Discerning drivers will appreciate the 2013 LINCOLN MKX. With fewer than 50,000 miles on the odometer, this 4 door sport utility vehicle prioritizes comfort, safety and convenience. It features a front-wheel-drive platform, an automatic transmission, and a refined 6 cylinder engine. A wealth of standard features means that you no longer have to sacrifice. Like heated seats, 1-touch window functionality, a tachometer, power front seats, a built-in garage door transmitter, a trip computer, an automatic dimming rear-view mirror, and leather upholstery. Lincoln ensures the safety and security of its passengers with equipment such as: dual front impact airbags with occupant sensing airbag, head curtain airbags, traction control, brake assist, a panic alarm, and 4 wheel disc brakes with ABS. With electronic stability control supplementing mechanical systems, you'll maintain precise command of the roadway. Our sales reps are extremely helpful & knowledgeable. They'll work with you to find the right vehicle at a price you can afford. Come on in and take a test drive!


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Schönox HPS North America, Inc.HPS Marketing2020-06-23T14:24:53-05:00
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Save time and money on your next job by renovating your subfloor instead of investing in costly demolition.
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Listed on the National Register of Historic Places, St. Andrews Episcopal Church was built in 1901 with a California Redwood frame and a rough-faced Virginia granite exterior. With almost 120 years of service, the church requires periodic renovation work completed with careful consideration of the structure and its historical significance. St. Andrews is one of many structures financed and organized by Grace Arents, a Christian activist and philanthropist working at the turn of the 20th century. While a strong subfloor and new floor covering were desired, the project goals also called for minimal impact on the structure. The project plan
Commercial Appeal Healthcare Conversion
Like several commercial facilities across the U.S., the four-story, 140,000 square foot, Commercial Appeal newspaper office and production building was converted for healthcare use in the wake of the COVID epidemic. The Commercial Appeal building's historic property location has been home to three Memphis newspapers including Commercial Appeal, as well as a Ford Model T factory. The most recent building on the site saw decades of newspaper office and production use with massive printing presses. U.S. Army Corps of Engineers and Tennessee Emergency Management Agency spearheaded the initiative with aggressive timelines for all facets of the project. The subfloors throughout
Green Bay's Hotel Northland
Listed on the National Register of Historic Places, Hotel Northland opened in Green Bay, Wisconsin, on March 21, 1924, as the largest hotel in the state. For more than 50 years, Hotel Northland, with its status as a boutique hotel well-appointed with the most luxurious amenities, served as the social hub of Green Bay.
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redpajama_set_name: RedPajamaCommonCrawl


text:
Q: C++\Win32 API - Difference between WC_BUTTON and "BUTTON" window classes Is there a difference or is it as simple as #define WC_BUTTON "BUTTON"? Also, if I use InitCommonControlsEx in place of InitCommonControls, do I still need to include a manifest?

A: Yes, its as you say:
CommCtrl.h

// Button Class Name
#define WC_BUTTONA  "Button"
#define WC_BUTTONW  L"Button"

You still need a manifest if you use InitCommonControlsEx as you need to use V6 of the common controls.

redpajama_set_name: RedPajamaStackExchange


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Dibaginjigaadeg Anishinaabe Ezhitwaad: A Tribal Climate Adaptation Menu
Title Dibaginjigaadeg Anishinaabe Ezhitwaad: A Tribal Climate Adaptation Menu
Authors Team, Tribal Adaptation
Pagination 54 p
Institution Great Lakes Indian Fish and Wildlife Commission
City Odanah, Wisconsin
Keywords adaptation, adaptation workbook, climate change, tribes
Abstract Climate change has impacted and will continue to impact indigenous peoples, their lifeways and culture, and the natural world upon which they rely, in unpredictable and potentially devastating ways. Many climate adaptation planning tools fail to address the unique needs, values and cultures of indigenous communities. This Tribal Climate Adaptation Menu, which was developed by a diverse group of collaborators representing tribal, academic, intertribal and government entities in Minnesota, Wisconsin and Michigan, provides a framework to integrate indigenous and traditional knowledge, culture, language and history into the climate adaptation planning process. Developed as part of the Climate Change Response Framework, the Tribal Climate Adaptation Menu is designed to work with the Northern Institute of Applied Climate Science (NIACS) Adaptation Workbook, and as a stand-alone resource. The Menu is an extensive collection of climate change adaptation actions for natural resource management, organized into tiers of general and more specific ideas. It also includes a companion Guiding Principles document, which describes detailed considerations for working with tribal communities. While this first version of the Menu was created based on Ojibwe and Menominee perspectives, languages, concepts and values, it was intentionally designed to be adaptable to other indigenous communities, allowing for the incorporation of their language, knowledge and culture. Primarily developed for the use of indigenous communities, tribal natural resource agencies and their non-indigenous partners, this Tribal Climate Adaptation Menu may be useful in bridging communication barriers for non-tribal persons or organizations interested in indigenous approaches to climate adaptation and the needs and values of tribal communities.
URL http://www.glifwc.org/ClimateChange/TribalAdaptationMenuV1.pdf


You asked for it – we did it. For Jenkem Mix 10, Brad Cromer picked out a couple of tracks, throwing in stuff you may be familiar with, next to some more obscure tracks. A refreshing change from the predictable skateboard Rap / Rock mixes, this one has a bit of everything and that signature nostalgic dreamy vibe which is apparent in all of Brad's skate parts and his own video LOFI. If Brad isn't one of your favorites yet, he will be soon. Pinky promise.


