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Muggles' Guide to Harry Potter/Characters/Argus Filch

Overview
Argus Filch is the caretaker at Hogwarts. He has a pet cat called Mrs. Norris who is usually on the prowl, keeping an eye out for him. He is bitter, cruel and seems to hate the students. He seems to work well with oppressors, seeing their use of rules as only natural and correct; he would be a perfect tool for a totalitarian regime. Every year he asks Dumbledore to read out what is banned. An example of things that are banned are Fanged Frisbees and, later, Weasleys' Wizard Wheezes products.

Philosopher's Stone
Harry and Ron get off on the wrong foot with Filch on the very first day of classes when he catches them trying to enter the forbidden corridor. They had not meant to visit that corridor; they had simply gotten lost on the way to Transfiguration class. They are saved from being locked in the dungeons by Professor Quirrell, who happens to be passing by.

At tea with Hagrid on the Friday of their first week, Harry is pleased that Hagrid refers to Filch as "that old git". Hagrid also says that he can't abide Mrs. Norris, and that Filch has apparently instructed Mrs. Norris to follow Hagrid around.

Shortly after this, Draco Malfoy challenges Harry to a Wizard's Duel. Harry and his second, Ron, followed by Hermione and Neville Longbottom, go to the Trophy Room, the designated site for the duel, but instead of finding Draco there, they hear Filch approaching. Trying to escape, Neville knocks over a suit of armour, and in the ensuing mad dash to escape they end up in the forbidden third floor corridor. Peeves has followed them as far as the door, but decides in the end that it would be more fun to taunt Filch than it would be to lead him to the four, thus allowing them to escape.

Trying to retrieve the copy of Quidditch Through the Ages that Harry had taken out of the library, and that Professor Snape had confiscated, Harry looks into the staff room, where he finds Filch binding up a wound on Snape's leg. Snape is incensed that Harry has seen this injury.

Harry receives an Invisibility Cloak for Christmas, and trying it out that night, opens a book in the Restricted Section of the library. The book starts screaming, and Harry runs, ducking under Filch's arm as Filch, wild-eyed, enters the Library. When Harry pauses for breath, he is alarmed to realize that, despite the distance he has traveled, Filch is approaching, saying that someone had been in the Restricted section. Harry is further dismayed to discover that the person Filch is talking to is Snape. The corridor is so narrow that the two of them won't be able to get past Harry, so Harry retreats though an open doorway, finding himself in a disused classroom containing the mirror of Erised.

When Hagrid's baby dragon, Norbert, is sent away, Hermione and Harry forget the Invisibility Cloak at the top of the tower. Filch catches them as they descend back into the school. Some time later, Filch escorts them, with Neville and Draco, who have also received detentions, over to Hagrid's, where they will be assisting Hagrid in searching for something that is killing unicorns.

Chamber of Secrets
At the Entrance Feast, Professor Dumbledore mentions that "our caretaker, Mr. Filch", has banned certain items; the full list of banned items is posted on his door.

Harry and Ron have received detention for driving a flying car into the Whomping Willow; at the end of the first week of classes, Professor McGonagall tells them that Ron's detention will be served with Filch, polishing the trophies, while Harry will be helping Gilderoy Lockhart answer his fan mail. Ron later says that he had a recurrence of the jinx he had tried to cast at Malfoy, and belched up a great lot of slugs on a Special Award for Services to the School, which he had then had to polish about ten times to get the slug slime off.

The Autumn weather is dismal and wet, and Harry, coming in from Quidditch practice, is sodden and muddy. Stopping to talk with Nearly Headless Nick, he is surprised by Filch's cat, Mrs. Norris, and, before he can make his escape, Filch himself. Filch, enraged, hauls Harry off to his office, where he begins writing him up for "befouling the castle". He is interrupted, however, by a loud crash from upstairs; shouting "Peeves!" he rushes off. Harry, left on his own, finds a letter from a company called "Kwikspell" on Filch's desk; looking at it, he sees that it is full of testimonials from people who say that the Kwikspell course had taught them magic when they had been unable to do any before. Harry, hearing Filch returning, puts the letter back on his desk. Filch returns, seemingly pleased: apparently Peeves has dropped a very valuable Vanishing Cabinet, and Filch seems to feel that this will compel Dumbledore to evict Peeves. Filch notices that the Kwikspell letter has been moved; he quickly shuffles it out of sight, then, looking embarrassed, tells Harry that he's free to go.

At Hallowe'en, Mrs. Norris is found Petrified and hanging from a torch bracket, near words scrawled on the wall: "The Chamber of Secrets has been opened. Enemies of the Heir, beware!". Enraged, Filch says that Potter has something to do with it, because he was in the vicinity at the time. Professor Dumbledore, arriving, takes Mrs. Norris off the torch bracket, and in company with Filch, Professor Snape, Professor McGonagall, Gilderoy Lockhart, Harry, Ron, and Hermione, carries her to Lockhart's office where he examines her. While it turns out that she is not dead, Dumbledore is unable to suggest how she was Petrified. Filch says that Harry must be involved, because he knows that Filch is... a Squib. Filch demands that someone be punished; Snape suggests that Harry must know more about things than he is telling, and suggests suspending him from the Quidditch team, a suggestion which McGonagall immediately resists. Professor Dumbledore reminds everyone that Harry is innocent until proven guilty, and tells Harry, Ron, and Hermione that they are free to go. Ron later explains why Filch was so upset; a Squib is a child of magical parents who is unable to do magic himself.

Over the next several months, we often see Filch wandering the hall trying to give students detention for "acting cheerful" or "breathing too loudly", sitting in a chair immediately under the torch bracket where Mrs. Norris was found, or trying to scrub the writing off the wall. Shortly after Christmas, Harry and Ron hear an outburst from Filch; peering around the corner, they find that he has abandoned his usual station, which turns out to be right outside Moaning Myrtle's bathroom, because Myrtle has turned on all the water and is flooding the hall. Investigating, Harry and Ron discover that someone has thrown a diary down a lavatory, and Myrtle is upset because it went through her head.

Filch does not play much more of a role in this book, but we do see him briefly at the end of the book when he is re-united with Mrs. Norris.

Prisoner of Azkaban
We don't see a lot of Filch in this book. At the first Hogsmeade weekend, Filch is checking people against a long list of names to see if they have permission to visit the village; Harry, not having permission, watches Ron and Hermione pass him, and then returns to Gryffindor tower. On the way, he is intercepted by Fred and George Weasley, who show him the Marauder's Map, a magical map that shows where everyone is in the castle. They say that they had stolen it from Filch's files once when they were being written up for setting off Dungbombs in the halls, but seeing how much greater Harry's need is than theirs, they give it to him, with instructions how to use it. This map is Harry's ticket to Hogsmeade, as it shows secret passages out of the school.

Filch is also present at Christmas dinner, and apparently it is rather ghastly watching him try to have a good time.

Goblet of Fire
Filch's role in this book is again minor. Harry notes that he is setting out extra chairs at head table at the feast celebrating the arrival of the two additional schools for the Tournament; Ron wonders why four chairs, as the only two guests that they know about are Madam Maxime from Beauxbatons, and Igor Karkaroff from Durmstrang. Ron's question is answered when Professor Dumbledore introduces the other two judges for the Triwizard Tournament, Ludo Bagman, and Bartemius Crouch. Shortly afterwards, Dumbledore asks Filch to bring out the casket that holds the Goblet of Fire.

When Harry, acting on a hint given to him by Cedric Diggory after the Yule Ball, visits the Prefects' Bathroom to try to decipher the clue in the Egg, he uses the Marauder's Map to see where Filch and Peeves are before venturing into the hallways. He checks again before heading back to Gryffindor Tower, and as he is doing so, he sees Bartemius Crouch in Snape's office. He chooses to investigate; getting his foot caught in a trick step, he drops the egg which immediately starts wailing. This summons Filch and, shortly, Snape. Filch believes that Peeves has stolen the Egg from one of the Champions and dropped it. Snape dismisses this concern, saying that someone has been in his office, and it must have been a wizard because of the charm he put on his door. The presence of the egg convinces Snape that Harry is there under his Invisibility Cloak. Professor Moody's arrival prevents Snape from finding Harry, and Moody sends both Snape and Filch on their separate ways before rescuing Harry from the trap he has gotten himself into.

Order of the Phoenix
Harry's scar pains him at the end of one of his sessions of detention with Dolores Umbridge, and he feels a need to write to Sirius Black, his godfather, to tell him about this. As he heads for the Owlery to mail the letter, he is spotted by Mrs. Norris. He is joined in the Owlery by Cho Chang, who is mailing off a birthday present for her mother. As they are talking, Filch bursts in, accusing Harry of preparing to mail off an order for Dungbombs. He demands to search Harry's pockets, but Cho defends him, saying that whatever it is, Harry had already sent it, she saw him.

When Harry heads to Hogsmeade for the next Hogsmeade weekend, Filch sniffs at him suspiciously; evidently he is carrying through on his threat in the Owlery that he will be watching for any scent of dungbombs on Harry. Harry mentions the episode in the Owlery to Ron and Hermione, wondering why Filch would have though that he would order Dungbombs. Hermione wonders who had tipped Filch off, and suggests that it might have been a ploy to get a look at Harry's mail.

When Hedwig returns with Sirius' answer, she has been attacked, and possibly the message that she carries has been read. This seems to confirm Hermione's suspicion that Filch had been instructed to try and read Harry's mail.

Shortly after Dumbledore leaves and Umbridge is appointed Headmistress, she asks Filch to summon Harry to her office. Filch is ecstatic, talking about how things will change now she's in charge. Umbridge has apparently told Filch that she is in favour of corporal punishment, and will be arranging to have Peeves evicted. Having told Harry all this, he announces Harry at Umbridge's door and then departs.

As Harry's interview with Umbridge is about to end, a series of explosions sounds in the main stairs. Umbridge and Filch run to investigate, but are powerless to handle the fireworks which Fred and George have set off. Having unsuccessfully tried to charm one of the fireworks away, Umbridge instructs Filch not to use magic against them; Harry is amused by this as he recalls that Filch, being a Squib, can't use magic anyway. Filch's attempt to dispose of a firework by hitting it with a broom is also unproductive, resulting only in a burning broom.

After Easter break, Fred and George become aware that Harry has need of Umbridge's fireplace, which is the only safe route he knows of to contact Sirius. They tell Harry that they are going to set off a diversion at 5PM. Though Hermione repeatedly advises against it, Harry decides to make use of the diversion to talk to Sirius. As he is speaking with Sirius, Harry hears someone entering Umbridge's office; hiding under his Invisibility Cloak, he watches as Filch enters the office and locates the forms to authorize whipping. Following Filch, Harry finds the twins, trapped by Umbridge in the Entrance Hall. Filch presents Umbridge with the necessary paperwork, and the twins, saying that they have had enough formal education, Summon their brooms and depart Hogwarts.

