sites which can contribute to this greater accuracy [1].
Thanks, in large part, to the availability of increasing sequence and structural information, various computational methods have been proposed to identify putative protein-protein binding sites utilizing evolutionary relationships [15–19], properties of surface patches [20, 21], residue hydrophobicity [22], etc. Recently, machine learning approaches such as neural networks [23–26], support vector machines [27–31] and Bayesian network [32] have been used to distinguish interface residues from non-interface residues based on sequence and structural properties.
All of these methods locate binding sites from protein surfaces, but none of them provide information about their binding partners (binding specificity). Therefore, methods that identify interacting protein binding sites are necessary. Inherently these methods would then allow more reliable determination of binary interactions. Docking approaches provide this information by predicting the binary complex of two known structures based on energetic or geometric complementary [33, 34]. However, long computation time is often required to determine each putative complex and most docking approaches are limited to rigid protein model analysis. Homology modeling [35] and multimeric threading [36] build an atomic model of a complex based on a template structure using sequence alignments. These two methods have been tested on large scale data sets [37, 38]. They both rely on the limited number of structure templates of complexes [39] and usually require sequence identity above 30% between homologs [40, 41]. Aytuna et al. [42] predicted protein-protein complexes by seeking pairs of proteins that share structurally and evolutionarily conserved residue similarity to 67 template interfaces. Pazos et al. [13] utilized correlated mutation for determining pairs of proteins that are likely to bind and also identified binding sites concurrently. Although structural information is not required for this method, a large set of multiple sequence alignment for each possible pair of proteins is needed.
Results and discussion
The contact preferences of interface residues
Ofran et al. have reported significant differences in residue composition and contact preferences between interfaces of hetero-obligomers, hetero-complexes, homo-obligomes, and homo-complexes [49]. In our data set, some differences between homo-dimer and hetero-dimer interfaces have also been observed. There was a higher tendency for hydrophobic-hydrophobic interactions in homo-dimers. On the other hand, more salt bridges and fewer contacts between residues with the same charge were preferred in hetero-dimers.
Several previous studies have provided detailed analysis of interaction preferences of different types of protein-protein interfaces in terms of amino acid, secondary structure or other properties [47–51]. The results of those previous studies and our studies show some variations because of the different composition of data sets and the definition of the interface residues. Nevertheless, the survey presented here indicates that information from sequence profile, secondary structure and accessible surface area (ASA) may be useful discriminators for defining contacting interface residues and can be captured by SVM predictors.
Identification of interacting binding sites using support vector machines
Prediction performances
We then evaluated the prediction method exploiting structural information. At a surface patch size of 1 (Figure 7(b)), incorporating information of secondary structure with the sequence profile increased the prediction accuracy significantly. However, further incorporation of information on the accessible surface area did not result in any additional improvement. As we increased the patch size to 3 (Figure 7(c)), we noticed that secondary structure and ASA had no impact on prediction. Therefore, for this study, we chose a sequence profile with a patch size 3 as the default input features.
The prediction performances
Accuracy for interacting binding sites, also known as recall (%)
Accuracy for non-interacting binding sites (%)
Average accuracy (%)
Precision (%)
Mix1 (sequence window)
Mix1 (putative binding sites)
The surface patch used here included only the two nearest surface residues, which are very likely to be located in the same sequence segment. For this reason we further performed a trial using the sequence profile with a window size 5 in sequence (that is, including 4 sequentially nearest residues). As expected, the ROC curves in Figure 7(a) indicates that the predictor using sequence information only was able to perform similarly to the predictor using a patch size of 3. At a threshold of 56%, 88.7% of interacting binding sites and 63.3% of non-interacting binding sites were correctly assigned. When the average accuracy reached its maximum (threshold: 64%), 78.5% of interacting binding sites and 76.9% of non-interacting binding sites were correctly assigned.
In this study, two binding sites were predicted to interact with each other if >56% of the total possible residue pairs between them were predicted to be in contact with each other. Raising the threshold increases the precision but decreases the recall (assigns less interacting binding sites and more non-interacting sites) and vice versa. In the data set, the contacting residue pairs for two interacting binding sites constituted, on average, only approximately 8% of the total possible residue pairs. Therefore, the threshold (56%) selected above seem to be very high. However, when we considered the 3 spatially nearest residues of each any two contacting residues to be in contact with each other across the interface, the fraction of contacting residue pairs out of the total possible residue pairs increased to 47%.
Predictions on putative binding sites
A pipeline was built to test if two putative binding sites would interact with each other (Figure 1). Given two proteins A and B, the pipeline first identifies the putative binding site of each protein (with predictor I) and then identifies the interaction between the two putative binding sites (with predictor II, which is the method presented in this study). This pipeline is able to provide information on both the location of binding sites and their binding partners.
