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Canadian Criminal Evidence/Documentary Evidence

Introduction
Documentary evidence is any kind of evidence on which relevant information is printed upon.

This generally includes paper records, such as court documents, business records, personal papers, etc.

It can also include electronic documents or materials reducible to writing that is stored on machines, including:
 * tape recordings
 * video tapes
 * microfiche
 * computer records

Documentary evidence in civil matters governed by provincial legislation have a variety of definitions in different jurisdictions.

Admissibility
All documents must be authenticated and established as relevant before they can be tendered into evidence. This is done either by oral or affidavit evidence.

The standard used to authenticate the document depends on whether the document is submitted as hearsay (where the contents of the letter helps establish some fact) or as non-hearsay (where the contents of the document is not relevant).

Unless provided by statute, all private documents must be proven to be admissible. It is usually necessary to prove execution before proof of contents. Execution may be proven by inference.

Non-Hearsay Documents
Documents that are used for non-hearsay purposes are admitted in the same way real evidence is admitted, which is by calling viva voce evidence of the person who can speak to it’s creation, use and the context of the document. The contents of the document need not be accurate, and where the witness cannot speak to the accuracy of the contents of the document, the contents will have little weight.

An example where the contents has no bearing is if a party were to attempt to establish that a letter was simply received by a person, which may have relevance to a case concerning actions prompted by the letter, the letter can be put into evidence by calling the person who received the letter and can confirm that it was the letter that they received and speak to the context of its receipt. By contrast, an example of a non-hearsay document where the contents is attested to as accurate is where a report is being tendered and the authenticating witness is the author of the report.

The document need not be an original, but rather can be authenticated by the witness as a fair and accurate representation of the document received.

Hearsay Documents
Documents that are submitted for the truth of their contents in lieu of oral evidence must generally be authenticated by someone who can speak with personal knowledge of the contents of the document. This can be direct personal knowledge or circumstantially personal knowledge.

The admissibility of documents for the truth of their contents is governed both by the common law and by statute, such as the Canada Evidence Act. The statutory law on documents compliments the common law, making alternative options for admissibility.

There is exception to this requirement under s. 29 (financial institution documents) and s. 30 (business records) of the Canada Evidence Act, as well as several other statutory hearsay exceptions.

Best Evidence Rule
Where the contents of a document are material to the case, the best evidence rule (or "documentary originals rule") requires that the party submit the original unless the party is unable to do so. The court can accept a secondary copy where it is satisfied that the original was lost, destroyed or otherwise unavailable.

In general, secondary evidence is admissible where the original was lost or destroyed accidentally or in good faith.

This rule arises from a time before the advent of computers and photocopiers when all copying was done by hand. It sometimes criticized as a rule that has outlived its purpose. There is some suggestion that a lack of original will merely go to weight.

Nevertheless, the best evidence rule is part of the common law. There are a number of statutory enactments that allow for exemption to this rule, such as CEA s. 29 [financial records], 30(3) [business records], 31(2)(c)[government records].

The rule does not preclude the admission of viva voce evidence of persons who viewed a video that was not in evidence.

Admissibility of Specific Types of Documents
Any document can be admitted without proof where the opposing party consents. Further, under s. 37(6.1) the court has a residual power to"receive into evidence anything that, in the opinion of the court, is reliable and appropriate, even if it would not otherwise be admissible under Canadian law, and may base its decision on that evidence."

There are generally three categories of documents:
 * 1) public documents
 * 2) judicial documents
 * 3) private documents

Types of Documents

 * Public and Judicial Documents
 * Private Documents
 * Business Records
 * Financial Institution Records

Electronic Documents
Electronic documents are governed by s.31.1 to 31.8 of the CEA. The provisions are meant to apply "in conjunction with either some common law general rule of admissibility of documents or some other statutory provision". The section, instead, have the effect of deeming electronically produced documents as "best evidence" (see s.31.1 and 31.2).