The diversion turns out to be a swamp, which now fills an entire corridor. Umbridge is unable to remove it, and the other teachers seem disinclined to try, so Filch is given the additional duty of taking students to their classes by punt. Additionally, in Fred and George's absence, many students are trying out for the role of chief troublemaker, and the halls are overwhelmingly redolent of dungbombs and stink pellets. Filch, along with Umbridge and her Inquisitorial Squad, are run ragged trying to catch troublemakers.

Presumably, Filch's life gets somewhat easier once Umbridge is fired, however, we don't hear of him again in this book.

Half-Blood Prince
Filch's role in this book is again diminished. We do hear from him that he feels that Umbridge is the best head Hogwarts has ever had; he seems to have forgotten the little matters of the swamp in the fifth floor corridor and the epidemic of dungbombs and stink pellets.

We hear that Filch has imposed a blanket ban on all products of Weasleys' Wizard Wheezes, and is scanning everyone who goes in and out of the school with Secrecy Sensors. He scans the Trio as they depart for their first Hogsmeade weekend. As they return, they are following behind Katie Bell, when she is Jinxed by a necklace she is carrying for someone at the school. Harry finds Hagrid to help get Katie back to school where she can be helped, and, carrying the necklace, follows. Meeting them at the school entrance, Professor McGonagall relieves Harry of the necklace, giving it to Filch to carry to Professor Snape.

Discussing this later, the Trio wonder exactly what was intended. With Filch scanning everything with his Secrecy Sensor, it is very unlikely that the package would have made it into Hogwarts, much less reached its eventual destination.

As Christmas, and Horace Slughorn's Christmas Slug Club Party, approach, Harry is the target of a large number of girls angling for invitations to the party from Harry. Hermione warns him to be careful of girls offering him things, they might well conceal love potions. Harry asks how they could get through Filch's secrecy sensors? Hermione points out that there isn't anything particularly Dark about love potions, and simply concealing them in perfume bottles, a service offered by Fred and George, would be sufficient to hide them.

Harry attends Slughorn's party with Luna Lovegood. Halfway through the party, Draco Malfoy is dragged in by Filch. Filch had caught him wandering the halls; Slughorn assumes that he was trying to gatecrash his party, and magnanimously invites him to join, to Filch's evident dismay. Draco and Snape, who is also present, very shortly manage to leave the party for a private discussion.

After Ron's birthday, at which he was first dosed with Romilda Vane's love potion, and then poisoned, Harry and Hermione leave the Hospital Wing with Hagrid to allow Ron's family to be with him. Hagrid mentions an angry conversation between Snape and Dumbledore which he had overheard, and Harry and Hermione are pressing him for more information when they are interrupted by the arrival of Filch, who is annoyed at students being out of bed at midnight. Hagrid angrily says that they are with him, a teacher, and as the quarrel starts to get loud, Harry and Hermione escape.

Harry interrupts Draco Malfoy when he is talking to Moaning Myrtle, and Draco retaliates by trying to hit Harry with the Cruciatus curse. Harry, in self defence, casts Sectumsempra. He is given detention for using Dark magic, and his detention is to recopy Filch's files that are beginning to deteriorate. These files have been specifically selected by Snape so that they include details of Harry's father's wrongdoings.

We do not see Filch again in this book.

Deathly Hallows
As almost none of the action in this book occurs in Hogwarts, we do not see very much of Filch. His appearance seems to be limited to a single cameo immediately before the first Battle at Hogwarts, where, much to his dismay, he is ordered to find Peeves and bring him to Professor McGonagall. We are told that he will be supervising the evacuation of the under-age students from Hogwarts, however.

Strengths
Through long residence in the castle, Filch knows pretty nearly everything there is to know about the physical layout of Hogwarts, and he is able to reach any location in the castle, from anywhere, almost immediately. Between himself and Mrs. Norris, Filch seems to be aware of everything going on in the castle, particularly if it is something forbidden.

Weaknesses
Argus Filch is a Squib, a child of wizard parents who has the inability to use magic. Harry discovers this in Harry Potter and the Chamber of Secrets when he spies Filch's "Kwikspell" letter, although he does not understand what that means until Filch says in front of him and Ron, "He knows I'm... I'm a Squib!" Even then, it is only when Ron explains what a Squib is that Harry understands the true significance of the Kwikspell letter and why Filch was so sensitive about it.

His lack of magical ability has made Filch singularly unsuited for almost any work available in the wizarding world; the caretaker position at Hogwarts is likely the only occupation available to him. Seeing this endless parade of wizarding children entering, gaining the skills he will never have, and leaving for a life he can only dream of, has left him bitter. This bitterness expresses itself in the endless restrictions he places upon the students and the powerful desire he has to torture them.

The author has stated that the Kwikspell course does not work for Filch; he is doomed to remain a Squib for all his life.

Relationships with Other Characters
Argus Filch has a lieutenant, his cat. Mrs. Norris is described as almost skeletally thin and dust-colored, and is apparently able to detect wrong-doing and report back to Filch, whereupon he appears on the scene to deal with the wrong-doer. She may be a magical cat-like animal known as a Kneazle, or like Crookshanks she may be a cat / Kneazle crossbreed. While many of the students have expressed a desire to harm Mrs. Norris for reporting their actions to Filch, she has never yet come to harm by a student. However, she was petrified by the monster from the Chamber of Secrets. Filch was desolated by her absence for the seven months before she was restored.

Filch is perpetually in a bad temper, and many of the deeds that he prosecutes students for are quite minor: he attempts to "write up" Harry for the unforgivable crime of dripping mud on the floor. This over-authoritative adherence to rules, many of which he makes up himself, has made Argus Filch an object of mild derision among the teachers, and widely disliked by the students.

In Dolores Umbridge, Filch seems to find a kindred spirit: it seems they both hate the students equally, and once she becomes Headmistress, Umbridge seems to be willing to allow Filch to start torturing the students. Filch seldom seems happier than when he is doing Umbridge's bidding.

It has been suggested that Irma Pince and Argus Filch have a relationship, by many fans, and in fact by Harry and Ginny in conversation. There is no evidence supporting this relationship anywhere else in the series (other than their standing together at Dumbledore's funeral), though they do seem to share a similar outlook on life and the students.

Mrs. Weasley tells us that Filch's predecessor was named Apollyon Pringle. Pringle had caught her and Arthur returning to the school after a 4AM stroll; apparently Mr. Weasley still bears the scars from that encounter.

Analysis
As is so often the case, the author is playing to a certain extent with classical mythology. In this case, the name "Argus" is likely selected from the mythical guardian with a thousand eyes. Given Filch's apparent awareness of all "malfeasance" within the school, this seems quite a reasonable parallel.

Questions

 * 1) Why does Argus Filch remain at Hogwarts when he often seems so miserable?
 * 2) How does Argus Filch feel about his lack of ability as a wizard?
 * 3) Why is Argus Filch so disdainful to the pupils of Hogwarts?
 * 4) To whom is Argus Filch related?
 * 5) Why is Argus Filch at Hogwarts? Why don't they just charm the castle clean?
 * 6) If Argus Filch is a cleaner, why are his clothes so dirty and ancient and his hair so greasy?

Greater Picture
It's certainly true that an establishment the apparent size of Hogwarts, occupied by that large a number of students, is going to need more than a single housekeeper; with magic, it would be possible, but the amount of space a single non-magical person can keep clean would be far less than the precincts of a castle. This is not helped by the teachers propensity to have their classrooms at the extreme ends of the castle - the Astronomy Tower, for instance, and Professor Trelawney's classroom at the top of the castle, and Professor Snape's classroom in the dungeons; nor can it be helped by the dormitories being similarly spread out, with Ravenclaw and Gryffindor in towers and Slytherin in a dungeon. It's only in the fourth book that we are informed that the castle also employs a large number of house-elves, who are charged with much of the domestic work including cleaning.

Given that the cooking, cleaning, and probably (to a large extent) mending is handled, what is the purpose of having a human housekeeper? We surmise that the main reason for the existence of the office is to manage the house-elves and maintain control over the students. House-elves would see students as "masters", as they see any human associated with the house that employs them, and so would allow the students to run riot. Additionally, a human overseer could be given instructions like "Maintain order, and keep the place clean," and would be able to break that down into suitable duties for the house-elves, presumably for other assistants like the portraits and the armor, in ways that these less-capable assistants could not. Additionally, a human would have the necessary authority to keep the students in line at times when the teachers were not available. Quite possibly some of this character goes back to the author's own childhood in grade school, where the janitor was a scary being simply because he was unknown.

So why Filch, why a squib in this important position where he might have to be dealing with magical children? We believe that in the series as a whole, this is in part meant to cast some light on Dumbledore's character. We know that Dumbledore has hired other squibs, notably Arabella Figg, and believe that this is a conscious choice on the part of the author to show that Dumbledore is particularly open-minded towards those who are unable to perform magic.


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User talk:65.96.61.1

Please stop adding nonsense to Wikibooks. It is considered vandalism. If you would like to experiment, use the sandbox. Thank you.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/

title: User talk:65.96.61.1


text: User talk:68.125.189.60

title: User talk:68.125.189.60


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Guide to Unix/Explanations/Real Networking Interfaces

Real Networking Interfaces are the actual physical network connections on a computer. For example, an Ethernet wire or wireless card is a real networking interface.

If an interface is only a tunnel through another interface, then it is a ../Fake Networking Interface.

Normally, there is somewhere in the ../Boot Process/ that configures network connections. Use the ifconfig command as root, though some Unix variants have a different command. A common configuration is to do DHCP with dhclient or pump command.

It is also possible to route packets between interfaces. This requires configuring the interfaces correctly and making a routing table. A firewall is a good idea.


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User:Lord Voldemort~enwikibooks/Topics

Ideas for topics that could reasonably permit textbooks to be written about:

Other Advanced Mathematics

 * You get the idea.

Other countries' history textbooks

 * I'm not going to list every country in the world, but you get the idea.

Anatomy & Physiology

 * You get the idea.

Etc.

 * You get the idea.

title: User:Lord Voldemort~enwikibooks/Topics


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Guide to Unix/Explanations/Pipes and Job Control

Pipes and Redirects
We can connect standard input, output, and error of commands to other commands or to files.

The   |    character is called a pipe and allows for the output of the command which precedes it to be redirected to the command which follows it (instead of being displayed as standard output).

The   >    character is a "shell redirection feature" and it redirects the output of the command which precedes it to the file whose name follows the said character. If the file already exists, then the   >    character will cause the file's contents to be wiped out by the new ones being redirected to it. An alternative is to use the   >>    pair of characters which will append the redirected contents to the file instead of wiping out the file's previous contents.

Job Control
You can run multiple commands at once, but only one can be in the foreground. The other commands can be in running at the background or suspended.