Putative binding sites of individual components of each complex in our data set were determined by a method modified from our previous work, using sequence and structural information [29] (predictor I, see methods). With this method, the recall was 65.6% and the precision was 45.2% at the residue level. The results are summarized as follows: 49.81% of the binding sites were precisely predicted, 71.30% of the binding sites were correctly predicted and 23.6% of the binding sites were partially covered by the predicted residues. If at least 70% of the residues at a site were identified, we defined this to be precisely predicted. If at least 50% of the residues at a site were identified, we considered this to be correctly predicted.
The pipeline consists of binding site identification (predictor I) and subsequent prediction of whether two of these identified sites interact (predictor II). Since predictor II depends little on spatially neighboring residues and is mostly sequence dependant, a sequence only predictor I could be substituted [19, 42].
We have developed a new method to predict interacting protein binding sites using a machine learning technique. To the best of our knowledge, this method is the first trial that predicts interacting binding sites without the constraint of using structure templates. An SVM was trained to learn the complementary information across interfaces and has been tested on a data set consisting of 584 non-redundant homo-dimer and 198 hetero-dimer interfaces. Our predictor successfully identified 87.4% of the interacting binding sites and 68.6% of the non-interacting binding sites. Separate training and testing on homo-dimers and hetero-dimers showed different prediction results, which might be caused by the differences in residue contact preferences between these two types of interfaces. For homo-dimers, 96.4% of the interacting binding sites and 67.5% of the non-interacting binding sites were correctly identified. For hetero-dimers, 66.3% of the interacting binding sites and 62.8% of the non-interacting binding sites were correctly identified. Better predictions are expected as more structures are determined and the number of homo-dimer and hetero-dimer complexes upon which to train increases.
We built a pipeline combining the method discussed here to a modified version of our previously developed method that identifies the location of binding sites. Taking both predictors together we showed that the prediction accuracy that were based on putative binding sites only decreased slightly over accurately known sites. Thus the pipeline enables the simultaneous prediction of binding sites and binding partners, identifying 87.3% of the interacting binding sites and 67.6% of the non-interacting binding sites in our data set. In the future, the pipeline can be used to search new protein binding sites and interactions in various biological systems, and therefore build interaction networks based on interaction details between proteins. It can also be used to validate existing networks.
At this time it is difficult to compare the results presented here with those of other methods since each uses different training sets and there is a lack of a common test set [41]. In addition, most existing methods have not been tested on negative data and hence prediction statistics (precision, recall, etc.) were not provided. Nevertheless, different methods have different limitations and exploit different information to various extents. For example, most docking procedures are computational expensive, homology modeling and multimeric threading rely on the availability of complex structure templates and correlated mutation methods need a large set of sequence alignment for each possible protein pair. Current efforts are directed at attaining higher prediction accuracy through incorporation of additional information such as local interface geometry or water mediated interactions into our predictor.
Data set
A non-redundant data set of dimer complexes was compiled using the method of Zhou et al. [26] modified as follows. All non-NMR multiple-chain protein entries with resolution better than 3.5 Å were collected from the PDB (March, 2004) [43]. For each entry, two chains were selected as an interacting protein pair if both have more than 20 residues that formed interfacial contacts with each other. A residue was considered to form an interfacial contact if the distance between any of its heavy atoms and any heavy atoms of its interacting proteins were <5 Å. The pairs containing chains with < 80 amino acids or SCOP class >= 8 were then filtered out.
Each of the collected chains was further compared against all other chains by BLAST. Chains were assigned to the same cluster if the sequence identity was > 30% and > 90% of the amino acids were aligned. All interacting protein pairs were mapped to these clusters and the representative pairs were selected. In order to consider dimers only, the representative pairs with chains interacting with more than one chain were discarded. Homo-dimers with both chains having > 30 interface residues and hetero-dimers with both chains having > 20 interface residues were collected, in order to roughly exclude those from crystallographic complexes [30]. This resulted in a non-redundant data set of 584 homo-dimers and 196 hetero-dimers. The data are available upon request from the authors.
The calculations of contact preferences of interface residues
We have surveyed the preferences of contacts between different groups of interface residues. We classified the residues into 20 groups in terms of amino acids, 3 groups in terms of secondary structures (alpha helix, beta strand, and others, including coil) and 2 groups in terms of the extent of water exposure (fully exposed: ASA >= 40% of a residue's nominal maximum area [59]; partially exposed: 15% <= ASA < 40%). The secondary structure and ASA of residues for each protein chain were calculated using the DSSP program [60] with the coordinates of a single chain obtained from the corresponding complex structure.