Under s. 31.8 of the CEA, "electronic documents" are defined as:

Authentication
The burden is upon the party tending the electronic document to prove its authenticity. (s.31.1)

The "best evidence rule" can be satisfied by establishing either:
 * "the integrity of the electronic documents system" that generated the document (s. 31.2(1)(a)) which is presumed (s. 31.3, see "presumption of integrity" below).
 * in the case of printouts, that the "printout has been manifestly or consistently acted on, relied on or used as a record of the information recorded or stored in the printout" (s. 31.2(2))
 * the presumption relating to electronic signatures (see s. 31.4)

Presumption of Integrity Under s. 31.3, in "absence of evidence to the contrary", the integrity of electronic documents are presumed where the is evidence of at least one of the following:
 * 1) "that at all material times the computer system or other similar device used by the electronic documents system was operating properly";
 * 2) if the device was not operating properly at all material times, that the malfunction "did not affect the integrity of the electronic document and there are no other reasonable grounds to doubt the integrity of the electronic documents system".
 * 3) that "the electronic document was recorded or stored by a party who is adverse in interest to the party seeking to introduce it"; or
 * 4) the document "was recorded or stored in the usual and ordinary course of business by a person who is not a party and who did not record or store it under the control of the party seeking to introduce it."

Admissibility
Once a computer record is authenticated, the records will usually be admissible under one of the following methods of admissibility for the truth of their contents:
 * CEA business records,
 * CEA financial records,
 * common law business documents,
 * principled exception to hearsay, or
 * real evidence

Where compilation was carried out by automated means, it may be possible to admit them through the common law business record method.

Evidence that is "automatically recorded by any means, other than by human labour, and the evidence so recorded can be reproduced in any form, intelligible to the human mind, the reproduction is admissible as real evidence." However, "The weight to be attached to such evidence will depend on the accuracy and integrity of the process employed."

See also: R. v. Nardi, 2012 BCPC 318 (CanLII)

Summaries of Voluminous Documents
Summaries of voluminous raw documents can be admissible for the purpose of assisting the trier-of-fact in understanding "the entire picture represented by voluminous documentary evidence" as long as source documents are also admitted. "The usefulness of the summaries depended entirely ... upon the acceptance ... the facts upon which the summaries were based."

In practice, spreadsheets of banking records that have not been admitted have been found acceptable where the tables can be authenticated as an accurate summary of the records it represents. The witness need not be the author of the spreadsheet or the source records.

Related to this principle from Schell, summaries can be admitted without admitting the source documents under the Voluminous Document Hearsay Exception.

Documents Found in Possession of Accused
Documents that are found in actual or constructive possession of the accused can be used to draw the inference that he has knowledge of the contents of the documents and has a state of mind about any transaction contemplated by it. However, where the document has been recognized, adopted or acted upon by the accused, the documents can be admitted for the truth of their contents.

Signatures
A signature is evidence suggesting the authorship of a document or knowledge and consent to the contents of it.

Where a party disputes the authenticity or identity of a signature, the signature can be proven by comparison "with any writing proved [...] to be genuine".

Forged Documents
Proving forged signature on documents will require an expert of handwriting analysis to determine the probability of matching the accused's signature and the document.

Errors in Documents
Certificates of analysis Errors and ambiguity in certificates of analysis in which there was a typographical error is not fatal to the case where it can be mended by way of viva voce evidence and where “the error was not of such a nature as to have misled the accused or to interfere with his right to make full answer and defense and receive a fair trial”.

Inadmissible Documents
Section 30(10) sets out several types of records which are inadmissible despite any other provision of the evidence act:
 * records "made in the course of an investigation or inquiry"
 * records "made in the course of obtaining or giving legal advice or in contemplation of a legal proceeding,"
 * privileged records
 * "a record of or alluding to a statement made by a person who is not, or if he were living and of sound mind would not be, competent and compellable to disclose in the legal proceeding a matter disclosed in the record;"
 * "any record the production of which would be contrary to public policy"
 * "any transcript or recording of evidence taken in the course of another legal proceeding."

Foreign Documents
The admissibility of foreign documents is governed by section 36 of the Mutual Legal Assistance in Criminal Matters Act, RSC 1985, c 30 (4th Supp) (MLAC).


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Canadian Criminal Evidence/Testimonial Evidence

Introduction
Testimonial evidence, also known as viva voce evidence or oral testimony, is evidence given by a witness in the form answers to posed questions.

Purpose of Testimonial Evidence
Testimonial evidence is the best way to ensure the most reliable and credible evidence is available for the trier of fact to consider.