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SB20s
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Squibs
J24s
Laser Sailing
Model Boats
Water Wag
Half Tonners
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Howth 17
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Ruffian 23
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Displaying items by tag: Bulman Buoy
A Lifetime in Kinsale Boats – Ships, Fishing, Piracy, Hanging & A Happy Ending
#islandnation – Entering Kinsale Harbour, east of the Bulman Buoy, is a prominent 200-foot cliff rising sharply above the sea. It is known as Hangman Point and was the location of a gibbet, a warning to everyone not to engage in piracy. Displayed there in 1675 was the head of one of six Irishmen who had murdered the Master and three crew aboard what was described as "a very rich ship," the St.Peter of Hamburg which had been bound for France. This gang sailed the vessel to the West Coast of Ireland where they were captured by the authorities led by Robert Southwell, Vice Admiral of Munster. Convicted and executed, their heads were displayed at different points along the coast, including one at Hangman Point.
The next time I am rounding the Bulman heading for Kinsale I'll take more note of Hangman Point about which I hadn't known a lot, though I did know of the roadside reminder out towards the Old Head of Kinsale of the female pirate Anne Bonney, another story of piracy from the locality. She was actually Anne Cormac, described as "a vivacious girl" who lived with her father, William, in a fine house on the edge of Bullen's Bay which was a haven for piracy on the south coast not far from Kinsale, providing a place to land stolen goods and get water and provisions.
She shared the maritime activities of the area, but her father was actually a successful Cork lawyer who emigrated from that area to the Carolinas in America where the doughty daughter was drawn to the sea, despite the best efforts of her father to steer her in other directions. This led her to falling for the charms of pirate and buccaneer 'Calico' Jack Rackham who was terrorising the coast of Bermuda.
Anne took to the life of piracy, engaged in it by boarding ships and capturing and looting them and was regarded as a tough fighter. Despite pregnancies, she had her children fostered to continue her cutlass-bearing life. Captured eventually, both 'Calico' and Anne were sentenced to hang. Because she was again pregnant she was reprieved and her last words to 'Calico' before he faced the hangman, according to legend were: "If you had fought like a man, you would not now be hanged like a dog!"
I am not sure I would particularly like such a female type aboard, but out towards the Old Head of Kinsale there is a roadside plaque reminding passersby of Anne Bonney.
The story is told by John Thullier, well-known in the maritime world and in sailing after a lifetime involvement with boats. He is the retired Director of Kinsale Further Education College and steeped in the maritime tradition of the town. The College evolved from projects designed to introduce the maritime environment to students and providing training in marine skills.
He has compiled the history of Kinsale Harbour and told me how, on walks around the seafront of the town with his grandfather who was a good boat builder timber needed would be spotted, with it all explained to him as a youngster about what a boat needed to be sturdy. John recalled to me how Sundays were the day of leisure, so the men would go sailing and, "in soft hat and with shirt and tie!" Those were times when there was a different approach to sailing clothing!
"Kinsale Harbour – A History," published by The Collins Press, was launched this week at Kinsale Yacht Club. In it John Thullier charts the history of a town now known best for its tourism and food, but which he says must retain its focus of being a port and a maritime location.
Nestling on the River Bandon as it sweeps to the sea, Kinsale emerged as a settlement in the 6th century and has seen many changes.
"Really there are three harbours here, the inner, the middle and the outer and Kinsale has changed over the years as it evolved to meet the many challenges," he said as we chatted overlooking the harbour from the front of the Trident Hotel where the statue of a fisherman, resting and thinking, reminds patrons that this too was once a big fishing port and still retains fishing boat activity.
"The harbour has always provided a safe anchorage and prospered during the golden age of sail, victualling shops bound for the American colonies, the West Indies and trading with English and Continental ports. Many people will remember it for the Battle of Kinsale, but there is much more to the town and the maritime tradition is its main reason for existence. There was a Naval base to restrict threats of foreign invasion, there were pirates and smugglers, it was a shipping port, it evolved when the size of ships changed, it was a big fishing industry centre, that changed too as the industry and stocks moved. It still retains some fishing and it became a sea angling centre which gave it a new life.
Now it is still very active in the marine, as a sailing centre. There have been difficult times here in Kinsale, but the way a town like this survives is to focus on what it has best, that is the maritime role, its maritime resources and facilities."
Even where we sat talking about Kinsale, where the Trident Hotel stands, he told me was once a dockyard.
"My mother's family was involved in the fishing industry, on my father's side the family were boatbuilders, owners and members of various boards and public bodies engaged in the affairs of the harbour.
"The story of Kinsale is the history of its connection with the sea. Everything about Kinsale is of the sea and so it should remain," says John Thullier, whose book about this major sailing location is well worth reading.
And if you want to know what happened to Anne the pirate, John Thullier says:
"No precise information is available about her after Rackham's hanging. There are reports that she abandoned piracy, was reconciled with her father, remarried and had eight more children."
I like a happy ending!
Twitter: @TomMacSweeney
Published in Island Nation
This island nation
Bulman Buoy
John Thullier
Cork Institute of Technology Win 2010 Student Yachting Nationals
Last weekend saw the Student Yachting Nationals take place at the Royal Cork Yacht Club. The students had the use of the ISA J80 Sailfleet for the event. Six college teams entered for the Nationals which was the Qualifier for the Student Yachting World Cup 2011.
Racing was scheduled for Cuskinny on Friday and conditions were ideal with 17-20 knots of breeze. Race Officer, Nathan Kirwan, got in four good races lasting some 40 to 50 minutes each. However, spinnakers were banned as some wipeouts had been observed by the ISA Bosun who exercised his judgment in this regard. Some two minutes after the start of the first race UCC skippered by Robert O'Leary suffered a snapped halyard but were refused redress. CIT skippered by George Kenefick lost their only winch handle overboard some three minutes before the start in race 1 but still managed to win the race by a comfortable margin. In race 2 UCC came back strongly to take the gun and pushing CIT into second place. At this stage match racing had begun between the two Cork colleges with each throwing dummy tacks to try to clear their air. In Race 3 TCD skippered by Alistair Kissane took the win with CIT in second and UCC third. The final race of the day was won by CIT with UCC third. Overall standings for Day One were: CIT 6pts, with UCC and TCD on 12 pts each. UCD had got off to a shaky start which was to prove costly for them as they were on form on days two and three.
On day two the Race Officer moved the course to the Curlane Bank and spinnakers were permitted. CIT found their rythym taking the bullet in race 5 with UCD in second and a poor mark rounding relegated UCC to third place. Race 6 saw the O'Leary and Kenefick teams doing circles at the pre start as the competition was intensifying and it was looking like a two horse race. UCC took first place with NUIG taking second and CIT third. Donagh Good of CIT went for a quick dip in the cold water but managed to grab on and was pulled back on board by George Kenefick and Kevin Goulding. Later during day 2 the wind was rising to 22 knots so spinnakers were once again banned. UCC found the conditions very much to their liking, taking the win, with TCD in second, UCC third and CIT fourth. Race 8 proved to be rather interesting with CIT managing to relegate UCC to last position and managing to keep UCC in their sight for the duration of the race. Downwind was difficult for CIT with UCC right on their tail but UCC were not successful in finding a passing lane. Again, UCD took their second bullet of the day with CIT and UCC in fifth and sixth positions some four to five minutes behind the rest of the fleet. CIT were able to discard their fifth position but UCC were unlucky in having to count their sixth as they also had a sixth from day one. TCD again got a second position. Results after day two were: CIT 14pts, UCC 19pts, UCD and TCD on 21pts each.
Day 3 was a non discardable coastal race from Crosshaven to Kinsale counting for 1.5pts. The start line was just off Roches Point with five knots of breeze and brilliant sunshine. UCC led the fleet and NUIG and CIT were in last position 300 metres behind the rest of the fleet. As the race went on the wind increased to a nice south westerly breeze of 12 to 14 knots. As this stage it looked as if it might be UCC's lucky day but Team CIT maintained their composure and by tacking close to the shore and keeping out of the tide managed to finish in third position at the Bulman Buoy with UCC first and UCD second. This result was to prove sufficient to give CIT the national student title for 2010.
Overall Results:
CIT	18.5pts
UCC	20.5pts
UCD	24pts
TCD	28.4pts
NUIG	33pts
UL	40pts
Published in Youth Sailing
Royal Cork Yacht Club
Cuskinny
Curlane Bank
NUIG
George Kenefick
Kevin Goulding
The Half Ton Class was created by the Offshore Racing Council for boats within the racing band not exceeding 22'-0". The ORC decided that the rule should "....permit the development of seaworthy offshore racing yachts...The Council will endeavour to protect the majority of the existing IOR fleet from rapid obsolescence caused by ....developments which produce increased performance without corresponding changes in ratings..."
When first introduced the IOR rule was perfectly adequate for rating boats in existence at that time. However yacht designers naturally examined the rule to seize upon any advantage they could find, the most noticeable of which has been a reduction in displacement and a return to fractional rigs.
After 1993, when the IOR Mk.III rule reached it termination due to lack of people building new boats, the rule was replaced by the CHS (Channel) Handicap system which in turn developed into the IRC system now used.
The IRC handicap system operates by a secret formula which tries to develop boats which are 'Cruising type' of relatively heavy boats with good internal accommodation. It tends to penalise boats with excessive stability or excessive sail area.
The most significant events for the Half Ton Class has been the annual Half Ton Cup which was sailed under the IOR rules until 1993. More recently this has been replaced with the Half Ton Classics Cup. The venue of the event moved from continent to continent with over-representation on French or British ports. In later years the event is held biennially. Initially, it was proposed to hold events in Ireland, Britain and France by rotation. However, it was the Belgians who took the ball and ran with it. The Class is now managed from Belgium.
At A Glance – Half Ton Classics Cup Winners
2017 – Kinsale – Swuzzlebubble – Phil Plumtree – Farr 1977
2016 – Falmouth – Swuzzlebubble – Greg Peck – Farr 1977
2015 – Nieuwport – Checkmate XV – David Cullen – Humphreys 1985
2014 – St Quay Portrieux – Swuzzlebubble – Peter Morton – Farr 1977
2013 – Boulogne – Checkmate XV – Nigel Biggs – Humphreys 1985
2011 – Cowes – Chimp – Michael Kershaw – Berret 1978
2009 – Nieuwpoort – Général Tapioca – Philippe Pilate – Berret 1978
2007 – Dun Laoghaire – Henri-Lloyd Harmony – Nigel Biggs – Humphreys 1980~
2005 – Dinard – Gingko – Patrick Lobrichon – Mauric 1968