The contact preference (L) for interface residues from group a and group b was calculated as follows [49]:
L(a, b) = F observed (a, b)/F expected (a, b)
where the observed contact frequency was defined as:
F observed (a, b) = N observed (a, b)/N total
and N observed (a, b) was the number of contact residue pairs between residue group a and group b. N total was the total number of all contacting residue pairs. The expected contact frequency was defined as:
F expected (a, b) = F(a) × F(b)
where F(a) and F(b) were the frequency of residue group a and group b at interfaces respectively. In this study, a residue was defined as a surface residue if its ASA was at least 15% of its nominal maximum area [59]. A surface residue was defined to be an interface residue (residue at a binding site) if it formed an interfacial contact. The definition of interfacial contact was described in the data set section.
Support vector machine (SVM) classifiers
The SVMs were trained to predict if two binding sites interact with each other. The SVM software used in this study was SVM light [61]. The radial basis function exp(-γ||b - a||2) was chosen as a kernel with γ = 0.01 and regularization parameter C = 10.
During the training process (Figure 5), two interface residues, each from interacting binding sites, were considered to form a contacting residue pair (positive class) if the distance between any of their respective heavy atoms was less than 5 Å. A non-contacting residue pair (negative class) was defined as any possible interface residue pair between two non-interacting protein binding sites (binding sites from two non-interacting protein chains). Non-interacting protein chains were generated from our data set having determined that two proteins were not reported to be in the same cellular location as defined by the UniProt database [62]. Since the number of non-interacting protein pairs greatly outnumbered the number of interacting protein pairs, we randomly selected a small portion out of the large pool to be representative data, making the number of non-interacting protein pairs equal to the number of interacting protein pairs. For example, for the combined data set of homo-dimers and hetero-dimers, there were 780 interacting protein pairs. The number of all possible non-interacting protein pairs was 460070. 780 non-interacting protein pairs were further randomly chosen from this pool.
To reduce the data redundancy and training time, for each binding site residue with multiple contacting residues at the other site, only the pairing with the smallest distance was selected to be included in the positive training set. Since there were many more non-interacting residue pairs than interacting residue pairs, a set of non-interacting residue pairs was randomly selected so that the ratio of positive to negative data was 1:1.
The SVM was fed two surface patches, each included a residue of an interface residue pair and its n spatially nearest surface residues (n was an adjustable parameter). The input features were different combinations of sequence profile, secondary structure and accessible surface area of residues in these 2 surface patches. If all three input features were used and surface patch size was set to 3, each residue pair was encoded as a feature vector with a dimension of 2 × 3 × 24: 2 × (the surface residue to be predicted + 2 nearest neighbors) × (20 amino acids + accessible surface area + 3 types of secondary structure). The sequence profiles were obtained from 3 iterations of a PSI-BLAST search against the NCBI non-redundant database (NR) with e = 0.001 and h = 0.001 [63]. The 3 categories of secondary structure were: alpha helix, beta sheet, and others, including coil regions (encoded 1 if it was in this category and -1 if it was not). All input values were scaled between -1 and 1.
During the testing process (Figure 6), two binding sites A and B were predicted to interact with each other if the number of positively predicted residue pairs between them were above a certain threshold:
N predicted ≥ P% × N total
where N predicted is the number of positively predicted residue pairs. N total is the number of total possible residue pairs between binding sites A and B. Given the threshold, the prediction performance was measured as follows:
Precision = TP/(TP +FP)
Accuracy for positive class, or recall, or true positive rate = TP/(TP + FN)
Accuracy for negative class = TN/(TN + FP)
False positive rate = FP/(FP + TN)
Average accuracy = (TP + TN)/(TP + TN + FP + FN)
where TP is the number of correctly predicted interacting binding sites, TN is the number of correctly predicted non-interacting binding sites, FP is the number of non-interacting binding sites incorrectly predicted to be interacting and FN is the number of interacting binding sites incorrectly predicted to be non-interacting.
Identification of the putative binding sites
The putative protein-protein binding sites were determined by a method modified from our previous work [29]. A SVM was trained to locate binding site residues on a protein surface by using sequence profile and accessible surface area of spatially neighboring surface residues. 976 non-redundant chains (584 chains from one of the components of homo-dimers, and 196 × 2 chains from both components of hetero-dimers) were trained and tested with 2 fold cross validation. Each of the other component of a homo-dimer was tested by the training set which didn't contain its homolog. The residues ranked as the top 30% by SVM were further clustered using the clustering method described in [29].
This work was supported by NIH grants GM63208 and GM08326.