Create the shell script "date_loop.sh" while : do date > datefile sleep 10 done
 * 1) !/bin/bash

(Note: the shell script can be created with Emacs: run emacs date_loop.sh, type in the above script, then press CONTROL-X CONTROL-S to save the script, then CONTROL-X CONTROL-C to quit Emacs.)

Make date_loop.sh executable: $ chmod +x date_loop.sh

Run the command in foreground:

$ ./date_loop.sh

Wait a while (about 30 seconds) then use CONTROL-Z to send SIGTSTP signal to the process: ^Z[2] + Stopped (SIGTSTP)       date_loop

Look at the last line of datefile: $ tail -1 datefile; sleep 10; tail -1 datefile Thu Apr 27 10:46:06 BST 2006 Thu Apr 27 10:46:06 BST 2006

Note, that while the process was runnable, it was suspended, thus new "times" were not appended to the file in the 10 second interval between respective tail commands.

Put the process into background: $ bg [2]    date_loop.sh&

The process is resumed and datefile is being updated again:

$ tail -1 datefile; sleep 10 ; tail -1 datefile Thu Apr 27 10:48:34 BST 2006 Thu Apr 27 10:58:54 BST 2006

Note that you can type commands at the command prompt.

Put the process back into foreground: $ fg date_loop.sh

Send a 'SIGINT to the process by typing "control-C". This terminates the process. We confirm that datefile is not being updated anymore:

^C $ tail -1 datefile; sleep 20; tail -1 datefile Thu Apr 27 10:59:55 BST 2006 Thu Apr 27 10:59:55 BST 2006


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Guide to Unix/Explanations/Choice of Shell

A great variety of shells is available for Unix, including Bourne-compatible shells (sh, bash, ksh, pdksh, ash, dash, etc.), C shell (csh, tcsh), Z shell (zsh), and the Friendly Interactive Shell (fish).

The default interactive shell in many Linux distributions is Bourne-Again Shell (bash). The default script-execution shell in some Linux distribution is Debian Almquist shell (dash). The default shell in macOS used to be Bash as well but is now Z shell (zsh).

Bourne-compatible shells
All Unix shells are similar, but they have different features. If you are beginning, and you are not aware of the differences between shells, then you probably want to start with a Bourne-compatible, POSIX (Portable Operating System Interface)-compatible shell such as bash or ksh.

Bourne-compatible shells:
 * sh is the original Bourne shell. On many non-Linux systems, this is an old shell without the POSIX features. Thus bash and ksh (or even csh and tcsh) are better choices than sh. On some systems though, sh is really the same as bash or ksh.
 * bash is the GNU Bourne-again shell. It is mostly Bourne-compatible, mostly POSIX-compatible, and has other useful extensions. It is the default on most Linux systems. If it is not the default, it is probably installed on Linux, and can also be installed on non-Linux systems.
 * ksh is one of the three:
 * Public domain ksh (pdksh) is Bourne-compatible and mostly POSIX-compatible.
 * AT&T ksh was a commercial shell. It has all of the features of pdksh, plus the ksh93 version has several interesting extensions, different from bash. It is licensed under an opensource license since 2005; Mac OS X 10.4 includes it.
 * mksh is the MirBSD enhanced version of the Public Domain Korn shell (pdksh)
 * ash, the Almquist shell, is a POSIX compliant shell that is much smaller than bash. It is the default shell in multiple BSD variants. Its variant Debian Almquist shell (dash) is the default shell in Debian and Ubuntu Linux distributions for execution of shell scripts as opposed to interactive use.

Links:
 * , wikipedia.org
 * , wikipedia.org
 * , wikipedia.org
 * , wikipedia.org

C shell
BSD introduced the C shell, which sometimes resembles slightly the C programming language. This shell is csh. The shell tcsh is csh with more features. These shells are NOT Bourne-compatible. Many of the features were later added to the Bourne-compatible shells (except old copies of sh). When these features work differently in C shell and Bourne-compatible shells, this guide will describe the Bourne-compatible shells.

If csh or tcsh is your default shell, you might benefit by using bash or ksh to get Bourne-compatibility and POSIX features. Some users still prefer the C shell.

Links:
 * , wikipedia.org
 * , wikipedia.org

Z shell
There are alternative shells such as zsh, the Z shell. The Z shell boasts extra and unusual features that make it the preferred shell of many (for example, it has a builtin ftp client). Though the Z shell is almost Bourne-compatible, it differs in enough ways that its default behaviour is not Bourne-compatible, though zsh is capable of masquerading as a Bourne shell when so instructed. It can also emulate ksh.

Links:
 * , wikipedia.org

Temporarily using a different shell
If you do not like the shell that you are using, you might want to use a different shell such as ksh or bash. Shells are normal programs, and can be run easily. The SHELL environment variable will still contain the default shell. The exit command will return you to the first shell. tcsh> echo $SHELL /bin/tcsh tcsh> bash bash$ echo $SHELL /bin/tcsh bash$ exit exit tcsh>

Permanently changing the default shell
Find list of shells by looking at /etc/shells (which can be done by executing more /etc/shells). The command passwd -e, on some systems chsh, will prompt for a new shell. To change from bash to tcsh one can simply execute chsh which will query the user to enter the absolute path to a new shell:

$ chsh Password: Changing the login shell for baldur Enter the new value, or press ENTER for the default Login Shell [/bin/bash]: /bin/tcsh

or the user can specify the shell:

$ chsh -s /bin/tcsh Password:

The shell must be specified using its absolute path, which may be found using which tcsh.

Links:
 * , wikipedia.org
 * , wikipedia.org

Related books

 * Bourne Shell Scripting
 * Bash Shell Scripting
 * C Shell Scripting

Links

 * Top 5 open source command shells for Linux, opensource.com
 * Unix Shells: Bash, Fish, Ksh, Tcsh, Zsh, hyperpolyglot.org
 * Evolution of shells in Linux, ibm.com
 * Why is Bash everywhere (in most if not all Linux distributions)?, superuser.com
 * 1.8 There Are Many Shells in Unix Power Tools by Peek, O'Reilly & Loukides, docstore.mik.ua
 * 2. Shell Command Language in The Open Group Base Specifications Issue 7, opengroup.org
 * , wikipedia.org
 * , wikipedia.org


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Guide to Unix/Explanations/Quoting and Filename Expansion

Special characters and substitution
The shell recognizes several special characters. The following are the special characters:
 * \ (backslash)
 * " (double quote)
 * ' (single quote)
 * # {number sign, pound sign, or hash)
 * $ (dollar sign)
 * ` (tick)
 * ~ (tilde)
 * { and } (braces or curly brackets)
 * ( and ) (parentheses)
 * * (asterisk, star or splat)
 * ? (question mark)
 * < (less than sign)
 * > (greater than sign)
 * & (ampersand)
 * (pipe)
 * ; (semicolon)
 * ! (exclamation point or bang)

They are all special characters in the Bourne shell, except for the exclamation point. However, many Bourne and non-Bourne shells also make special the exclamation point. When the shell sees special characters, it does something more complex than simply running the command that you typed.

Some special characters trigger substitution, when parts of the command are replaced with other text. One common form of substitution is filename expansion, which saves you work when typing longer filenames and lists of filenames.

To test substitution, we need the echo command. This command simply echoes its arguments (including any changes made to the arguments by the shell). All options except "-n" are ignored. $ echo -lnQ arg1 arg2 arg3 -lnQ arg1 arg2 arg3

Quoting
Quoting is used to preserve the literal meaning of special characters.

Here is an example of several types of quoting, which will be referred to in the rest of this section (there are many unnecessary things in this which you should find after reading this section, but are used for the sake of example):

$ echo There is \"a small possibility\" that '/etc/*tab' are " not " text and a backslash will not be printed after this. \\ There is "a small possibility" that /etc/*tab are not  text and a backslash will not be printed after this. \

Backslash
A backslash (\) simply stops the shell from thinking that certain characters are special. In the example above, it was used to print literally the doublequote character.

To print a backslash, use two backslashes in a row.

Now commands that want special shell characters for input will work.

Paired quoting characters
Paired characters affect whatever is between them.

Single quotes
Single quotes prevent all expansion, thus preserving the literal meaning for all chars.

In the example, single quotes were used to prevent the * from expanding.

Single quotes can't be used within single quotes. Any 2nd single quote always terminates the 1st, whereas a 3rd single quote begins the next pair.

Double quotes
Double quotes are like single quotes, but don't preserve the literal meaning of $, \ when followed by a dollar sign, tick, double quote, or backslash, and `.

In the example, double quotes were used to preserve the literal meaning of spaces.

Filename expansion
Filename expansion uses the following characters to avoid typing long lists of files: * ? { }

* and ?
The shell globbing characters of * and ? are used to form patterns. The shell searches for existing files that match the patterns and does a subsitution.
 * * matches 0 or more characters, except /
 * ? matches any 1 character except /

When more than one file is matched, the files are separated by spaces, as separate arguments.

For example, /etc/ss* means all of the files inside the /etc directory which begin with the letters ss. The echo command demonstrates the substitution. The results may differ on your system, depending on what files you have. $ echo /etc/ss* /etc/ssh /etc/ssl

The echo command did this because it thinks that you ran echo /etc/ssh /etc/ssl. The shell substituted those names for /etc/ss*. Though /etc/ssh/ssh_config exists on many systems, it appeared not above, because <tt>*</tt> never matches <tt>/</tt>.

Now here is something more useful. We will use substitution with a command other than "echo". We will combine filename expansion with the ls command. $ ls /etc/ss* /etc/ssh: ssh_config                ssh_host_key               ssh_host_rsa_key.pub ssh_host_dsa_key          ssh_host_key.pub           sshd_config ssh_host_dsa_key.pub      ssh_host_rsa_key /etc/ssl: lib         openssl.cnf  private      x509v3.cnf

Notice how the * reduced extra typing. If we did <tt>ls /etc/s*</tt>, we would probably further reduce the amount the user needs to type.