Home » Collaborative Post » How Do I Prevent My Pup From Soiling The Carpet?
Elizabeth Gorski April 2, 2019 April 2, 2019 No Comments on How Do I Prevent My Pup From Soiling The Carpet?
If you've decided to adopt a puppy, you need to know that, despite their cuteness, puppies can cause a lot of damage at home! Indeed, contrary to kittens who can learn to be clean from a very young age, puppies can need several months to adjust; several months during which you are likely to have to clean the unpleasant mess they leave behind them. As a rule of the thumb, it can take up to 6 months to toilet train your puppy, although larger breeds can need up to a year while smaller dogs get the hang of it quicker. However, you are not powerless. There are some tips you can use to protect your beloved carpet.
First of all, you need to understand that training a dog takes time. Indeed, if the puppy used to live in a safe outdoor area, he may not yet fully understand that he can't use the house as his very own toilet! You will need to establish clear rules that your puppy can follow. Do make sure to reward positive behaviors, such as asking to go outside, to reinforce them. You might be tempted to punish your dog when he soils the carpet, but be patient. Positive reinforcement through treats and petting is likely to achieve better results quicker. Additionally, if you're experiencing difficulties, you can refer your dog to a professional trainer who can help you to introduce the right environment for learning.
Knowing that your pup will need several months before being fully toilet trained means that you have to find alternative solutions to protect your carpet. You can find a changeable diaper for your dog, which can be a useful incentive to encourage your pup to ask to go out. After all, each time the dog asks, you can remove the diaper. More importantly, a diaper can be used at night for young dogs who may not be able to wake until you wake up in the morning. Additionally, they can be a useful alternative if you're visiting friends.
If you work during the day, it means that your puppy is likely to stay at home for sometimes 10 to 12 hours. Ultimately, you couldn't last that long without going to the toilet. The same principle applies to your dog. Your dog needs to relieve himself regularly throughout the day. If you put him in a situation where he can't go outside to pee, you need to be ready to clean the carpet. Ultimately, it would be unhealthy for your dog to wait an entire day.
Well… Do you really need a carpet?
While carpets are cozy, they are a terrible solution when you have a dog. Indeed, even with a quality vacuum cleaner, you might find it challenging to remove all pet hair and dust. Additionally, you're more likely to get dirty stains from walking your dog in bad weather. Maybe the best way to save the carpet from your pup is to have no carpet at all!
House training your puppy is going to take on average 6 months. With dedicated training and helpful gear, you can keep your house almost spotless! However, as a pet owner, you should review your interior style for efficient pet management!


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One of the leading sluggers of his era, Darryl Strawberry was an 8-time All Star outfielder and earned World Series rings with the New York Mets (1986) and the New York Yankees (1996, '98 and '99). In a major league career that spanned 17 seasons, Strawberry had reached the pinnacle of the baseball world but his personal world was crumbling. Addictions, failed marriages, and a struggle with depression brought him to the brink. His dramatic testimony of how Christ changed his life is recorded in his autobiography Straw: Finding My Way (2009). Now an ordained pastor, he and his wife Tracy (whom he met while in drug rehab) have co-authored The Imperfect Marriage: Help for Those Who Think It's Over.
Alex Kendrick is a pastor, author and screenwriter, film director and actor—and also a husband and the father of six children. Concerned that movies had become more influential in modern society than churches, he and his brother Stephen formed a film production company based out of their church in Albany, Georgia. Since its founding in 2002, Sherwood Pictures has brought to 21st century America a number of remarkable and powerful faith-based films, including: Facing the Giants, Fireproof, Courageous, War Room and, most recently, Like Arrows. Alex is a powerful speaker and is passionate about presenting the Christian life in its practical and relevant expressions.
The youngest brother of the famed acting clan, Stephen Baldwin's varied career has included writing, producing, and directing as well as acting in television shows and feature films, including Born on the Fourth of July and The Usual Suspects. His 2006 autobiography, The Unusual Suspect, describes his life in the secular Hollywood lifestyle and his conversion to Christ, which was triggered by the impact of September 11, 2001. Stephen has founded ministries to work with teens and active military personnel, and is a regular guest on television and radio talk shows. He and his wife live in New York and have two daughters.
A legendary football coach and television commentator, Lou Holtz brings to his work an intuitive feel for the game, an outgoing personality and a great sense of humor. His career included coaching stints at William & Mary, North Carolina State, Arkansas, Minnesota, Notre Dame (where he won a consensus national championship in 1988), and South Carolina, as well as a single season as head coach of the New York Jets. He is a member of the College Football Hall of Fame, and author of the motivational books Wins, Losses and Lessons and Winning Every Day: The Game Plan for Success. He speaks regularly on principles of leadership and faith. He and his wife of 57 years live in Orlando, and have four children.


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Voices of Support
Message from SRSG
World Day Q&A
World Day News/Media
Planning and Promoting Your Events
Religious and Spiritual Resources
Category: World Day News
Salesians to Support the World Day of Prayer and Action for Children
The Salesians of Don Bosco, a world-wide Roman Catholic religious order, has called on all its members to unite in celebrating the World Day of Prayer and Action for Children, an initiative promoted by the Global Network of Religions for Children.
In a letter addressed to Salesian chapters worldwide, the order's Rector Major, Fr. Pascual Chávez, said that "only if religious leaders and all of us join together in our efforts will it be possible to respond adequately to the dramatic and massive violations to the dignity and to the fundamental rights of children in the world." The letter is available in five languages on the sdb.org site and in the Service Section of ANS www.infoans.org.
The Salesian Society is the third largest missionary organization in the world, counting some 20,000 members in 130 countries. Its mission is to care for children and young people and promote human rights education. More information on the Salesian work in the human rights area is available on the Platform www.donbosco-humanrights.org.
The eight Salesian NGOs, coordinated by the Don Bosco Network, also published the message of the Rector Mayor on the website www.donbosconetwork.org. One of the NGOs, VIS, is promoting the Day of Prayer and Action in all the countries where it is present (www.volint.it).
Ethics Education
End Child Poverty
Prayer and Action
Initiated by the global non-governmental faith-based organization, Arigatou International, Prayer and Action is a global social movement that has promoted prayer and action for the well-being of children on Universal Children's Day since 2008.
Council Memebers
Stop Violence Against Children


Each diamond which is extracted from mother Earth is unique. This can be specially felt in a tiny minority of extremely rare diamonds that show a variety of colour, known in the trade as Natural Fancy Colour Diamonds, the most popular among consumers being Yellow or Canary colour diamonds with a sunny or orangey hue. These are naturally formed due to the presence of nitrogen within rock formations.
Blue diamonds, which are extremely scarce have a presence of the rare metalloid boron. Green diamonds, also very rare, indicate their exposure to radioactivity during their formation. The colour in the news, Pink diamonds, are almost exclusively mined in the Argyle mine in Australia are a result of "the distortion of the internal structure of the stone" according to John King of the GIA. These diamonds often fetch record prices in top auction houses across the world. A cut above all the rest are Red Colour Diamonds with only a handful recovered and polished to perfection, the most notable of them being the De Young Red and the Moussaieff Red.
Black diamonds, which are also unfairly termed as Fancy Colour Diamonds in the generic trade are generally treated for colour and are actually found in abundance with price levels of £100-300 per carat. Natural Black Diamonds are more uncommon but price levels are lower in comparison to Yellows. In the same instance, with the advent of technology, Yellow, Blue and Pink Diamonds can also be "lab grown" or "Treated for colour" which result in severe price reductions. For eg, a "Treated" Yellow Diamond can be easily sourced for £800-2000 for a one carat stone. At Marlows Diamonds, we do NOT recommend purchase of any "treated or lab grown diamonds", hence we do not normally stock any form of treated diamond, unless specifically requested by a client.
Fancy Colour Diamonds, like White diamonds come in a variety of clarities ranging from Flawless to I2 (being heavily marked) with prices varying accordingly. Further, Natural Fancy Colour Diamonds, in addition to coming in their pure colour form (eg. Natural Fancy Yellow or Natural Fancy Intense Yellow) also come in different mixed colour attributes (eg. Natural Fancy Greenish Yellow), showing a mixture of colours. Many coloured diamonds show some form of fluorescence due to the presence of additional minerals in them. The rarest and most expensive are the Pure Colours with None, Faint or Medium fluorescence as graded by the GIA or IGI. The saturation of colour is also shown on the GIA report, for eg. Yellow diamonds start from Faint Yellow – Very Light Yellow – Light Yellow – Fancy Yellow – Fancy Intense Yellow – Fancy Deep Yellow – Fancy Vivid Yellow (being the most expensive and most saturated in the Yellow category).
If you wish to find out more or require further knowledge and assistance with buying that one special Fancy colour diamond of your choice, a visit to Marlows in the famous Jewellery Quarter of Birmingham is a must, as we have one of the largest retail stock of Natural Fancy Colour Diamonds outside of Bond Street brands with their associated high price structures. A visit would enlighten you to the actual prices associated with Fancy Colour Diamonds as they do not have an international pricing structure like White Diamonds of D-Z colours and can be extremely frustrating to source, with consumers ending up paying many thousands of pounds for diamonds worth a few hundred pounds. We look forward to your visit.