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Over the years since Amon Düül II released Yeti (it was 1970, in case you forgot), quite a number of listeners have noticed that "Archangel's Thunderbird" is a really catchy song. Here's a recent cover of it as a reminder.
by Jon Davis, Published 2015-08-25
Filed under: Video
Related artist(s): Amon Düül I / II, Cary Grace
Help MoonJune Bring Great Music to Life – Like many music lovers around the world, we've been thrilled and amazed to hear the recordings that have been released by MoonJune from sessions at La Casa Murada in Spain. Such label stalwarts as Mark Wingfield, Markus Reuter, Asaf Sirkis, Tony Levin, Dusan Jevtovic, Vasil Hadzimanov, and many more have gathered in various combinations at the studio to produce some of the most creative music in recent years. Now, label head Leonardo Pavkovic is offering a compilation, La Casa Murada - MoonJune Sessions, Volume One, as a fundraiser for upcoming sessions. » Read more
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Freedom to Spend Unearths June Chikuma's Archives – Jun (June) Chikuma is well known for her video game and anime soundtracks, but she also released an album of experimental electronic music back in 1986 called Divertimento where she indulged the kind of spontaneity that wouldn't work in a soundtrack. RVNG Int'l label Freedom to Spend is bringing this overlooked item to broader attention with a deluxe reissue. » Read more
Seaprog 2019 Lineup Almost Complete – The Seaprog festival in Seattle is scheduled for June 7-9 this year, and they've announced their lineup of performers. The revitalized Trettioåriga Kriget will cap Friday night, perennial favorites Marbin are on Saturday, and District 97 will finish off the fest on Sunday night. In support, they've booked a stellar variety of artists from the Northwest and around the world, including EchoTest, Markus Reuter and Trey Gunn, and the live debut of the amazing Troot project. » Read more
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Hecenia - La Couleur du Feu – If you've ever heard Hecenia's first album, Légendes from a few years ago, with vocals, drum machines, and all, you might want to push all that out of your mind now. This new album is... (1995) » Read more
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Steve Hackett - Genesis Revisited – After Steve Hackett left Genesis in 1977, he continued to create imaginative music while his cohorts gradually faded into a massive commercial success. With the Genesis of old long gone, Steve returns... (1997) » Read more


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by William
(Kent, Wa. )
Our blue and gold macaw "Sunshine" bites his claws and actually acts like he gets mad at them.
Why would he do this? Does he need some special vitamin or mineral he could be missing. He eats very well and has a large variety of foods he likes, bird as well as people food?
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During the Second World War there was a shortage of nylon hose. I remember one old friend guarding her one good pair, keeping them in a fruit jar with the lid on tight. She wore them only on good weather Sundays and to funerals, rationing being what it was.
One Saturday while uptown, I noticed a long line, even out to the sidewalk, at Murphy's. I investigated and found a shipment of hose had just come in. They had moved the boxes to the back of the store and were selling them from there, only one pair per person. I bought mine, then went to the end of the line and bought a pair for my mother. I went again for a pair for my sister. Now as I observe the well-stocked nylon shelves and read their expensive ads, I think of that time when one good pair of nylons was really a treasure.
Florence Palmer
Marshall, Illinois
Back in 1955 a call went out from the editors of the then Capper's Weekly asking for readers to send in articles on true pioneers. Hundreds of letters came pouring in from early settlers and their children, many now in their 80s and 90s, and from grandchildren of settlers, all with tales to tell. So many articles were received that a decision was made to create a book, and in 1956, the first My Folks title – My Folks Came in a Covered Wagon – hit the shelves. Nine other books have since been published in the My Folks series, all filled to the brim with true tales from Capper's readers, and we are proud to make those stories available to our growing online community.


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New in these parts
I guess it's customary to introduce oneself, so here it is.
I live in the New York metro area and love to cook, but have never made bread in all my 39+ years until now. I love this site, and came to it because I was looking for a pizza dough recipe; pizza is, of course, the perfect food, and I wanted to make the pesto pizza that Whole Foods started to offer this year - without the hefty price tag.
I found the Pizza Primer here (http://www.thefreshloaf.com/recipes/pizza) and it was great. The pesto pizza - dough slathered with a mix of olive oil, fresh basil, garlic, salt & pepper, topped with mozzarella cheese, topped with fresh sliced garden tomatoes - was truly superb. And I loved the silkiness of the fresh dough; I still have one dough ball in my freezer, too.
In fact, I have a lunch pizza-making date this weekend with a friend who asked if I'd teach her how to make it! The blind leading the blind, essentially - but at least we have the recipe!
Anyway, I've started to make everything I eat, instead of buying anything, and have found that my expenses have essentially been halved. I've begun making cookies, cakes, and breads of all types; I've made the gingerbread, too - http://www.thefreshloaf.com/recipes/gingerbread - and that's another long-time favorite of mine. I have my eye on these bagels, too: http://www.thefreshloaf.com/recipes/bagels - but can't seem to find the malt powder.
My goal is to make everything I eat by hand - because, you know, I'm just so sick of reading those long lists of chemicals in everything - and also without electricity as I am short in the equipment area. Late to the bread game, IOW, but ardent!
Thanks, everybody, for your wonderful recipes and for this site! It's terrific.