Here is an example of the ? character at work: $ ls /etc/ssh/ssh_host_???_key /etc/ssh/ssh_host_dsa_key /etc/ssh/ssh_host_rsa_key

When expansion fails
Sometimes, when using * or ?, no files are found. In this case, the shell does not give an error; it simply does no substitution. Suppose that in the machine on the example above, we make a mistake and typed <tt>/etc/sss*</tt> which matches nothing. Then the shell would do no substitution: $ echo /etc/sss* /etc/sss*

Curly brackets expansion
The curly brackets help when typing several similar arguments, especially filenames. The filenames do not need to actually exist. Example: $ echo /etc/ss{h,l,ssnakes} /etc/ssh /etc/ssl /etc/ssssnakes

They are very useful for long lists of files in the same directories: $ echo /bin/{ls,mv,cp} /sbin/{halt,reboot} /bin/ls /bin/mv /bin/cp /sbin/halt /sbin/reboot

You can also use them to print the alphabet (or numbers): $ echo {z..a} z y x w v u t s r q p o n m l k j i h g f e d c b a


text:
User:Etscrivner

I am someone who is extremely interested in the fields of computer science and mathematics. I've written several computer emulators namely:

 * NeoPSX
 * NeoChip8
 * NeoGameBoy

And also several emulator plugins:

 * PADzenogais[DX9]
 * PS2SP

I'm hoping to contribute a substantial amount to the Emulation wikibook, in order to create a unified resource for people looking to write an emulator in any langauge.

title: User:Etscrivner


text:
User talk:12.215.248.159

Please stop adding nonsense to Wikibooks. It is considered vandalism. If you would like to experiment, use the sandbox. Thank you.

title: User talk:12.215.248.159


text:
User talk:204.210.151.66

Please stop adding nonsense to Wikibooks. It is considered vandalism. If you would like to experiment, use the sandbox. Thank you.

title: User talk:204.210.151.66


text:
User talk:68.68.4.190

Please stop adding nonsense to Wikibooks. It is considered vandalism. If you would like to experiment, use the sandbox. Thank you.

title: User talk:68.68.4.190


text:
Cookbook talk:Risotto

I think this should be merged with the Cookbook:Risotto article, preferably under that name. 'Italian Risotto' sounds a little redundant to me, I have never heard of any other risotto's. risk 01:38, 22 November 2005 (UTC)

title: Cookbook talk:Risotto


text:
Handbook of Genetic Counseling/Cri-du-chat syndrome - deletion 5p

Cri-du-chat syndrome - deletion 5p

Contracting

 * Introduction
 * Ask about what their main concerns are
 * Explain that we will update medical and developmental history since her last visit to genetics
 * Doctor will perform physical examination
 * We will discuss your concerns and any recommendations we have

Interim History
(Follow form, but specifically ask about list of potential health problems located below Overview)
 * Cri du chat is a syndrome that is associated with a deletion of the short arm of chromosome 5
 * French for "cat's cry"
 * incidence is 1:50,000 (Van Buggenout et al., 2000 ) may be as high as 1:20,000 (OMIM)

Characteristic features

 * usually suspected at birth based on characteristic monochromatic, high-pitched cry
 * poor suck, vomiting, failure to thrive, respiratory distress and jaundice present in 60-92%
 * microcephaly
 * round face
 * hypertelorism
 * epicanthal folds
 * down-slanting palpebral fissures
 * low-set ears
 * micrognathia
 * psychomotor retardation
 * high arched palate
 * as individuals with 5p deletion get older change of phenotype is noted and it is less striking and harder to diagnose (face lengthens, face becomes "coarse", prominent supra-orbital ridges, deep-set eyes, hypoplastic nasal bridge, severe dental malocclusion, relatively large mouth, and full lower lip)

Potential health problems

 * several cardiac anomalies described in a small number of patients (ASD, VSD, tetralogy of fallot and PDA)
 * cleft palate (rare)
 * gastrointestinal abnormalities include malrotation and Hirschprung disease
 * teeth abnormally erupted
 * Apnea
 * Strabismus
 * Minor vision problems
 * Gastric reflux
 * Chronic constipation (well managed in most cases)
 * Colic
 * Frequent ear and upper respiratory infections
 * Scoliosis
 * Sleep disorders
 * Saliva control problems (if not resolved during childhood surgery can help correct)
 * Minor hearing impairment

Growth

 * compared with the standard population, most children with cri-du-chat syndrome are small at birth
 * as they grow most have significant microcephaly
 * weight compromised for age
 * slow growth frequently observed
 * may be evidence of intrauterine growth retardation

Life expectancy

 * Difficult to predict
 * 10% mortality in first year due to respiratory or cardiac complications
 * Believed that if no major health problems present life span would be in normal range

Learning

 * study of 26 children ages 6 yr. 4 mths and 15 yr 5 mths
 * moderate to severe learning difficulties and developmental delay are usually observed
 * 24 were in severe learning disability range
 * better receptive than expressive language
 * study of seven patients
 * 6 severe or profound MR
 * 1 mild MR
 * Language comprehension may not be as impaired as language production
 * Clear benefit shown in those children that received early intervention services compared to those that did not
 * Developed many self-care skills
 * Communicate through short sentences, words, signs, or gestures

Behavior

 * study examined the range, distinctiveness, and correlates of maladaptive behavior in 146 subjects using the Aberrant *Behavior Checklist as a standardized measure
 * Hyperactivity was the most significant and frequent problem in the sample
 * Subjects also showed aggression, tantrums, self-injurious behavior
 * some of these problems were more pronounced in individuals with lower cognitive-adaptive levels, as well as in those with histories of previous medication trials
 * Autistic-like features and social withdrawal were more characteristic of individuals with translocations as opposed to deletions, even when controlling for the lower adaptive level of the translocation group
 * head banging, hitting the head against body parts, self-biting and rumination are the most frequently occurring behaviours in CCS
 * Aggressive behaviour was reported for 88%, with a statistically significant negative correlation between age and the number of aggressive behaviors reported
 * Study of 7 older patients most had periods of destructive behavior, self mutilation and aggression
 * Other reported behaviors include:
 * Repetitive movements
 * Obsessive attachment to objects
 * Hypersensitivity to sensory stimuli
 * Feeding and sleeping problems
 * Mood disorders

Genetics

 * 85% are sporadic deletions *10-15% are familial (usually parental translocation rarely a familial inversion)
 * PARENTAL CHROMOSOMES SHOULD BE DONE SO ACCURATE RECURRANCE RISKS CAN BE CALCULATED
 * Gene that makes Delta-catenin (an adherends junction protein involved in cell motility and expressed early in neuronal development)
 * delta-catenin maps to a specific region in 5p15.2 that has been implicated in the mental retardation phenotype
 * strong correlation between the hemizygous loss of delta-catenin and severe mental retardation

Genotype-phenotype correlation

 * Patients show phenotypic and cytogenetic variability
 * Genotype-phenotype correlation in 62 patients with terminal deletions highlighted a progressive severity of clinical manifestation and psychomotor retardation related to the size of the deletion (Mainardi et al., 2001). Whereas other study reported no correlation with size of deletion and severity in 50 patients (Marinescu et al., 1999).
 * The analysis of seven patients with interstitial deletions and one with a small terminal deletion confirmed the existence of two critical regions, one for dysmorphism and mental retardation in p15.2 and the other for the cat cry in p15.3
 * study lends support to the hypothesis of a separate region in p15.3 for the speech delay
 * One family with deletion 5p where breaking point is slightly distal to 15.3 showed only

Patient resources/ references

 * 5p- Society (Cri-du-Chat) -- support group
 * 11609 Oakmont
 * Overland Park, KS 66210
 * Phone: (913) 469-8900
 * E-mail: fivepminus@aol.com
 * Web Site: http://www.fivepminus.org/
 * Conference in SLC Aug 15-19, 2002

 * Chromosome Deletion Outreach
 * P.O. Box 724
 * Boca Raton, FL 33429-0724
 * E-mail: cdo@worldnet.att.net
 * Web site:members.aol.com/cdousa/cdo.htm
 * Cri Du Chat Support Group of Australia Inc.
 * Email: info@criduchat.asn.au
 * Web: http://www.criduchat.asn.au


text:
Handbook of Genetic Counseling/Cystic Fibrosis Carrier Screening-1

Cystic Fibrosis Carrier Screening

Disease Characteristics

 * Autosomal recessive (use visual aide to describe)
 * Build up of mucus in lungs and pancreas
 * Failure to thrive
 * Diarrhea
 * Pneumonia
 * Small intestine obstruction
 * Pulmonary disease
 * Pancreatic disease
 * Male infertility
 * Survival rate= aprox. average of 35 years
 * Cognitive function is typically not impaired

Incidence rates

 * 1/3300 live births - Caucasian
 * 1/15300 - African American
 * 1/32000- Asian

Carrier frequencies

 * 1/26 in the Ashkenazi Jewish Population
 * 1/25 N. and S. European
 * 1/46 Hispanic
 * 1/60 African American
 * 1/90 Asian American

Who should be tested

 * Individuals with a family history and their partners
 * Couples planning pregnancy from the high risk ethnic backgrounds
 * Gamete donors
 * Spouses of a known carrier
 * NIH recommended in April 1999 that all pregnant couples get offered this test and all planning pregnancies

Types of testing

 * DNA - PCR using DF508 and 7 other mutations (use visual aide to describe)
 * Done by a multiple of centers
 * $235.00
 * Turnaround time is 7-10 days
 * Carrier test detection rate
 * 80-90% (depends on center)
 * Blood sample
 * 10-15cc
 * lavender EDTA
 * DNA chip - 86 mutations
 * Done by Genzyme (1-800-848-4436): http://www.genzymegenetics.com/Our-Services/Reproductive-Testing/cf-plus.aspx
 * 7-14 days turnaround
 * $235.00
 * Carrier Test Detection Rates
 * 90% for N. Europeans
 * 70% for S. Europeans
 * 97% for Ashkenazi Jewish
 * 75% for African American
 * Blood samples
 * 20cc for adults
 * 5-7cc for children
 * yellow-top ACD-A
 * lavender top EDTA
 * Linkage - extremely rare mutations in a family


text:
Handbook of Genetic Counseling/Cystic Fibrosis Carrier Screening-2

Cystic Fibrosis

What is CF?

 * Cystic Fibrosis (CF) is one of the most common inherited diseases, affecting about 1 in 3300 live births in the United States.
 * It is most common in Caucasians.
 * CF is a complex multisystem disease that affects the respiratory tract, pancreas, intestine, reproductive tract, and hepatobiliary system.
 * CF causes many parts of the body to produce thick mucus leading to pneumonia, diarrhea, poor growth, and infertility. This is due to the faulty transport of sodium and chloride within cells lining certain organs.

Diagnosis

 * The median age at diagnosis is 6 to 8 months; nearly two-thirds of individuals are diagnosed before 1 year of age.
 * The diagnosis of CF is established in individuals with one or more characteristic phenotypic features of CF plus evidence of an abnormality in CFTR function based upon ONE of the following:
 * Presence of two disease-causing mutations in the CFTR gene
 * Two abnormal quantitative sweat chloride values
 * An abnormal value for the transepithelial nasal potential difference (NPD)
 * The sweat test has been the "gold standard" for diagnosing CF for more than 40 years.
 * It is a diagnostic procedure that determines the amount of sodium and chloride (salt) in the sweat.
 * It is painless, relatively inexpensive, and gives definitive answers.
 * The test can be performed on individuals of any age.
 * A colorless, odorless chemical known to cause sweating is applied to a small area on the arm or leg.
 * An electrode is attached to stimulate a weak electrical current to the area. Patients may feel a tingling sensation in the area or a feeling or warmth. This lasts approximately 5 minutes.
 * The stimulated area is then cleaned, and sweat is collected on filter paper or in a plastic coil. This is analyzed for increased amounts of sodium and chloride.
 * The diagnosis of CF may be made in the absence of phenotypic features of CF in the following circumstances:
 * Confirmed diagnosis of CF in a sibling and an abnormal sweat chloride value or presence of the same two disease-causing mutations in the CFTR gene as identified in the affected sibling.
 * Diagnosis in a newborn screening program.
 * As of November 2001, Colorado, Wisconsin and Wyoming offer CF in the newborn screen.
 * Connecticut, Massachusetts, and Montana either test in a select population, have a pilot program, or are planning to begin CF newborn screening.
 * In utero diagnosis by CFTR mutational analysis.
 * 10.3% of newly diagnosed patients in 1999 were diagnosed by newborn screening or prenatal diagnosis.