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UC Admissions: 7 Facts You Need to Know
By Lynn O'Shaughnessy on June 2, 2010 in Academics, Admission practices, Admissions, California universities, Community colleges, Money
The University of California's admission practices generated a lot of angst and speculation in recent months, which led to a lot of curiosity about how the UC schools would handle the the latest crush of college applications with money tighter than ever.
Now that the most recent UC admission season is history, here are 7 facts about who got in and who didn't at the UC campuses.
UC Admissions Fact No. 1: About 100,000 students applied to UC campuses for the 2010-2011 school year. It represent the highest number of applicants in history and the fewest number of applicants offered admission. All the UC campuses, except for UC Riverside and UC Merced, recorded their lowest admission rates ever.
UC Admissions Fact No. 2: Systemwide, the number of out-of-state and foreign students accepted at UC campuses for the fall increased 25% from 7,634 to 9,552. Why are the UCs embracing so many nonresidents? It's simple. Nonresidents pay three times as much in tuition as Californians and the UCs are desperate for money.
UC Admissions Fact No. 3: UC Berkeley offered admission to 12,915, which is only 50 less than last year. However, only 9,420 of this year's successful UC applicants were Californians. The rest were those outsiders with deep pockets.
UC Admissions Fact No. 4: The UC schools used waiting lists for the first time, but only a fraction of the 10,700 on UC waiting lists got offered an admission spot. Only 1,866 students received late acceptances and they came from only two schools — UC Davis and UC Santa Barbara.
UC Admissions Fact No. 5: Total costs for current students at UC campuses is estimated at $26,985 for one year. This includes UC fees ($9,285), room and board ($12,600), books/supplies, health insurance, and transportation. Cost will rise even more for the 2010-2011 year.
UC Admissions Fact No. 6: Starting in 2012, only the top 9% of graduating high school seniors in California will be guaranteed a spot at a UC. Since 1960, the guaranteed admission was extended to the top 12.5%.
UC Admissions Fact No. 7: There was a nearly 21% increase in applicants from transfer students from the state's community colleges during the most recent admission season. Final admission figures aren't in yet, but the UC system expects that it will have accepted at least 500 more transfer students than last year.
Read More About UC schools:
The Shrinking Odds of Getting Into UC Berekely
How I Graduated From Berkeley in Two Years
6 Questions to Ask a State University
Lynn O'Shaughnessy also write a college blog for CBSMoneyWatch and she has just released her new eBook, Shrinking the Cost of College: 152 Ways to Shrink the Cost of a Bachelor's Degree. This week it's on sale for as low as $14.95.
UC, UC admissions, University of California, Waiting list
Shrinking the Cost of College: Twitter Chat Tonight
A Law Professor's Take on College Admissions


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Michelle Yeoh asked Quentin Tarantino why she wasn't in 'Kill Bill'
Michelle Yeoh has revealed why she wasn't cast in Quentin Tarantino's Kill Bill, after asking the director herself.
According to Tarantino, the 1992 action film Supercop, starring Yeoh and Jackie Chan, was a source of inspiration for Uma Thurman during filming on the 2003 martial arts film.
READ MORE: Is 'Everything Everywhere All At Once' the year's maddest, most exciting movie?
The director also encouraged Yeoh to come out of retirement after she suffered an on-set injury filming 1996's The Stunt Woman. "I must say, Quentin, he's persistent," Yeoh told Town & Country. "He is who he is today because he's full of passion and love, so he wore me down.
"Suddenly we became animated. So then I thought, maybe I'm not ready to give up on this."
Quentin Tarantino CREDIT: Daniele Venturelli/WireImage
Considering his admiration for her, Yeoh revealed that she asked the director why she wasn't cast in Kill Bill. "I asked Quentin the same question," Yeoh said.
"He's very smart. He said, 'Who would believe that Uma Thurman could kick your ass?'"
Kill Bill stars Thurman as Beatrix 'the Bride' Kiddo, who swears revenge on a team of assassins after they try to kill her at her wedding. A sequel, titled Kill Bill: Volume 2, was released in 2004.
Yeoh's career has hit new heights following roles in Crazy Rich Asians, Marvel's Shang-Chi And The Legend Of The Ten Rings, and Everything Everywhere All At Once. The latter, directed by Daniel Kwan and Daniel Scheinert, has become the highest-grossing release ever for studio A24.
Her previous credits include James Bond film Tomorrow Never Dies, 2000's Crouching Tiger, Hidden Dragon, and as Captain Philippa Georgiou in Star Trek: Discovery.
The actor is set to play Dr. Karina Mogue in Avatar: The Way Of Water, director James Cameron's sequel to 2009's Avatar. The film is scheduled to be released on December 16, 2022.


text:
\section{Introduction}

The number of completely sequenced bacterial and archaeal genomes are rising steadily,
such an increasing makes it possible to develop novel kind of large scale approaches
to understand genomes structure and evolution over time. Gene content prediction and genome comparison have both provided new important information and
deciphering keys to understand evolution of prokaryotes ~\cite{varani2011issaga}.
 Important sequences in understanding rearrangement of genomes during evolution are so-called
transposable elements (TEs), which are DNA fragments or segments that
have the ability to insert themselves into new chromosomal locations, and often
make duplicate copies of themselves during transposition process~\cite{nref1hawkins2006differential}. Remark that, in
bacterial reign, only cut-and-paste mechanism of transposition can be found, the
transposable elements involved in such a move being the insertion sequences (ISs).

Insertion sequences
range in size from 600 to more than 3000
bp.  They are divided into 26 main different families in prokaryotes, as described in
ISFinder\footnote{\url{www-is.biotoul.fr}}~\cite{siguier2006isfinder}, an international
reference database for bacterial and archaeal ISs that includes background information on
transposons.  The main function of ISFinder is to assign IS names and to produce a focal
point for a coherent nomenclature for all discovered insertion sequences.
This database includes over than 3500 bacterial ISs~\cite{emma6hickman2010integrating,zhou2008insertion}.
Data come from a detection of repeated patterns, which can be
easily found by using homology-based techniques~\cite{chr4feschotte2007computational}.
Classification process of families, for its part, depends on transposases homology
and overall genetic organization. Indeed, most ISs consist of short inverted repeat
sequences that flank one or more open reading frames (ORFs, see Figure~\ref{ISfig}),
whose products encode the transposase proteins necessary for transposition process.
The main problem with such approaches for ISs detection and classification
is that they are obviously highly dependent on
the annotations, and existing tools evoked above only use
the NCBI ones, whose quality is limited and very variable.

In this research work, the authors' intention is to find an accurate method for discovering insertion sequences in prokaryotic genomes.
To achieve this goal, we propose to use one of the most recent computational tool
for automated annotation of insertion sequences, namely OASIS, together with the
international database for all known IS sequences (ISFinder).
More precisely, OASIS works with genbank files that have fully
described genes functionality: this tool identifies ISs in
each genome by finding conserved regions surrounding already-annotated
transposases. Such technique makes it possible to discover new insertion sequences, even
if they are not in ISFinder database.
A novel pipeline that solves the dependence on NCBI annotations,
and that works with any annotation tool (with or without description of
gene functionality) is then proposed.
The output of our pipeline contains all detected IS sequences supported with other important information like inverted repeats (IRs) sequences, lengths, positions, names of family and group, and other details that help in studying IS structures.