Witnesses are encouraged to be honest, accurate, and complete by requiring them to give evidence under the requirements that:
 * 1) the witness give an oath or affirmation to their evidence;
 * 2) their personal presence is necessary;
 * 3) they will be subject to cross examination

Topics

 * Competence and Compellability
 * Refreshing Memory
 * Video Testimony
 * Witness Screens

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


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Canadian Criminal Evidence/Character

Introduction
Character evidence is evidence that invites the trier of fact to make an inference that the person is of a certain "type", thus inferring that the person acted consistently with that type of character. Character evidence can often become prejudicial to the accused and so must be taken with care.

Character of Victim
The accused is generally permitted to introduce evidence of the deceased's victim's prior record as well as transcripts of the a related proceedings to establish a propensity for violence.

Topics

 * Character of Accused
 * Similar Fact Evidence
 * Alternative Suspect Evidence

title: Canadian Criminal Evidence/Character


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Canadian Criminal Evidence/Hearsay

Introduction
Hearsay evidence is any statement, either written or oral, which was made out of court, but is presented in court to prove the truth of that statement. It is a type of evidence that is generally considered inadmissible.

The hearsay rule has stated as: Written or oral statements, or communicative conduct made by persons otherwise than in testimony at the proceeding in which it is offered, are inadmissible, if such statements or conduct are tendered either as proof of their truth or as proof of assertions implicit therein.

The definition has been addressed in several cases.

Courts generally do not allow such evidence as it is generally said to be untrustworthy for several reasons:
 * 1) The admission of such evidence lends itself to the perpetration of fraud. This is in part due to the lack of oath on the part of the source.
 * 2) Hearsay evidence results in a decision based upon secondary and, therefore, weaker evidence, rather than the best evidence available. Related to this, there is no opportunity to cross-examine or otherwise test the evidence of the source.
 * 3) There is no opportunity to observe the demeanour of the declarant, thus making it harder to assess the quality of the evidence.
 * 4) The introduction of such evidence will lengthen trials.

Elements of Hearsay
Where hearsay potentially arises there are four elements to consider if the rule is engaged:
 * 1) a declarant
 * 2) a recipient
 * 3) a statement and
 * 4) a purpose for introducing the statement

The first three are almost always made out, the fourth requirement is usually the source of controversy. Not every out of court statement is hearsay.

The prohibited purpose consists of admission for the purpose of proving the “truth” of its contents. Otherwise, it is admissible evidence. That is, statements that used to show the recipient had notice, knowledge or motive, or was in some way probative, then it is otherwise admissible.

If it is for the “truth of its contents” then it is presumptively inadmissible unless it fits in a traditional categorical exception or under the principled exception.

Computer Records
The absence of data in a computer system is not generally hearsay. For example, enquiries into the police records regarding a suspect that result in a negative result was found not to be hearsay.

Opinion Evidence
Non-specific hearsay opinion evidence is inadmissible.

Phone Calls
Drug purchase phone calls, usually where the police are on the other end of a call, have a history of litigation to exclude them as hearsay. More often than not they have been admitted as either necessary and reliable or as non-hearsay.

Others
See also Canadian Criminal Evidence/Credibility/Prior Consistent Statements - a form of hearsay

Topics

 * Traditional Exceptions
 * Principled Exceptions

Case Digests

 * Case Digests on Hearsay

title: Canadian Criminal Evidence/Hearsay


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Interests
I have many computing interests such as Web Programming. I have tried to contribute to many of these wikibooks including PHP and CSS.

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My name is David Biesack. I work at SAS Institute, Inc.

On WikiBooks, I'm contributing to the Java Programming module, which I helped form as an alternative to the Programming:Java module which needed work and reorganization.

Most recently, I've been working on a replacement for Java Programming/First Java Program; see my draft /First Java Program.

I've been developing in Java since 1996. I served on the JSR 201 expert group which added new language syntax to Java (enhanced for loops, type safe enums, static imports, autoboxing).

title: User:Djb


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Java Programming/Preface

"The beautiful thing about learning is nobody can take it away from you."