Prognosis

 * Median survival has increased from 18 years in 1976 to 30.1 years in 1995. Current approximation is 36.5 years (geneclinics.org).
 * Pulmonary disease is the major cause of morbidity and mortality in CF. Patients have lower airway inflammation and chronic endobronchial infection, which often progresses to end stage lung disease characterized by extensive airway damage.
 * Patients with pancreatic sufficiency (<10%) have a milder clinical course with greater median survival (56 years according to 1995 CFF Patient Registry) as compared to those with pancreatic insufficiency.
 * There is a wide variability of disease expression from death in early childhood to patients presenting as young adults with a history of recurrent sinusitis and bronchitis or male infertility.

Features of CF

 * Intelligence is normal.
 * Phenotypic feature of CF may include:
 * Chronic sino-pulmonary disease
 * Including chronic cough, sputum production, chronic wheeze, obstructive lung disease on lung function test, chronic chest radiograph abnormalities, and digital clubbing.
 * Gastrointestinal/nutritional abnormalities
 * Such as malabsorption/pancreatic insufficiency, distal intestinal obstructive syndrome, rectal prolapse, recurrent pancreatitis, chronic hepatobiliary disease, failure to thrive, hypoproteinemia, and fat-soluble vitamin deficiencies.
 * Infertility
 * More than 95% of males with CF are infertile due to azoospermia resulting from altered Wolffian duct structures.
 * Most women with CF are fertile, although some have abnormal cervical mucus which may contribute to infertility
 * Salt-loss syndrome

Management

 * Referral to a regional CF center is strongly recommended for individuals with CF.
 * Epidemiological data show that patients followed on a regular basis in accredited CF centers have improved clinical outcome.
 * Respiratory:
 * Patients are regularly followed with pulmonary function studies, chest radiographs, and specific blood and urine tests.
 * Intervention to treat or prevent pulmonary complications may include oral, inhaled or I*antibiotics, bronchodilators, anti-inflammatory agents, mucolytic agents, and chest physiotherapy (postural drainage with chest percussion).
 * Gastrointestinal:
 * Nutritional therapy may include special formulas for infants to enhance weight gain, supplemental feeding to increase caloric intake, and additional fat-soluble vitamins to prevent vitamin deficiencies.
 * Pancreatic insufficiency is treated with oral pancreatic enzyme replacement.
 * Pregnancy:
 * With increasingly better pulmonary treatment and improved nutrition, pregnancies today are well tolerated, especially in women with mild to moderate disease.
 * The risk for congenital anomalies in the fetus has not been seen to be increased.
 * Breastfeeding is possible.
 * Gene therapy is in a research phase only and is not able to control or treat the symptoms related to CF at this time.
 * U.S. Congress appropriated $40 million to the NIH to establish nine CF gene therapy centers, which will run clinical trials for the development of gene therapy technology.
 * Pilot and feasibility studies are currently active at the following gene therapy centers:
 * Cornell University Medical College, New York, New York
 * Institute for Human Gene Therapy at the University of Pennsylvania, Philadelphia
 * Johns Hopkins University School of Medicine, Baltimore, Maryland
 * University of North Carolina at Chapel Hill
 * University of Washington, Seattle
 * University of Iowa, Iowa City
 * University of Alabama at Birmingham.

Inheritance

 * CFTR gene mutations are inherited in an autosomal recessive manner.
 * Parents of a proband are obligate carriers.
 * Carriers are asymptomatic. They have no biochemical or physiologic alterations by which they could be readily identified.
 * Siblings of a proband have a 25% chance of being affected, a 50% chance of being an unaffected carrier, and a 25% chance of being unaffected and not a carrier.

Molecular Study

 * CF's causative gene, CFTR (cystic fibrosis transmembrane conductance regulator), and its mutations were characterized in 1989.
 * The normal gene product of the CFTR gene is a 1,480 amino acid integral membrane protein that functions as a regulated chloride channel in epithelial cells.
 * The CFTR gene is 230 kilobases, contains 27 exons, and produces a 6.5 kilobase mRNA product.
 * There are over 900 mutations known; almost all are point mutations or small (1-84 bp) deletions and are specific to an affected family.
 * The most common mutation is delta F508, which accounts for about 30-80% of mutant alleles depending on the ethnic group.
 * There is a panel of 25 CFTR alleles recommended by the American College of Medical Genetics for general population CF carrier screening.
 * Mutations in CFTR can affect the CFTR protein quantitatively and/or qualitatively.
 * The best correlation between genotype and phenotype occurs in the area of pancreatic sufficiency. The most common mutations have been classified as pancreatic-sufficient (PS) or pancreatic-insufficient (PI).
 * Patients with pancreatic sufficiency usually have either one or two PS alleles.
 * In contrast, genotype-phenotype correlation is generally poor for pulmonary disease in CF.
 * Many mutations are sufficiently rare that genotype-phenotype predictions cannot be made on the basis of empirical studies of populations of patients.

Population Genetics

 * The CFTR mutation detection rate varies with ethnic background.
 * The following chart approximates incidence and carrier frequency by ethnicity:
 * Group Incidence Carrier Frequency
 * Caucasian 1/3,300 1/28
 * Hispanics 1/8-9,000 1/46
 * African American 1/15,300 1/61
 * Asian Americans 1/32,100 1/90

Genetic Testing

 * Molecular genetic testing for disease causing mutations in the CFTR gene (7q31) is used:
 * To establish or confirm the diagnosis of CF in symptomatic individuals.
 * For carrier detection in population screening programs, in at-risk relatives, and their reproductive partners.
 * In prenatal testing of at-risk pregnancies and for pregnancies in which fetal echogenic bowel has been identified.
 * The GeneTests-GeneClinics Laboratory Directory lists 64 worldwide labs that offer clinical testing for CF.
 * This list is not comprehensive because laboratory participation is voluntary.
 * There are additional laboratory sites that offer research testing for CF.
 * Genzyme Genetics: http://www.genzymegenetics.com/Our-Services/Reproductive-Testing/cf-plus.aspx
 * Genzyme has a mutation panel containing 97 of the most common mutations, including those found in diverse ethnic populations or associated with mild disease.
 * Many commercial testing facilities offer only the recommended panel of 25 mutations.
 * Specimen Requirements:
 * 1. Blood: ACD-A (yellow-top) or EDTA (lavender-top) tube. Adult: 10 ml whole blood; 30 ml whole blood if ordering multiple tests.
 * 2. Dried Blood Spot: Dried blood spots collected on Genzyme provided filter paper/test requisition. Fill a minimum of three circles completely with blood. Please Note: If prenatal carrier screening for cystic fibrosis is ordered in conjunction with first trimester screening all six circles should be filled.
 * 3. Mouthwash: Please Note: Patient should not eat, drink, smoke or chew gum for at least one hour prior to collection. (See specimen kit for detailed instructions). Mouthwash samples can be sent when ordering up to two tests. When ordering more than two tests, blood samples are required. 10 ml of Scope® mouthwash that has been swished vigorously for at least 1 minute. Collect in orange-top 50 ml polypropylene tube.
 * 4. Prenatal: Please Note: Call a laboratory genetic coordinator prior to obtaining any specimens. In some circumstances, specimens from other family members may be required. All prenatal specimens (including cord blood) must be accompanied by a maternal blood or mouthwash specimen for analysis of possible maternal cell contamination. Discard first 2 ml; then 15 ml amniotic fluid in 15 ml orange-top polypropylene tube, 10-15 mg chorionic villi in laboratory-provided screw-top tubes with sterile transport medium or 1 T-25 flask of confluent cells. Additional sample must be obtained for back-up culture at one of our cytogenetics laboratories or another facility. If additional testing is desired, more amniotic fluid is needed. For example, chromosome analysis requires an additional 15-25 ml (see Cytogenetics – Amniotic Fluid Chromosome Analysis test page: http://www.genzymegenetics.com/Our-Services/Reproductive-Testing/amniotic-fluid-testing.aspx) and AFAFP requires an additional 2 ml (see Amniotic Fluid Alpha-Fetoprotein - AFAFP test page: http://www.genzymegenetics.com/Our-Services/Reproductive-Testing/afafp-test.aspx).
 * Genzyme provides a brief informed consent for DNA testing for the patient: http://www.genzymegenetics.com/For-Clients/informed-consent-forms-reproductive.aspx
 * Ambry Genetics Corporation
 * On 10/17/01, a press release from Ambry Genetics reported the development of "The Ambry Test: CF, the most comprehensive genetic test analyzing the CF gene."
 * This test is a PCR based assay analyzing exonic and surrounding intronic regions of the patient's genomic DNA.
 * Sequence analysis of the full CFTR gene allow for detection of novel mutations.
 * As of 01/20/02 Ambry reports having found 64 different mutations, and seven of those are novel variants found in patients with CF.
 * The cost is $285, and results are available in 1-4 weeks.
 * This test may be useful for patients diagnosed with CF who have received a negative test result from the Genzyme panel analysis.
 * CHMCC
 * The Children's Hospital has a contract agreement with Genzyme; so standard CF testing is done with them.
 * The cost of the blood test is $270, but 60% of that cost is in added charges from the CHMCC laboratory. Genzyme offers the test for $110.
 * Blood specimens are typically used for carrier testing; 20 cc of blood in a purple top (EDTA) tube is sent at room temperature.
 * Patients can be sent to the test referral center with the Genzyme test requisition form: http://www.genzymegenetics.com/For-Clients/test-requisitions.aspx, and the test referral center will take care of all processing.
 * Samples should be drawn on Monday through Wednesday or Thursday before noon.
 * Results typically take 2 weeks and are faxed to the lab unless you write in the fax number for the Human Genetics Department.
 * The original report is mailed to the referring physician, and the patient is typically phoned with the results.
 * Don't forget that the referring physician MUST sign the test requisition form!

Prenatal Diagnosis

 * Prenatal testing is available for pregnancies at 25% risk in which the disease-causing mutations of the CFTR gene have been identified in both parents.
 * It is also available for pregnancies in which fetal echogenic bowel and/or dilated bowel is observed on ultrasound examination.