The contributions of this article can be summarized as follows. (1)
A pipeline for insertion sequences discovery and classification is proposed, which does not depend
on NCBI annotations. It uses unannotated genomes and embeds various annotation tools
specific to Bacteria (such as Prokka, BASys, and Prodigal) in its
process. (2) Overlapping and consensus problems that naturally appear after
merging annotation methods recalled above are solved, in order to obtain large and accurate number of ISs with their names of families and groups. And finally (3) the pipeline is tested
on a set of 23 complete genomes of \emph{Pseudomonas aeruginosa}, and
biological consequences are outlined.

\begin{figure}[ht!]
\centering
\includegraphics[scale=1]{1471-2164-9-36-1.jpg}
\caption{IS element types~\cite{zhou2008insertion}}
\label{ISfig}
\end{figure}

\color{black}
The remainder of this article is organized as follows. In Section~\ref{sec:state}, various tools
for discovering IS elements in different species of Bacteria and Archaea are presented.
The suggested methodology for increasing both the number and accuracy of detecting
IS elements is explained in Section~\ref{sec:methods}. The pipeline is detailed in
Section~\ref{sec:pip}, while an application example using 23 completed genomes of
\emph{P. aeurigonsa} is provided in Section~\ref{sec:result}.
This article ends by a conclusion section, in which the contributions are summarized and
intended future work is detailed.

\section{State of the art in ISs detection or annotation}
\label{sec:state}

The study on the plant-pathogenic prokaryote \emph{Xanthomonas oryzae pv. oryzae (Xoo)}, which causes
bacterial blight (one of the most important diseases of rice) was published in 2005
by Ochiai \emph{et al.}~\cite{art1ochiai2005genome}. They used GeneHacker~\cite{yada1996detection}, GenomeGambler version 1.51, and Glimmer program~\cite{delcher1999improved} for coding sequence prediction.
Insertion sequences were finally classified by a BLAST analysis using ISFinder database evoked previously.

\textbf{IScan}, developed by Wagner \emph{et al.}~\cite{emma2Wagner01082007}, has then
been proposed in 2007. Inverted repeats are found using smith waterman local
alignments on transposase references found with BLAST and used
as a local database. This tool has been
applied on 438 completely sequenced bacterial genomes by using BLAST with referenced
transposases, to determine which transposases are related to insertion sequences.
Touchon \emph{et al.}, for their parts, have analyzed  262 different
bacterial and archaeal genomes downloaded from GenBank NCBI
in 2007~\cite{art4touchon2007causes}. A coding sequence has then been considered as an IS element if its
BLASTP best hit in ISFinder database  has an e-value lower than $10^{-10}$.

\textbf{ISA} has been created by Zhou \emph{et al.} in 2008~\cite{zhou2008insertion}.
This annotation program depends on both NCBI annotations and ISFinder.
More precisely, authors manually collected 1,356 IS elements with both sequences
and terminal signals from the ISFinder database, which have
been used as templates for identification of all IS elements and map
construction in the targeted genomes.
ISA, which is not publicly available, has finally been used for an analysis of
19 cyanobacterial and 31 archaeal annotated genomes downloaded from NCBI.

In 2010, Plague \emph{et al.} analyzed the neighboring gene
orientations (NGOs) of all ISs in 326 fully sequenced bacterial chromosomes. They obtained primary annotations from the Comprehensive Microbial Resource database (release 1.0-20.0) at the Institute for Genomic
Research\footnote{\url{http://cmr.tigr.org/tigr-scripts/CMR/CmrHomePage.cgi}}.
Their approach for extracting IS elements from these genomes was to consider
that a coding sequence with a best BLASTX hit e-value lower than $10^{-10}$ is
an insertion sequence~\cite{art2plague2010intergenic}.
\textbf{ISsage}, for its part, has been developed in 2011 by Varani
\emph{et al.}~\cite{varani2011issaga}. They used eight different bacterial genomes downloaded from NCBI, and produced a web application pipeline that allows semi-automated annotation
based on BLAST against the ISFinder database. However ISsage cannot
automatically identify new insertion sequences which are not already present in
ISFinder database.

A new computational tool for automated annotation of ISs has then been
released in 2012 by Robinson \emph{et al.}~\cite{robinson2012oasis}.
This tool has been called \textbf{OASIS}, which stands for ``Optimized
Annotation System for Insertion Sequences''. They worked with 1,737 bacterial and archaeal genomes downloaded from NCBI.
OASIS identifies ISs in each genome by finding conserved regions surrounding already-annotated transposase genes. OASIS uses a maximum likelihood algorithm
to determine the edges of multicopy ISs based on conservation between their
surrounding regions. For defining inverted repeats, the same strategy as IScan
was used (Smith-Waterman alignment). Authors also used hierarchical
agglomerative
clustering to identify groups of IS lengths. The ISs set is then classified
according to the family and group after a BLASTP best hit in ISFinder database
with an e-value lower than $10^{-12}$. When a cluster
cannot match with any entry of the database, the IS set is
considered as new. Thus OASIS has the ability to discover new
insertion sequences, that is, which cannot be found in ISFinder.

\begin{table}[H]
\center
\caption{Input set of 23 complete genomes of \emph{P. aeruginosa}}
\scalebox{0.7}{%
\begin{tabular}{|c|c|c|c|c|c|}
\hline
\textbf{} & \textbf{} & \textbf{INSDC(Genbank)} & \textbf{Refseqs} & \multicolumn{ 2}{c|}{\textbf{Input Cenomes}} \\ \hline
\textbf{Index } & \textbf{ GenomeName } & \textbf{ GID} & \textbf{ GID} & \textbf{GID} & \textbf{Accession no.} \\ \hline
1 &  PACS2  & 106896550 &  \_ & 106896550 & AAQW01000001.1 \\ \hline
2 &  PAO1  & 110227054 & 110645304 & 110645304 & NC\_002516.2 \\ \hline
3 &  UCBPP-PA14  & 115583796 & 116048575 & 116048575 & NC\_008463.1 \\ \hline
4 &  PA7  & 150958624 & 152983466 & 152983466 & NC\_009656.1 \\ \hline
5 &  19BR  & 343788106 & 485462089 & 485462089 & NZ\_AFXJ01000001.1 \\ \hline
6 &  213BR  & 343788107 & 485462091 & 485462091 & NZ\_AFXK01000001.1 \\ \hline
7 &  M18  & 347302377 & 386056071 & 386056071 & NC\_017549.1 \\ \hline
8 &  DK2  & 392316915 & 392981410 & 392981410 & NC\_018080.1 \\ \hline
9 &  B136-33  & 477548288 & 478476202 & 478476202 & NC\_020912.1 \\ \hline
10 &  RP73  & 514245605 & 514407635 & 514407635 & NC\_021577.1 \\ \hline
11 &  c7447m  & 543873856 &  \_ & 543873856 & CP006728 \\ \hline
12 &  PAO581  & 543879514 &  \_ & 543879514 & CP006705 \\ \hline
13 &  PAO1-VE2  & 553886202 &  \_ & 553886202 & CP006831 \\ \hline
14 &  PAO1-VE13  & 553895034 &  \_ & 553895034 & CP006832 \\ \hline
15 &  PA1  & 557703951 & 558672313 & 558672313 & NC\_022808.1 \\ \hline
16 &  PA1R  & 557709751 & 558665962 & 558665962 & NC\_022806.1 \\ \hline
17 &  MTB-1  & 563408818 & 564949884 & 564949884 & NC\_023019.1 \\ \hline
18 &  LES431  & 566561164 & 568151185 & 568151185 & NC\_023066 \\ \hline
19 &  SCV20265  & 567363169 & 568306739 & 568306739 & NC\_023149 \\ \hline
20 &  LESB58  &  \_ & 218888746 & 218888746 &  NC\_011770.1 \\ \hline
21 &  NCGM2.S1  &  \_ & 386062973 & 386062973 & NC\_017549.1 \\ \hline
22 &  PA38182  & 575870901 &  \_ & 575870901 & HG530068.1 \\ \hline
23 &  YL84  & 576902775 &  \_ & 576902775 & CP007147.1 \\ \hline
\end{tabular}}
\label{inputset}
\end{table}

Finally, in 2014, the analysis of the NGOs for all IS elements within 155 fully sequenced Archaea genomes was presented by Florek
\emph{et al.}~\cite{art3florek2014insertion}. To do so,
they have launched a BLASTP in the ISFinder, with an e-value
less than or equal to $10^{-10}$, for
all protein coding sequences downloaded from NCBI which are related to IS
elements.