- B.B. King (5 October 1997)

Learning a computer programming language is like a toddler's first steps. You stumble, and fall, but when you start walking, programming becomes second nature. And once you start programming, you never cease evolving or picking up new tricks. Learn one programming language, and you will "know" them all — the logic of the world will begin to unravel around you.

Are you new to programming?

If you have chosen Java as your first programming language, be assured that Java is also the first choice for computer science programs in many universities. Its simple and intuitive syntax, or grammar, helps beginners feel at ease with complex programming constructs quickly.

However, Java is not a basic programming language. In fact, NASA used Java as the driving force (quite literally) behind its Mars Rover missions. Robots, air traffic control systems and the self-checkout barcode scanners in your favorite supermarkets can all be programmed in Java.

Programming with Java™
By now, you might truly be able to grasp the power of the Java programming language. With Java, there are many possibilities. Yet not every programmer gets to program applications that take unmanned vehicles onto other planets. Software that we encounter in our daily life is somewhat humble in that respect. Software in Java, however, covers a vast area of the computing ecosphere. Here are just a few examples of the ubiquitous nature of Java applications in real-life:

 * OpenOffice.org, a desktop office management suite that rivals the Microsoft Office suite has been written in Java.
 * The popular building game Minecraft is written in Java.
 * Online browser-based games like Runescape, a 3D massively multi-player online role playing game (MMORPG), run on graphics routines, 3D rendering and networking capabilities powered by the Java programming language.
 * Two of the world's renowned digital video recorders, TiVo and BSkyB's Sky+ use built-in live television recording software to record, rewind and play your favorite television shows. These applications make extensive use of the Java programming language.

The above mentioned applications illustrate the reach and ubiquity of Java applications. Here's another fact: almost 80% of mobile phone vendors adopt Java as their primary platform for the development of applications. The most widely used mobile-based operating system, Android, uses Java as one of its key application platforms — developers are encouraged to develop applications for Android in the Java programming language.

What can Java not do?
Well, to be honest, there is nothing that Java can't do, at least for application programming. Java is a "complete" language; the only limits are programmer imagination and ability. This book aims to get you acquainted with the basics of the language so you can create the software masterpiece of your dreams. The one area where Java can't be used is for direct interaction with computer hardware. If you want to write an operating system, you will need to look elsewhere!

title: Java Programming/Preface


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Java Programming/Statements

Now that we have the Java platform on our systems and have run the first program successfully, we are geared towards understanding how programs are actually made. As we have already discussed, a program is a set of instructions, which are tasks provided to a computer. These instructions are called statements in Java. Statements can be anything from a single line of code to a complex mathematical equation. Consider the following line:

This line is a simple instruction that tells the system to initialize a variable and set its value as 24. If the above statement was the only one in the program, it would look similar to this:

Java places its statements within a class declaration and, in the class declaration, the statements are usually placed in a method declaration, as above.

Variable declaration statement
The simplest statement is a variable declaration:

It defines a variable that can be used to store values for later use. The first token is the data type of the variable (which type of values this variable can store). The second token is the name of the variable, by which you will be referring to it. Then each declaration statement is ended by a semicolon.

Assignment statements
Up until now, we've assumed the creation of variables as a single statement. In essence, we assign a value to those variables, and that's just what it is called. When you assign a value to a variable in a statement, that statement is called an assignment statement (also called an initialization statement). Did you notice one more thing? It's the semicolon, which is at the end of each statement. A clear indicator that a line of code is a statement is its termination with an ending semicolon. If one was to write multiple statements, it is usually done with each statement on a separate line ending with a semicolon. Consider the example below:

You do not necessarily have to use a new line to write each statement. Just like English, you can begin writing the next statement where you ended the first one as depicted below:

However, the only problem with putting multiple statements on one line is, it's very difficult to read it. It doesn't look that intimidating at first, but once you've got a significant amount of code, it's usually better to organize it in a way that makes sense. It would look more complex and incomprehensible written as it is in Listing 3.4.

Now that we have looked into the anatomy of a simple assignment statement, we can look back at what we've achieved. We know that...
 * A statement is a unit of code in programming.
 * If we are assigning a variable a value, the statement is called an assignment statement.
 * An assignment statement includes three parts: a data type, the variable name (also called the identifier) and the value of a variable. We will look more into the nature of identifiers and values in the section Variables later.