NIH Consensus Statement

 * A NIH Consensus Development Conference was held in 1997 to address the issue of genetic testing for CF.
 * The conclusion was that genetic testing for CF should be offered to adults with a positive family history of CF, to partners of people with CF, to couples currently planning a pregnancy, and to couples seeking prenatal care.
 * The panel did not recommend offering CF genetic testing to the general population or newborn infants.
 * They felt that the offering of CF carrier testing should be phased in over a period of time to ensure that adequate education and appropriate genetic testing and counseling services are available to all people being tested.

Resources

 * Cystic Fibrosis Foundation
 * Phone: (800) 344 4823
 * Email: info@cff.org
 * Website: www.cff.org

 * NCBI Genes and Disease Webpage at www.ncbi.nlm.nih.gov/disease/CF


text:
Handbook of Genetic Counseling/Cystic Fibrosis - Prenatal Diagnosis-1

Cystic Fibrosis - Prenatal Diagnosis

Introduction and Contracting

 * What are your main reasons for seeking genetic counseling?
 * Do you have any particular questions or concerns you would like to discuss?
 * Address any immediate concerns or indicate that they will be addressed later during the discussion
 * Outline the session including the information they want to know
 * First I'll obtain more information about medical and family history to determine if there is anything else that we may want to discuss today
 * Then we can discuss cystic fibrosis and answer any questions you have

Review Genes and Chromosomes
FACTS ABOUT CF
 * Sometimes it is helpful to review some basic genetics principles because it is not something most people think about every day.
 * Review genes and chromosomes and explain autosomal recessive inheritance

CF Overview

 * CF is one of the most common inherited diseases (affects 1 in 3300 live births in US)
 * occurs in individuals of all races and ethnicities, but is most common in Caucasians
 * Due to changes in both copies of a gene that instructs the body about how to make a protein channel that transports sodium and chloride into cells that line certain organs
 * These channels are either not made or don't work properly
 * This leads to production of thick mucus in the lungs which then leads to an increased risk of infections and pneumonia that may require periods of hospitalization
 * It can also cause interference with digestion, which can lead to diarrhea and poor growth
 * It also often causes infertility in males and may cause decreased fertility in females

Features of CF
decreased fertility in females due to abnormal cervical mucus that can contribute to infertility
 * normal intelligence
 * features may include
 * chronic sino-pulmonary disease: cough, sputum production, wheezing, obstructive lung disease, chronic chest radiograph abnormalities, digital clubbing
 * gastrointestinal/ nutritional abnormalities: malabsorption/ pancreatic insufficiency (foul, bulky, fatty stools) distal intestinal obstructive syndrome, rectal prolapse, recurrent pancreatitis, chronic hepatobiliary disease, failure to thrive, hypoproteinemia, fat soluble vitamin deficiencies
 * infertility: 98% of males with CF infertile due to unilateral or bilateral agenesis of vas deferens

Diagnosis

 * median age diagnosed is 6-8 months (2/3 dx before age 1)
 * diagnoses established in people with one or more phenotypic features and one of following
 * presence of 2 disease-causing mutations in the CFTR (cystic fibrosis transmembrane regulator) gene
 * two abnormal quantitative sweat chloride values (the "gold standard")
 * painless, relatively inexpensive, definitive answer)
 * abnormal value for the transepithelial nasal potential difference (NPD)
 * diagnosis established in absence of phenotypic characteristics when
 * confirmed dx of sibling and abnormal sweat chloride value or presence of same two mutations as in the sibling

Prognosis

 * survival increased from 18 years 1976 to 30.1 years 1995 currently approximated at 33 yrs (geneclinics)
 * pulmonary disease major cause morbidity and mortality
 * patients with pancreatic sufficiency (<10%) have milder course and greater survival (56 yrs 1995 CFF Patient Registry
 * wide variability in disease expression

Incidence

 * Caucasians 1/2,500
 * African-Americans 1/18,000
 * Asian Americans 1/90,000
 * 30,000 affected in US 8,000,000 carriers in US
 * carrier rates see chart in visual aids

CF gene and common mutations

 * located on 7q
 * 250,000 bp, 27 exons and 1,480 aa's
 * functions as a regulated chloride channel in epithelial cells
 * over 900 known mutations (most point mut. or small del.)
 * genotype/phenotype correlation (both severe and mild mutations)
 * delta F508 most common (30-80% of mutations)

CF Carrier Screening
Results take about 2 weeks according to genzyme
 * As mentioned CF occurs more frequently in Caucasians than other ethnicities (one in 25,000 Caucasians affected and 1 in 28 are carriers)
 * AR inheritance, both parents must be carriers to have child with CF
 * a blood test is offered that can determine if an individual is a carrier of CF
 * assess whether interested in this testing
 * testing at CHMC now offered and screens for 25 of most common mutations
 * now CHMC does the panel for ________????
 * GENZYME panel of 87
 * carrier detection rate with the panel is 90% if of Northern European Descent and 70% if of Southern European descent.
 * The 87 mutation analysis by genzyme detects 85-90% of carriers if Caucasian
 * cost was $265 when done through CHMC, but sent to genzyme CHMC added on a lab fee

Options for Pregnancy and Future Pregnancies if Both Were Carriers

 * Testing can determine if a fetus is affected before they are born
 * Amnio can be performed to test and see if fetus has CF and it is greater than 99% accurate if the mutations that parents carry are known
 * Future pregnancies also have option of CVS performed earlier than amnio 10-12 weeks
 * Describe if interested
 * preimplantation genetic diagnosis-Where they perform genetic testing on embryos obtained using in vitro fertilization techniques. Then only implant those that don't have CVS
 * If interested would be important to review costs and success rates

Review

 * Assess if there are any questions or other concerns throughout the session
 * Assess how they feel about carrier testing
 * Offer patient literature on CF

Psychosocial Considerations

 * May be nervous about pregnancy due to earlier loss
 * Normalize early losses
 * May not know much about partner's history
 * Check to determine who she has for support family friends
 * Assess their experience with CF and make certain to explain that the symptoms and how affected someone is varies even among family members with same mutation
 * May think risk is higher than it is for CF so get a feel for how likely she thinks it is


text:
Handbook of Genetic Counseling/Cystic Fibrosis - Prenatal Diagnosis-2

Cystic Fibrosis - Prenatal Diagnosis

Introduction and Contracting

 * Acknowledge any prior contact
 * Ask them what they hope to gain from the session
 * Do you have any particular questions you would like to discuss?
 * Address any immediate concerns or indicate that they will be addressed later during the discussion
 * First I'll obtain more information about medical and family history
 * Then review CF and discuss family planning options including prenatal testing and PGD

Obtain Medical and Family History

 * Ask them to describe their experience with receiving a diagnosis of CF in their daughter
 * What type of testing did your daughter receive to confirm diagnosis?
 * Were the mutations identified?
 * Were there any complications with the pregnancy?
 * Have you had any other pregnancies?
 * I'm going to take a family medical history. Some of the questions I will ask will help us determine if there are any other hereditary disorders that we may want to discuss

CF

 * You seem to have a lot of experience with CF how do you feel about your chances of having another child with CF?
 * Get them to explain their understanding of their risks
 * AR inheritance (1 in 4 of having CF and ½ or 50% chance they will be a carrier)
 * Any questions about the genetics or biological cause of CF?

Facts About CF
(I don't think it will be necessary to review all of this because they probably know more than I do about CF, but this is for my benefit)

What is it?

 * CF is one of the most common inherited diseases (affects 1 in 3300 live births in US)
 * most common in Caucasians
 * multisystem disease affects resp. tract, pancreas, intestine, reproductive tract, hepatobiliary system
 * causes body to produce thick mucus lead to pneumonia, diarrhea, poor growth, and infertility
 * due to faulty transport of sodium and chloride within cells lining certain organs

Features of CF
decreased fertility in females due to abnormal cervical mucus that can contribute to infertility
 * normal intelligence
 * features may include
 * chronic sino-pulmonary disease: cough, sputum production, wheezing, obstructive lung disease, chronic chest radiograph abnormalities, digital clubbing
 * gastrointestinal/ nutritional abnormalities: malabsorption/ pancreatic insufficiency (foul, bulky, fatty stools) distal intestinal obstructive syndrome, rectal prolapse, recurrent pancreatitis, chronic hepatobiliary disease, failure to thrive, hypoproteinemia, fat soluble vitamin deficiencies
 * infertility: 98% of males with CF infertile due to unilateral or bilateral agenesis of vas deferens

Diagnosis

 * median age diagnosed = 6-8 months (2/3 dx before age 1)
 * diagnoses established in people with one or more phenotypic features and one of following
 * presence of 2 disease-causing mutations in the CFTR (cystic fibrosis transmembrane regulator) gene
 * two abnormal quantitative sweat chloride values (the "gold standard")
 * painless, relatively inexpensive, definitive answer)
 * abnormal value for the transepithelial nasal potential difference (NPD)
 * diagnosis established in absence of phenotypic characteristics when
 * confirmed dx of sibling and abnormal sweat chloride value or presence of same two mutations as in the sibling

Prognosis

 * survival increased from 18 years 1976 to 30.1 years 1995 currently approximated at 33 yrs (geneclinics)
 * pulmonary disease major cause morbidity and mortality
 * patients with pancreatic sufficiency (<10%) have milder course and greater survival (56 yrs 1995 CFF Patient Registry
 * wide variability in disease expression

Incidence

 * Caucasians 1/2,500
 * African-Americans 1/18,000
 * Asian Americans 1/90,000
 * 30,000 affected in US 8,000,000 carriers in US
 * carrier rates see chart in visual aids

CF gene and common mutations

 * located on 7q
 * 250,000 bp, 27 exons and 1,480 aa's
 * functions as a regulated chloride channel in epithelial cells
 * over 900 known mutations (most point mut. or small del.)
 * genotype/phenotype correlation (both severe and mild mutations)
 * delta F508 most common (30-80% of mutations)
 * Later on we will be discussing what testing is available for family planning and CF testing. This same prenatal testing can detect some birth defects and chromosomal abnormalities also.