Two major concerns with the state of the art detailed above
can be emphasized. Firstly, most of them cannot detect new insertion sequences.
Secondly, all these tools are based on NCBI annotations of very relative
and variable qualities -- except ISsaga, which could work with other annotation tools (but it depends only on transposase ORFs that have been already defined in ISFinder). Our objective in the next section is to propose a pipeline
that solves these two issues, being able to deal with unannotated genomes
and to detect unknown ISs.

\section{Prediction and Modules based on OASIS}
\label{sec:methods}

For illustration purpose, the proposed pipeline system for IS elements prediction will be
presented using 23 complete genomes of \emph{P. aeruginosa} available on the
NCBI website, RefSeq and INCDS/Genebank databases, see Table~\ref{inputset}
(RefSeq genomes were prefered when available).
The prediction of IS elements in the proposed pipeline depends on both OASIS~\cite{robinson2012oasis} and ISFinder~\cite{siguier2006isfinder}.

\subsection{Prediction of IS elements from \emph{Pseudomonas aeruginosa}}

OASIS is used in this pipeline for predicting insertion sequences in prokaryotic
genomes.
This latter detects ISs in each genome by finding conserved regions
surrounding already-annotated transposase genes, which are identified by the
word \emph{$¨$transposase$¨$} in the ``product'' field of the GenBank file.
Obviously OASIS highly depends on the quality of annotations~\cite{robinson2012oasis}, while to determine whether a given gene is a transposase or not
is a very difficult task (indeed transposases are among
the most abundant and ubiquitous genes in nature~\cite{aziz2010transposases}, and they are widely separated in Prokaryote genomes).
OASIS deals with files having genbank format. It takes
them as input and then produces two output files for each provided genome.
The first one is a fasta file that contains all IS nucleotide sequences,
with start and end positions. It also contains the amino acid sequence for each ORF.
The second file is a summary table providing attributes
that describe the insertion sequence: set-id, family, group,
IS positions, inverted repeat left (IRL) and right (IRR),
and orientation. Remark that most of these information are
in the ISFinder database too. Indeed  OASIS find them alone but
it extracts family names and group from ISFinder.

The main problem found in OASIS is solved in the proposed pipeline by
using different types of annotations: NCBI will not be used alone,
and gene functionality taken from annotation tools will either or not
be used depending on the situation. Finally, transposases
within IS will be verified using ISFinder database.
OASIS can thus be used in two different ways in our pipeline, depending on the
provided genbank file. These two modules have been named NOASIS,
which  uses the original input genbank genome file provided by the NCBI (as it is, without any modification), and DOASIS, which deals with modified genbank files that have been updated to obtain more accurate results than NOASIS.
These modules are described thereafter.

\subsection{Normal OASIS (NOASIS)}

For finding predicted IS in NOASIS module, we simply applied OASIS on the input
set of genomes with their NCBI annotations,
that is, with the original downloaded genbank file.
Using the reference genome named PAO1, the summary outputted by the pipeline is
given in Tables~\ref{pao1}
and~\ref{pao2}. In these NOASIS tables, the summary produced by OASIS is enriched
with new features
described below:
\begin{itemize}
	\item{\textit{\textbf{Real IS}}}
	IS sequences that have best match (first hit) when using BLASTN with ISFinder database, an e-value equal to 0.0, and with a functionality of each ORF within the IS recognized as a transposase.
	\item{\textbf{\textit{Partial IS}}}
Sequences that match part of known IS from ISFinder (\emph{i.e.}, have e-value lower
than $10^{-10}$) and have  also a transposase gene functionality for the ORFs.
    \item{\textit{\textbf{Putative New IS}}}
	Sequences with bad score after making a BLASTN with ISFinder, but
	with a transposase.
	They may be real insertion sequences not already added in ISFinder database
	or false positives, requiring human curation.

\end{itemize}

Applying this slightly improved version of OASIS in the 23 genomes
of \emph{Pseudomonas} leads to a major issue: surprisingly,
NOASIS found no real insertion sequences in some genomes
like PACS2 or SCV20265.
The problem is that OASIS find
multiple copies of IS elements in each genome by identifying
conserved regions surrounding transposase genes. However some
of the considered genomes either have no information about transposase gene
into their feature genbank tables or have simply no feature
table in their genbank format files. This issue is at the
basis of our improved module called DOASIS, which is explained below.

For the sake of comparison, Figure \ref{IS_tuber} contains similar results for \emph{Mycobacterium tuberculosis} genus.
\color{black}

\begin{figure}[ht!]
\centering
\includegraphics[scale=0.25]{MicroTuber.png}
\caption{IS elements detect in 28 \emph{Mycobacterium tuberculosis}}
\label{IS_tuber}
\end{figure}

\subsection{Developed OASIS (DOASIS)}

The main idea for DOASIS module is that information about transposases within genbank files
are potentially incorrect (\emph{i.e.}, may all be false positives). So  we
simply decide to remove all transposase words in the product fields
from all inputted genomes. We thus update these information as follows.
\begin{description}
\item[Step 1: genbank update.] Inputted genbank files are modified following one of the three methods
 below.
\begin{enumerate}
\item \textbf{All-Tpase}: we consider that all the genes may potentially be a transposase.
So all product fields are set to ``transposase''.
\item \textbf{Zigzag Odd}: we suggest that genes in odd positions are putative transposases and we update the genbank file adequately. Oddly, this new path will produce new candidates which
are not detected during All-Tpase.
\item \textbf{Zigzag Even}: similar to Zigzag Odd, but on even positions.
\end{enumerate}

We checked also a randomized method (\emph{i.e.}, by putting ``transposase'' in randomly picked genes).
However we found poorer
number of predictive real ISs or new real ISs compared with the three methods previously presented.
For these reasons, we will not further investigate the randomized method.

\color{black}

\begin{figure}[ht!]
\centering
\includegraphics[scale=0.4]{random}
\caption{Comparison of predicted ISs between randomization method and all/odd/even methods.}
\label{randomfig}
\end{figure}

\item[Step 2.] We apply OASIS three times (\emph{i.e.}, one time per method)
on all genomes, and then
we take the output fasta file that
contains both nucleotides and amino acids sequences for each IS element.
\item[Step 3.]  A BLASTN with ISFinder is applied on each IS sequence.
If the e-value of the first hit is 0.0, then  the ORF within this
IS belongs to known (Real) IS already existing in the ISFinder database. Else,
if the e-value is lower than $10^{-10}$, then we found a Partial IS.
\item[Step 4.] Collect all Real IS from previous three methods (ALL\_Tpase, Zigzag
odd, and Zigzag even) and then remove overlaps among them. Finally, produce best
Real IS with all information. Remark that the problem of finding consensus
and overlaps can be treated as a lexical parsing problem
\end{description}

\section {The Proposed Pipeline}
\label{sec:pip}

It is now possible to describe the proposed pipeline that can use the two modules
detailed in the previous section. This pipeline, depicted in Figure~\ref{ISpip},
will increase the number of
Real IS detected on the set of  \emph{P.aeruginosa} genomes under consideration
(indeed, the detection is improved in all categories of insertion sequences,
but we only focus on Real IS in the remainder of this article, for the sake
of concision).
Its steps are detailed in what follows.

\begin{figure}[ht]
\centering
\includegraphics[scale=0.6]{pipeline.png}
\caption{The proposed pipeline}
\label{ISpip}
\end{figure}

\begin{description}
\item[Step 1: ORF identification.]
Our pipeline is currently compatible with any type of annotation
tools, having either functionality capability or not, but for comparison we only focus
in this article on the following tools: \emph{BASys}, \emph{Prokka}, and \emph{Prodigal}.
 BASys (Bacterial Annotation System) is a web server that performs
automated, in-depth annotation of bacterial genomic (chromosomal and plasmid)
sequences.
It uses more than 30 programs to determine nearly 60 annotation subfields for each gene.
Remark that genomes must be sent online manually, and that some
curation stage may be required to remove some DNA ambiguity on
returned genbank files.