Now, before we move on to the next topic, you need to try and understand what the code below does.

The first two statements are pretty much similar to those in Section 3.3 but with different variable names. The third however is a bit interesting. We've already talked of variables as being similar to gift boxes. Think of your computer's memory as a shelf where you put all those boxes. Whenever you need a box (or variable), you call its identifier (that's the name of the variable). So calling the variable identifier  gives you the number , calling   would give you   hence when you add the two up, the answer should be. That's what the value of the last variable  would be. The part of the third statement where you add the numbers, i.e.,  is called an expression and the expression is what decides what the value is to be. If it's just a plain value, like in the first two statements, then it's called a literal (the value is literally the value, hence the name literal).

Note that after the assignment to  its value will not be changed if we assign different values to   or , like in line 5.

With the information you have just attained, you can actually write a decent Java program that can sum up values.

Assertion
An assertion checks if a condition is true:

Each  statement is ended by a semi-colon. However, assertions are disabled by default, so you must run the program with the -ea argument in order for assertions to be enabled.

Program Control Flow
Statements are evaluated in the order as they occur. The execution of flow begins at the top most statement and proceed downwards till the last statement is encountered. A statement can be substituted by a statement block. There are special statements that can redirect the execution flow based on a condition, those statements are called branching statements, described in detail in a later section.

Statement Blocks
A bunch of statements can be placed in braces to be executed as a single block. Such a block of statements can be named or be provided with a condition for execution. Below is how you'd place a series of statements in a block.

Branching Statements
Program flow can be affected using function/method calls, loops and iterations. Of various types of branching constructs, we can easily pick out two generic branching methods.

 * Unconditional Branching
 * Conditional Branching

Unconditional Branching Statements
If you look closely at a method, you'll see that a method is a named statement block that is executed by calling that particular name. An unconditional branch is created either by invoking the method or by calling,  ,   or  , all of which are described below.

When the name of another method is encountered in a flow, it stops execution in the current method and branches to the newly called method. After returning a value from the called method, execution picks up at the original method on the line below the method call.

The program flow begins in the  method. Just as  is invoked, the flow travels to the called method. At this very point, the flow branches to the other method. Once the method is completed, the flow is returned to the point it left off and resumes at the next statement after the call to the method.

Return statement
A  statement exits from a block, so it is often the last statement of a method:

A return statement can return the content of a variable or nothing. Beware not to write statements after a return statement which would not be executed! Each  statement is ended by a semi-colon.

Conditional Branching Statements
Conditional branching is attained with the help of the  and   statements. A conditional branch occurs only if a certain condition expression evaluates to true.

Conditional Statements
Also referred to as  statements, these allow a program to perform a test and then take action based on the result of that test.

The form of the statement:

(condition) { do statements here if condition is true } {   do statements here if condition is false }

The condition is a boolean expression which can be either or. The actions performed will depend on the value of the condition.

Example:

If statements can also be made more complex using the else if combination:

(condition 1) { do statements here if condition 1 is true }  (condition 2) { do statements here if condition 1 is false and condition 2 is true } {   do statements here if neither condition 1 nor condition 2 is true }

Example:

If there is only one statement to be executed after the condition, as in the above example, it is possible to omit the curly braces, however Oracle's Java Code Conventions explicitly state that the braces should always be used.

There is no looping involved in an if statement so once the condition has been evaluated the program will continue with the next instruction after the statement.

If...else statements
The ... statement is used to conditionally execute one of two blocks of statements, depending on the result of a boolean condition.

Example:

Oracle's Java Code Conventions recommend that the braces should always be used.

An statement has two forms:

(boolean-condition)

and

(boolean-condition)

Use the second form if you have different statements to execute if the is true or if it is false. Use the first if you only wish to execute if the condition is true and you do not wish to execute alternate statements if the condition is false.

The code section 3.13 calls two methods,   and , stores the results, then uses an  statement to test if   is less than y and if it is, the  body will swap the values. The end result is x always contains the larger result and y always contains the smaller result.