Explanation of Advanced Maternal Age

 * As women get older their risk for having a baby with a change in chromosome number increases. There is no magic age at which a woman goes from no risk to high risk. However, at age 35 the risk is considered high enough to offer some standard testing options that we will discuss today.
 * Explain chromosomes and genes
 * Explain nondisjunction
 * Briefly describe the common trisomies (21 (Down Syndrome), 18, 13, 47XXY)
 * Chance of having a baby with one of these chromosomal changes increases with maternal age

Chromosome abnormalities
(Details I won't go into very much again fro my benefit)
 * Explain nondisjunction
 * This mistake that occurs in cell division is a random chance event that does not run in families
 * Although it is a random event, it does occur more often as a woman gets older
 * When there is an extra copy we call it trisomy because there are three copies instead of the usual two copies
 * Any time there is extra genetic material there are changes in the way the fetus grows and develops

Down Syndrome

 * The most common type of trisomy is called Down Syndrome or trisomy 21 because it is caused by an extra copy of chromosome 21
 * You mentioned a distant cousin with Down syndrome-- how familiar are you with this condition?
 * Children with Down syndrome are all unique, but often have distinguishable physical characteristics that you might recognize.
 * They are all mentally retarded and this is most often mild to moderate
 * They also often have heart defects and are at an increased risk for some other specific medical concerns

Trisomy 18, 13

 * Two of the other common trisomies are trisomy 18 and 13.
 * Children with these conditions are more severely affected than those with Down Syndrome.
 * They usually have a variety of birth defects and are severely mentally retarded.
 * Many miscarry and those that are born often do not live past 1 year of age

Other chromosome abnormalities involving the sex chromosomes

 * Other chromosome abnormalities that you may be at an increased risk for involve the sex chromosomes
 * Babies can have an extra copy of one of the sex chromosomes and sometimes you can't even tell
 * They may have learning disabilities.
 * They don't have increased risks for severe medical complications, but may be infertile.

Age Related Risks

 * Age related risks (refer to chart in visual aids)
 * Age 38 risks
 * Live born baby with Down Syndrome 1 in 189 or 0.53%
 * Live born with chromosomal abnormality 1 in103 or 0.97%
 * chance of having a liveborn child with normal chromosomes is 99.03%

Prenatal Testing Options

 * 2 are diagnostic tests (CVS and amniocentesis) which will tell you with nearly 99.7% certainty if the fetus has one of the chromosomal changes discussed and almost 100% certainty whether the fetus has CF
 * Ultrasound will help in determining the overall development of the major organs and can show some birth defects (may show fetal echogenic bowel and/or dilated bowel which can be an indication of CF)

Chorionic Villus Sampling Overview

 * Often referred to simply as CVS
 * CVS is a technique in which a sample of placental tissue is obtained
 * The little fingerlike projections of the placenta that are sampled are called chorionic villi
 * The villi are derived from the same original cells as the fetus so these cells should have the same genes and chromosomes as the fetus and we can look at the chromosomes in these cells and detect the chromosomal abnormalities discussed earlier
 * CVS is performed between 10 and 12 weeks gestation
 * CVS has been around since 1983 in US

Amniocentesis Overview

 * Have you heard about amniocentesis?
 * It is a simple medical procedure that is usually performed after 15 weeks gestation that is used to rule out many chromosomal abnormalities including the ones we just discussed that you are at increased risk for
 * A small sample of the amniotic fluid that surrounds the baby is taken
 * Within the fluid are skin cells that have been sloughed off by the baby.
 * These cells can be grown in a lab and then the chromosomes can be looked at

Amniocentesis VS. CVS

 * Review visual aid that compares the two procedures on timing, risk, accuracy etc.

What Information These Procedures Can Provide

 * determine if the fetus has one of the chromosomal abnormalities we discussed with >99% accuracy for amnio and 98-99% accuracy for CVS
 * DNA obtained from the sample can also be used to test for CF with almost 100 % accuracy
 * determine the babies sex if you would like to know.
 * The fluid obtained during an amnio also used to test for open neural tube defects such as anencephaly and spina bifida, but CVS can't (should have blood test)
 * Spina bifida is where the spinal cord didn't form properly and nervous tissue is exposed
 * It can cause motor impairments along with other health concerns
 * Risks for these do not increase with age, but it is tested for at the same time and the test is able to detect 99% of ONTD's (if measuring AFP and acetylcholinesterase)
 * CVS does not test for NTD's Therefore it is recommended that a woman has a blood test at about 16 weeks to determine if the fetus is at increased risk for a neural tube defect

Limitations

 * Most birth defects cannot be detected by amnio or CVS. (Amnio can detect about 10% of birth defects including the ones we discussed).
 * For example cleft lip, cleft palate, congenital heart defects, small chromosomal abnormalities, and many types of mental retardation will not be detected.
 * Doesn't routinely test for other heritable disorders unless ordered specifically
 * Most women tested receive news that their child doesn't have chromosomal abnormalities but it doesn't guarantee a healthy baby. (3-5 out of every hundred babies has a birth defect).

There are some risks associated with the procedures

 * .5% additional risk for pregnancy loss with amnio (1 out of every 200 women who have an amnio will have a miscarriage that is due directly to the procedure) 1% with CVS These risks are above the baseline risk of miscarriage that all women have.
 * Life threatening problems to the mother are extremely rare
 * Infection can occur but rare (less than 1 in 1,000 women)
 * Blood group sensitization (Rh - mothers will receive RhoGam following procedure)
 * Routine amnio is not associated with increased risks of birth defects in the fetus
 * Scarring of the baby is possible but is thought to be very uncommon
 * Extremely low risk of uterine infection
 * Some studies reported a possible risk of limb defects with CVS while other studies have not. Most of the defects were noted if the procedure was performed before 10 weeks because the limbs develop between 4-10 wks. If there is an increased risk it is about 1 in 3000.
 * Risks are lower if the physician is highly experienced
 * There is a very small chance of lab error and the need to repeat the procedure
 * CVS has higher risk of error 1-2%

Reasons some women choose CVS
(This is a personal decision and each woman places different emphasis on the things that are important to her)
 * Permits termination at earlier gestational age
 * 1st trimester and people often don't know that she is pregnant
 * Early termination has been reported to be easier emotionally and physically
 * Allows treatment for a fetus with 21-hydroxylase deficiency (CAH) autosomal recessive condition in which shots of dexamethosone can be given
 * They want reassurance that the fetus does not have a chromosomal abnormality

Reasons some women choose amniocentesis

 * Lower risk of pregnancy loss 0.5% instead of 1%
 * Results are slightly more accurate >99% compared to 98-99%
 * Offers detection of open neural tube defects (90-96%)
 * However, a maternal blood test (MSAFP) can be performed later in pregnancy (14-22 wks) and will detect 85% of open NTD's
 * Procedure is easier and more hospitals perform it
 * With CVS there is a greater likelihood of needing further testing due to
 * Laboratory failure
 * Maternal cell contamination
 * Frequency 1.9%
 * Not problematic for cytogenetics, can be for DNA or biochemical testing
 * Can be detected by DNA analysis using a maternal blood sample
 * Mosaic or ambiguous results
 * Presence of two or more groups of cells that differ in their chromosome make up
 * Occurs in 1-2% of CVS samples
 * less concerning in CVS than amnio because the placental cells are more distantly related they split off from the cells in the embryo early on so fetus might not share same genetic make up
 * Insufficient sample
 * They want reassurance that the fetus does not have a chromosomal abnormality

Reasons some women choose not to undergo either procedure

 * They don't want to take that added risk of miscarriage
 * They are more anxious about the procedure than they are about having a child with a chromosomal abnormality
 * They feel comfortable not knowing if there is one of these problems until they deliver the child
 * They don't feel a need for reassurance and would not abort the fetus regardless of the result
 * Moral or religious views

Detailed description of the amnio procedure
(I WON'T go into this much detail)
 * Spend more time on the procedure details if she is interested or if needed to make an informed decision
 * The entire procedure from when you arrive to when you leave will last about 20-45 minutes and you can return home after it is completed
 * Some physicians require you to have a full bladder
 * Abdomen is cleaned and sterilized
 * A local anesthetic is often given to numb the outer layers of skin (this is similar to the shot your dentist uses)
 * Ultrasound is used before and during the procedure to visualize where the baby is and find a pocket of fluid.
 * A needle about the width of a needle used to draw blood, but longer (3") is inserted through the abdomen into the uterus and amniotic sac.
 * The needle may seem long but it is the width that is felt
 * The needle is only in for one or two minutes while amniotic fluid is drawn up through it.
 * Most women report that the needle insertion is not as painful as they had expected, but that there is some discomfort.
 * Some report a stinging sensation when the needle first enters the skin
 * Some report that they feel a sharp pain or a contraction as the needle enters the uterus.
 * Others describe it as feeling similar to blood draw.
 * Some experience a sensation of pressure in their lower abdomen as the fluid is drawn up through the needle.
 * It is also common for women to report some minor uterine cramping (similar to menstrual cramps) during and/or after the procedure.
 * Usually the first little bit of fluid is discarded because it might have some of your cells mixed in.
 * The sample will be about 20cc or 1-2 tablespoons. This fluid is quickly replaced by the baby.
 * The babies heart is monitored by U/S after the procedure

What to expect and do after the amnio

 * Mild cramping is common
 * Spotting occurs in a small percentage of women
 * After the test avoid strenuous activities for 24 hours
 * Call the doctor immediately if you experience any of the following:
 * severe and persistent abdominal pain and cramps
 * vaginal bleeding
 * vaginal leakage of amniotic fluid
 * anything that seems unusual
 * The results will be available in about 1.5 to 2 weeks

Description of CVS

 * There are two ways the procedure can be performed: Transcervical and Transabdominal
 * Contraindications for both types include:
 * Active vaginal bleeding (must have stopped at least 1 week ago)
 * Rh sensitization (if already sensitized) if not sensitized Rhogam given to Rh negative women to prevent sensitization
 * Maternal bleeding disorder
 * Fibroids not avoidable
 * Multiple gestation? (usually not attempted)
 * Transcervical
 * Procedure is similar to a pap smear
 * Vagina and cervix are cleaned
 * Under the visual guidance of ultrasound, a thin tube (catheter) inserted through the vagina, cervix, and into the placenta
 * Once the catheter is in place a syringe is attached
 * Suction is applied to remove the villi while the catheter is removed
 * After the sample is obtained it is viewed under a microscope to be sure the size and quality is sufficient and another sample is not needed
 * Sample is placed in a tube of tissue culture medium and sent to a lab for testing
 * Most women report minimal discomfort during the procedure although it varies
 * The actual procedure only takes about 5 minutes
 * The baby's heart beat will be monitored
 * Bleeding occurs in up to 10% of women
 * (Easiest to perform with posterior placenta close to cervix)
 * (Contraindications for transcervical CVS include: cervical polyps, overly curved sampling pathway, active genital herpes or other infections)
 * (Large sample is obtained including whole villi)
 * Transabdominal
 * Abdomen is cleansed and xylocaine injection is given to numb the upper layers (similar to shot given at the dentist)
 * Using ultrasound as visual guidance, spinal needle is guided through the abdominal wall, uterine wall, and into the placenta
 * Once in place a syringe is attached to supply suction
 * While suction is supplied the needle is moved back and forth through the placenta
 * After sample is obtained it is viewed to make sure there is enough and another sample is not required
 * Sample is then placed in a tube of tissue culture medium and sent to a lab for testing
 * There is a wide range of responses when it comes to how women report the procedure felt. When the needle is inserted it may burn for a few seconds. Women report everything from mild cramping to painful, heavy cramping.
 * The actual procedure takes about 5 minutes
 * The heartbeat of the fetus will be monitored
 * Bleeding is rare
 * Contraindications for transabdominal CVS include: interceding bowel, the placenta is too far from the maternal abdominal surface (obesity)
 * (Easiest to perform with anterior or fundal placenta)
 * (Smaller sample size (pieces of the villi) obtained)
 * (Can be performed after 12 weeks, but usually only if there is not enough amniotic fluid for an amniocentesis)