Prokka (rapid prokaryotic genome annotation), for its part, is
a classical command line software for fully annotating draft bacterial genomes,
producing standards-compliant output files for further analysis~\cite{seemann2014prokka}.
Finally,
Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm)
is an accurate bacterial and archaeal genes finding  software
provided by the Oak Ridge National Laboratory~\cite{hyatt2010prodigal}.
\item[Step 2: IS Prediction.] The second stage of the pipeline consists in using
either NOASIS or DOASIS for predicting IS elements. Notice that NOASIS
cannot be used with Prodigal, as this module requires information
about gene functionality (both NOASIS and DOASIS can be use with
Prokka and BASys annotations).
\item[Step 3: IS Validation.] This step is realized by launching BLASTN on each
predicted IS sequence with ISFinder. The e-value of the first hit is then checked:
if it is 0.0, then the ORF within this sequence is a Real IS known by ISFinder. As
described previously, it will be considered as Partial IS if
its e-value is lower than $10^{-10}$. Both IS names of family and group are returned
too.
\end{description}

\section{Results and Discussion}
\label{sec:result}

We can firstly remark in Figure~\ref{fig:all_annot} that,
using either Prokka or BASys for genes detection
and functionality prediction is better than taking directly the annotated genomes
from NCBI: a larger number of Real IS can be found. Additionally, this comparison
shows that Prokka outperforms BASys in 3 families of ISs (namely: IS3, IS30, and
ISNCY), while BASys seems better for detecting insertion sequences belonging
in the IS5, IS1182, and TN3 families. This variability may be explained by
the fact that functionality annotations of these tools depend probably on
IS families that where known when these tools have been released.

\begin{figure}
\centering
\includegraphics[scale=0.5]{all_annot_tools.jpg}
\caption{Comparison between Prokka, BASys, and NCBI functionality annotations}
\label{fig:all_annot}
\end{figure}

\begin{table}[htbp]
\caption{Summary table produced by NOASIS (begining)}
\centering
\scalebox{0.7}{%
\begin{tabular}{|c|c|c|c|c|c|c|c|c|c|}
\hline
\textbf{Name} & \textbf{Genome} & \textbf{Start} & \textbf{End} & \textbf{Orientation} & \textbf{SetID} & \textbf{ISFinder\_name} & \textbf{Family} & \textbf{Group} & \textbf{Length} \\ \hline
PAO1 & NC\_002516.2 & 499832 & 501193 & - & 1 & ISPa11 & IS110 & IS1111 & 1361 \\ \hline
PAO1 & NC\_002516.2 & 2556875 & 2558236 & + & 1 & ISPa11 & IS110 & IS1111 & 1361 \\ \hline
PAO1 & NC\_002516.2 & 3043478 & 3044839 & - & 1 & ISPa11 & IS110 & IS1111 & 1361 \\ \hline
PAO1 & NC\_002516.2 & 3842002 & 3843363 & - & 1 & ISPa11 & IS110 & IS1111 & 1361 \\ \hline
PAO1 & NC\_002516.2 & 4473550 & 4474911 & + & 1 & ISPa11 & IS110 & IS1111 & 1361 \\ \hline
PAO1 & NC\_002516.2 & 5382524 & 5383885 & - & 1 & ISPa11 & IS110 & IS1111 & 1361 \\ \hline
PAO1 & NC\_002516.2 & 54041 & 54835 & + & 2 & ISStma5 & IS3 & IS3 & 794 \\ \hline
\end{tabular}}
\label{pao1}
\end{table}

\begin{table}[htbp]
\caption{Summary table produced by NOASIS (end)}
\centering
\scalebox{0.7}{%
\begin{tabular}{|c|c|c|c|c|}
\hline
\textbf{IRR=IRL} & \textbf{Locus\_tag(gbk)} & \textbf{Product(gbk)} & \textbf{E Value} & \textbf{IS\_type} \\ \hline
ATGGACTCCTCCC & [['PA0445']] & [['transposase']] & 0.0 & Real IS \\ \hline
ATGGACTCCTCCC & [['PA2319']] & [['transposase']] & 0.0 & Real IS \\ \hline
ATGGACTCCTCCC & [['PA2690']] & [['transposase']] & 0.0 & Real IS \\ \hline
ATGGACTCCTCCC & [['PA3434']] & [['transposase']] & 0.0 & Real IS \\ \hline
ATGGACTCCTCCC & [['PA3993']] & [['transposase']] & 0.0 & Real IS \\ \hline
ATGGACTCCTCCC & [['PA4797']] & [['transposase']] & 0.0 & Real IS \\ \hline
AAAGGGGACAGATTTATTTTCCCTGCTCTAAT & [['PA0041a']] & [['transposase']] & 0.23 & Putative New IS \\ \hline
\end{tabular}}
\label{pao2}
\end{table}

The effects of DOASIS module compared to single OASIS
on annotated NCBI genomes are depicted in
Figure~\ref{fig:all_ncbi}. The improvement in real IS
discovery is obvious, illustrating the low quality and inadequacy of
NCBI annotations for studying insertion sequences in bacterial genomes,
and the improvements when using our pipeline. This chart
shows too that a zigzag path in the annotation can oddly
improve the detection of insertion sequences.

The prediction of real ISs is based on finding conserved regions (\emph{i.e.}, inverted repeats (IRs)) surrounded by transposase genes.
Some ISs have been lost in All\_Tpase, for the following reason: when we suggested that all genes are transposases, OASIS found predicted ISs that consist of large sets of transposases surrounded by IR in their left and right boundaries. But when these predicted ISs have been verified using ISFinder database, we did not find any good match. Contrarily, in Zigzag methods, good matches have been found (real ISs), because many of these elements consist of one or two transposase genes flanked by IRs.
These results are listed with detail in Table~\ref{basys} using BASys annotation tools.

\begin{figure}[H]
\centering
\includegraphics[scale=0.35]{image1.jpg}
\caption{NOASIS (NCBI annotation) versus DOASIS}
\label{fig:all_ncbi}
\end{figure}

\begin{table}[H]
\caption{BASys annotation using NOASIS and DOASIS}
\begin{center}
\scalebox{0.6}{%
\begin{tabular}{|c|c|r|r|r|r|r|}
\hline
\textbf{BASys} &  & \multicolumn{1}{c|}{\textbf{Normal}} & \multicolumn{1}{c|}{\textbf{All Transpos}} & \multicolumn{1}{c|}{\textbf{Zigzag Odd}} & \multicolumn{1}{c|}{\textbf{Zigzag Even}} & \multicolumn{1}{c|}{\textbf{(All\_T/odd/even)}} \\ \hline
Name & Genome & \multicolumn{1}{l|}{Real IS} & \multicolumn{1}{l|}{Real IS} & \multicolumn{1}{l|}{Real IS} & \multicolumn{1}{l|}{Real IS} & \multicolumn{1}{c|}{\textbf{Best Real}} \\ \hline
PACS2 & 106896550 & 2 & 1 & 2 & 0 & 2 \\ \hline
PAO1 & 110645304 & 9 & 6 & 0 & 0 & 6 \\ \hline
UCBPP-PA14 & 116048575 & 3 & 8 & 8 & 1 & 8 \\ \hline
PA7 & 152983466 & 13 & 0 & 0 & 0 & 0 \\ \hline
LESB58 & 218888746 & 2 & 3 & 5 & 2 & 6 \\ \hline
M18 & 386056071 & 1 & 2 & 2 & 1 & 2 \\ \hline
NCGM2.S1 & 386062973 & 15 & 0 & 12 & 0 & 12 \\ \hline
DK2 & 392981410 & 8 & 9 & 10 & 8 & 11 \\ \hline
B136-33 & 478476202 & 3 & 5 & 3 & 3 & 5 \\ \hline
19BR & 485462089 & 5 & 0 & 0 & 10 & 10 \\ \hline
213BR & 485462091 & 5 & 4 & 4 & 4 & 4 \\ \hline
RP73 & 514407635 & 4 & 5 & 5 & 2 & 5 \\ \hline
c7447m & 543873856 & 9 & 0 & 9 & 9 & 10 \\ \hline
PAO581 & 543879514 & 9 & 6 & 8 & 0 & 8 \\ \hline
PAO1-VE2 & 553886202 & 8 & 6 & 9 & 6 & 9 \\ \hline
PAO1-VE13 & 553895034 & 8 & 6 & 8 & 8 & 8 \\ \hline
PA1R & 558665962 & 4 & 4 & 4 & 5 & 5 \\ \hline
PA1 & 558672313 & 5 & 5 & 5 & 6 & 6 \\ \hline
MTB-1 & 564949884 & 0 & 1 & 0 & 1 & 1 \\ \hline
LES431 & 568151185 & 5 & 14 & 13 & 8 & 14 \\ \hline
SCV20265 & 568306739 & 5 & 14 & 13 & 8 & 14 \\ \hline
PA38182 & 575870901 & 1 & 3 & 1 & 2 & 4 \\ \hline
YL84 & 576902775 & 7 & 7 & 7 & 7 & 7 \\ \hline
 &  & \multicolumn{1}{c|}{131} & \multicolumn{1}{c|}{109} & \multicolumn{1}{c|}{128} & \multicolumn{1}{c|}{91} & \multicolumn{1}{c|}{157} \\ \hline
\end{tabular}}
\end{center}
\label{basys}
\end{table}

We can thus wonder if the source of a wrong prediction of
real IS is due to a wrong coding sequence prediction, or to
functionality errors. Switching between NOASIS and DOASIS
allows us to answer this question. We can conclude
from Table~\ref{correlation} that (1) annotation errors are more frequent on NCBI, while Prokka annotates well the sequences related to ISs (see NOASIS columns), and that (2) both NCBI and Prokka have a better coding sequence prediction than BASys, at least when considering sequences involved in IS elements (see DOASIS columns and the correlation line). More precisely, the correlation is based on the number of predicted real IS elements between NOASIS and DOASIS.

\begin{table}[H]
\caption{Correlation table for different annotation tools}
\begin{center}
\scalebox{0.7}{%
\begin{tabular}{|c|c|c|c|c|c|c|}
\hline
 \textbf{} & \multicolumn{ 2}{c|}{\textbf{NCBI}} & \multicolumn{ 2}{c|}{\textbf{BASys}} & \multicolumn{ 2}{c|}{\textbf{Prokka}} \\ \hline
 & \textbf{NOASIS} & \textbf{DOASIS} & \textbf{NOASIS} & \textbf{DOASIS} & \textbf{NOASIS} & \textbf{DOASIS} \\ \hline
 Number of Real IS & 110 & 169 & 131 & 157 & 169 & 176 \\ \hline
 \textbf{Correlations} & \multicolumn{ 2}{c|}{0.3985580752} & \multicolumn{ 2}{c|}{0.357346472} & \multicolumn{ 2}{c|}{0.926355615} \\ \hline
\end{tabular}}
\end{center}
\label{correlation}
\end{table}

Prodigal has been studied separately, as it does not provide genes functionality.
The number of Real ISs per genome returned by our pipeline
using prodigal is given in Figure~\ref{prod}. As shown in Table~\ref{high throughput},
the quality of  coding sequences predicted with prodigal compared
with other annotation tools allows us to discover the best number of real ISs.
In particular, we have improved a lot of results produced
by OASIS and ISFinder on NCBI annotations, which is usually used in the
literature that focuses on bacterial insertion sequences.
Furthermore, this table illustrates a certain sensitivity of
coding sequence prediction tools with functionality annotation capabilities
to detect ISs in some specific genomes like PA7.
Indeed we discovered,
during other studies we realized on this set of \emph{Pseudomonas} strains,
that PA7 has a lot of specific genes, that is, which are not in the core genome of all \emph{Pseudomonases}, which may explain such a sensitivity.
\begin{figure}[h]
\centering
\includegraphics[scale=0.5]{prodigal_bestIS.jpg}
\caption{Real ISs found by our pipeline using Prodigal}
\label{prod}
\end{figure}

\begin{table}[htbp]
\caption{Final comparison using our pipeline}
\centering
\scalebox{0.7}{%
\begin{tabular}{|c|c|c|c|c|c|c|c|c|c|}
\hline
\textbf{} & \textbf{NCBI} & \textbf{BASys} & \textbf{Prokka} & \textbf{Prodigal} & \textbf{} & \textbf{NCBI} & \textbf{BASys} & \textbf{Prokka} & \textbf{Prodigal} \\ \hline
\textbf{Name} & \textbf{DOASIS} & \textbf{DOASIS} & \textbf{DOASIS} & \textbf{DOASIS} & \textbf{Name} & \textbf{DOASIS} & \textbf{DOASIS} & \textbf{DOASIS} & \textbf{DOASIS} \\ \hline
PACS2 & 0 & 2 & 2 & 3 & c7447m & 10 & 10 & 10 & 12 \\ \hline
PAO1 & 10 & 6 & 10 & 12 & PAO581 & 10 & 8 & 10 & 8 \\ \hline
UCBPP-PA14 & 4 & 8 & 4 & 8 & PAO1-VE2 & 10 & 9 & 10 & 9 \\ \hline
PA7 & 15 & 0 & 14 & 18 & PAO1-VE13 & 10 & 8 & 10 & 9 \\ \hline
LESB58 & 3 & 6 & 3 & 6 & PA1R & 4 & 5 & 4 & 5 \\ \hline
M18 & 3 & 2 & 3 & 3 & PA1 & 5 & 6 & 5 & 6 \\ \hline
NCGM2.S1 & 11 & 12 & 19 & 14 & MTB-1 & 1 & 1 & 1 & 2 \\ \hline
DK2 & 12 & 11 & 13 & 17 & LES431 & 6 & 14 & 6 & 6 \\ \hline
B136-33 & 5 & 5 & 5 & 7 & SCV20265 & 15 & 14 & 15 & 15 \\ \hline
19BR & 8 & 10 & 5 & 11 & PA38182 & 7 & 4 & 7 & 7 \\ \hline
213BR & 8 & 4 & 8 & 10 & YL84 & 7 & 7 & 7 & 8 \\ \hline
RP73 & 5 & 5 & 5 & 5 & \textbf{Total IS} & \textbf{84} & \textbf{71} & \textbf{91} & \textbf{114} \\ \hline
\end{tabular}}
\label{high throughput}
\end{table}

\section {Conclusion}
\label{sec:conclusion}

Insertion sequences of bacterial genomes are usually studied using
OASIS and ISFinder on NCBI annotations. We have shown in this
article that a pipeline can be designed to improve the accuracy
of IS detection and classification by improving the coding sequence
prediction stage, and by considering a priori each sequence as a transposase. The source code for this pipeline can be download from the link~\footnote{\url{http://members.femto-st.fr/christophe-guyeux/en/insertion-sequences}}.
A comparison has been conducted on a set of \emph{Pseudomonas aeruginosa},
showing an obvious improvement in the detection of insertion
sequences for some particular configurations of our pipeline.

In future work, we intend to enlarge the number of coding sequence
and functionality prediction tools and to merge all the Real IS results
in order to improve again the accuracy of our pipeline. We will then focus
on the impact of IS elements in \emph{P.aeruginosa} evolution,
comparing the phylogenetic tree of strains of this species with
a phylogeny of their insertion sequences. Insertion events will then
be investigated, and related to genomes rearrangements found in this
collection of strains. We will finally enlarge our pipeline to
eukariotic genomes and to other kind of transposable elements.

\bibliographystyle{plain}

redpajama_set_name: RedPajamaArXiv


This unusual radish looks like a watermelon when sliced. The round white roots have shoulders and are 2 inches in diameter. The inside flesh is red to pink sweet and crisp. Large tops make for easy picking. Best when picked small.
To grow the best radishes the crop must grow quickly therefore the soil must be loose and enriched with fertilizer. Water in the absence of rain.