Recommendations for after the procedure

 * No exercise or strenuous activity for 24 hours
 * No sexual intercourse, douching, tub baths, or tampon use for 72 hours
 * Notify the OB in any of the following occur:
 * Fever greater than 100.4 degrees F
 * Heavy bleeding or cramping
 * Amniotic fluid leakage
 * Return for follow up ultrasound (if that is standard practice)
 * Blood test (MSAFP) at 16-18 weeks to check for NTD's
 * Ultrasound is recommended at 18-20 weeks

Test Results

 * Results will be available anywhere between 1-2 weeks depending on which lab it is sent to (Genzyme 7 days, CHMC about 2 weeks)
 * More than 95% of women receive reassuring news
 * Remind them that sometimes further follow-up testing is needed
 * Ask them how they would like to receive their results and if they want to know the sex of the fetus

Preimplantation Genetic Diagnosis

 * Performed at only few centers in US
 * Closest is Regional Genetic Institute in Chicago
 * First attempt in 1989
 * Can be used to detect any genetic condition for which there is a sufficient sequence information
 * Can detect common aneuploidies and translocations
 * As many as 40 PGD centers have been established in 17 countries
 * By this time, these centers performed approximately 3,000 clinical cycles, resulting in more than 500 pregnancies (over 20% pregnancy rate), and the birth of nearly 300 healthy children.
 * More than two thirds of these clinical cycles were performed in USA, from which the largest number (1,200 cycles) was contributed by RGI. This resulted in 250 pregnancies and birth of approximately 200 healthy children
 * At present, RGI (Chicago) is the only center in the world offering Preimplantation Diagnosis by sampling the first and second polar bodies.
 * he first polar body is discarded during oocyte maturation, prior to fertilization and contains one set of duplicated chromosomes
 * the second polar body is discarded after fertilization and contains one set of chromatids
 * test the polar bodies for genetic disease to determine if egg has mutation
 * offered to couples who are known carriers of genetic diseases detectable by DNA analysis
 * RGI physicians have already performed over 100 clinical cycles involving preimplantation diagnosis many genetic diseases including CF
 * diagnosis of Down syndrome and other common aneuploidies
 * analysis of the chromosome number (13, 16, 18, 21) in both the first and second polar body by FISH
 * Only embryos resulting from the fertilization of eggs with normal number of these particular are transferred
 * patients may choose which embryos they wish to be transferred or frozen. The procedure has been offered to over 600 IVF couples
 * resulted in 131 births of healthy children and dozens ongoing pregnancies confirmed to be unaffected by CVS or amniocentesis
 * Preimplantation diagnosis via blastomere biopsy is also performed for other specific disorders involving paternal genes or sex selection for X-linked disorders and if doing IVF cycle outside of
 * Cost (probe development $1,000, PGD for one cycle $3,000, IVF one cycle $7,500 IVF meds $2,000-$4,000, cost to send embryologist to your IVF center $2,000 Total $13,500-$17,500 per cycle

Review

 * Assess if there are any questions or other concerns throughout the session
 * Assess again how she feels about the test options
 * Offer patient literature (already sent according to chart note)


text:
Talk:Prolog/Lists

added a section about the reverse predicate. hopefully I will add an alternative and much better implementation later. -sgt

Other exercises that could be added: I'll do some of these soon if I have time... -MatrixFrog (talk) 07:32, 11 April 2008 (UTC)
 * sorting a list (many possible solutions, of course)
 * finding permutations of a list
 * finding the highest or lowest value in a list of numbers
 * flattening a list (i.e. turning 1,2],[3,[4] into [1,2,3,4]
 * While these would be great exercises, we should remember that this is a very early chapter and most readers will not be comfortable enough with prolog to do all of these. We haven't even explained cuts yet. I think most of these would be better suited to a later section of the book. risk (talk) 21:33, 17 September 2008 (UTC)

Length
The definition of length is horribly wrong. (by 83.104.248.190, risk (talk))

Changes by 83.104
I've reverted the rewrite of 11:13, 6 September 2008 by 83.104.248.190, as I disagreed with nearly all of it. It removes a lot of essential explanation of structure and terminology, necessary to read other texts about prolog. As an example. A list in prolog isn't just a list like java's list, it's the primary way of dealing with collections of objects (rather more like java's array, other collections are constructed from it). Just saying "this is how you do a list" neglects the point of what lists are and why they're necessary. If you explain don't that you need them, starting to talk about lists as if the reader should already know about it will confuse people. I have similar reservations about most of the other changes. risk (talk) 21:29, 17 September 2008 (UTC)

I've reverted your revert because the article was made considerably worse by doing so. If you want to add or clarify explanation do so. Do not revert to a definition of length/2 that uses is/2 because this is not acceptable Prolog code. Prolog lists are not like java, drawing an analogue with java is unhelpful.

 * It was harsh of me to simply revert your edits. Sorry about that. I have now edited some specific points. Regarding the first line; you say "prolog lists are not like java", I say the exact same thing in my comment (seriously, read it again). What I mean is that there are certain things that you want from a language when you come into it fresh. You want to do arithmatic, you want to control flow, you want to store values, and you want to store collections of values. Prolog may turn all these things completely on their head, but these are the expectations that users have when they start learning prolog. We need to say this is how you store multiple values. "This is how you do lists" just suggests that it's some functionality for handling ordered collections of values, but it is in fact, the only way to handle collections fo values. Wether you want sets, or maps or dictionaries, you'll have to use lists. That's the analogy to java's array's
 * I would also ask you to keep in mind (I do hope you'll continue editing the book) that we're writing for people new to prolog and possibly new to the world of computer science as a whole. Using words like "nondeterminism" and "base case" will confuse anybody without some sort of academic background, unless we've explained them properly. On that note, your definition of length, using succ may be technically better, but the succ predicate hasn't been introduced yet. In fact no builtin predicates have been introduced at this point, and the reader who's just started learning prolog three days ago can hardly be expected to know about succ. (Granted, the math behind L is L1 + 1 hasn't been introduced yet either, so maybe it should be moved to the next chapter). Could you perhaps show the original answer first, then explain why it's not perfect and why the reader should use succ instead? Thanks. risk (talk) 14:53, 23 October 2008 (UTC)

 * Indeed. "succ" has not been introduced yet. I solved the excercise as follows:

 * --84.138.228.89 (talk) 17:35, 28 June 2009 (UTC)

Is listsplit still a valid rule?
I'm running through this tutorial right now. When I tried the listsplit command, I got an "Undefined procedure" error on SWI Prolog. Is listsplit still a standard Prolog command? (I'd remove it myself, but as I'm just learning, I'm not completely sure that listsplit is wrong, and I wouldn't know what to replace it with ): ) 129.93.5.129 (discuss) 05:26, 8 December 2013 (UTC)

title: Talk:Prolog/Lists


text:
Handbook of Genetic Counseling/Developmental Delay and Mental Retardation

Developmental Delay and Mental Retardation

Etiology

 * Cause unknown in about 50% of cases
 * Often multifactorial with genetic and environmental components
 * Low birth weight, prematurity, and perinatal complications may be associated - not known if they cause mental retardation or if factor causing these problems also caused MR
 * Approximately 2000 known genetic causes
 * Chromosomal abnormalities
 * Metabolic or endocrine disorders
 * Hereditary degenerative disorders
 * Hormonal deficiency
 * Hereditary syndromes or malformations
 * Acquired causes
 * Prenatal: infection, irradiation, or exposure to toxins
 * Perinatal: prematurity, anoxia, cerebral damage, or infection
 * Postnatal: brain injuries, anoxia, poisons, hormonal deficiencies, metabolic dysfunction, postimmunization encephalopathy, sociocultural, kernicterus, epilepsy
 * In United States, 1-3% of people meet cognitive and functional criteria

Clinical Features

 * It is a, medical and mental, developmental disorder
 * Affects developmental and cognitive abilities
 * Substantial limitations in functioning
 * IQ scores below 70
 * Mild MR: IQ range 50-55 to 70
 * Moderate MR: IQ range 35-40 to 50-55
 * Severe MR: 20-25 to 35-40
 * Profound MR: Below 20-25
 * Majority of individuals with mental retardation have IQ scores of 55-69
 * Able to live independently or with support in group homes
 * Less than 10% of all people with mental retardation have severe to profound impairments
 * May have limited ability to develop some adaptive skills
 * Communication
 * Home living
 * Work
 * Self-care
 * Social/interpersonal skills
 * Self-direction
 * Functional academic skills
 * Leisure
 * Health and safety
 * Use of community resources
 * Can affect abilities in key developmental areas
 * Language development
 * Visual and auditory perception and discrimination
 * Abstract problem solving
 * Onset must occur before age 18

Management options

 * No treatment or cure
 * Early intervention services
 * Provided by the county in Ohio to children between birth and age 3
 * Studies show the earliest experiences in learning sets the pattern for later information processing
 * Begins with comprehensive developmental assessment
 * May be performed here by CCDD or by private service
 * Assessment used to develop intervention strategy
 * After age 3, school system provides special services
 * Develop an Individualized Education Plan (IEP)
 * Early education focuses on cognitive development and special services such as speech therapy
 * Later education may focus on developing life skills
 * Can attend school until age 21
 * Adult services
 * Handled in Ohio by the Board of MRDD
 * Focuses on job training, vocational education
 * Community or group homes are available for semi-independent living

Recurrence Risks

 * Can calculate a much more accurate risk if etiology is known
 * Other factors to consider:
 * Possibility of consanguinity
 * Whether one or both parents are affected
 * Developmental disabilities may be exacerbated by environmental factors
 * Unsafe or unstimulating home environment
 * Substandard health care
 * Unadequate schooling or lack of services
 * Empiric risk figures when parents affected with mental retardation of unknown etiology
 * 39.4% if both parents affected
 * 7.8% if only father affected
 * 19.6% if only mother affected (higher due to prevalence of X-linked inheritance for conditions such as Fragile X)

Psychosocial Issues

 * Provision of adequate services
 * Burden of taking care of a child/adolescent/adult with mental retardation
 * Impact on siblings and other family members
 * Denial, grief, disappointment, or feeling of loss
 * Interruption of career goals, family routines, or plans for the future
 * Financial and insurance issues


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