... statements also allow for the use of another statement,. This statement is used to provide another statement to the conditional that can only be executed if the others are not true. For example:

The  statement is useful in this case because if one of the conditionals is true, the other must be false. Keep in mind that if one is true, the other will not execute. For example, if the statement at line 2 contained in the first conditional were changed to, the second conditional, the  , would still not execute. However, when dealing with primitive types in conditional statements, it is more desirable to use  rather than multiple   statements.

Switch statements
The conditional statement is basically a shorthand version of writing many ... statements. The syntax for statements is as follows: {  case : ; break; case : ; break; default: ; break; } This means that if the variable included equals one of the case results, the statements following that case, until the word  will run. The  case executes if none of the others are true. Note: the only types that can be analysed through statements are, , , or  primitive types. This means that variables can not by analyzed through  statements. However, as of the JDK 7 release, you can use a String object in the expression of a switch statement.

In this example, since the integer variable  is equal to 2,   will execute, make   equal to 4. Thus, 4 is returned by the method.

Iteration Statements
Iteration Statements are statements that are used to iterate a block of statements. Such statements are often referred to as loops. Java offers four kinds of iterative statements.

 * The  loop
 * The  loop
 * The  loop
 * The  loop

The while loop
The  loop iterates a block of code while the condition it specifies is.

The syntax for the loop is:

(condition) { statement; }

Here the condition is an expression. An expression as discussed earlier is any statement that returns a value. condition statements evaluate to a boolean value, that is, either  or. As long as the condition is, the loop will iterate the block of code over and over and again. Once the condition evaluates to, the loop exits to the next statement outside the loop.

The do...while loop
The do-while loop is functionally similar to the while loop, except the condition is evaluated AFTER the statement executes {   statement; } (condition);

The for loop
The for loop is a specialized while loop whose syntax is designed for easy iteration through a sequence of numbers. Example: The program prints the numbers 0 to 99 and their squares.

The same statement in a while loop:

The foreach loop
The foreach statement allows you to iterate through all the items in a collection, examining each item in turn while still preserving its type. The syntax for the foreach statement is:

(type item : collection) statement;

For an example, we'll take an array of s denoting days in a week and traverse through the collection, examining one item at a time.

Notice that the loop automatically exits after the last item in the collection has been examined in the statement block.

Although the enhanced for loop can make code much clearer, it can't be used in some common situations.

 * Only access. Elements can not be assigned to, eg, not to increment each element in a collection.
 * Only single structure. It's not possible to traverse two structures at once, eg, to compare two arrays.
 * Only single element. Use only for single element access, eg, not to compare successive elements.
 * Only forward. It's possible to iterate only forward by single steps.
 * At least Java 5. Don't use it if you need compatibility with versions before Java 5.

The continue and break statements
At times, you would like to re-iterate a loop without executing the remaining statement within the loop. The statement causes the loop to re-iterate and start over from the top most statement inside the loop.

Where there is an ability to re-iterate the loop, there is an ability to exit the loop when required. At any given moment, if you'd like to exit a loop and end all further work within the loop, the  ought to be used.

The  and   statements can be used with a label like follows:

Throw statement
A  statement exits from a method and so on and so on or it is caught by a  /  block. It does not return a variable but an exception:

Beware not to write statements after a  statement which would not be executed too! Each  statement is ended by a semi-colon.

try/catch
A /  must at least contain the   block and the   block:

Question 3.1: How many statements are there in this class?

5 One statement at line 3, two statements at line 6, one statement at line 7 and one statement at line 11.

title: Java Programming/Statements


text:
Java Programming/Execution

There are various ways in which Java code can be executed. A complex Java application usually uses third party APIs or services. In this section we list the most popular ways a piece of Java code may be packed together and/or executed.

JSE code execution
Java language first edition came out in the client-server era. Thick clients were developed with rich GUI interfaces. Java first edition, JSE (Java Standard Edition) had/has the following in its belt: With JSE the following Java code executions are possible:
 * GUI capabilities (AWT, Swing)
 * Network computing capabilities (RMI)
 * Multi-tasking capabilities (Threads)
 * Stand alone Java application : (Figure 1) Stand alone application refers to a Java program where both the user interface and business modules are running on the same computer. The application may or may not use a database to persist data. The user interface could be either AWT or Swing.
 * The application would start with a  method of a Class.  The application stops when the   method exits, or if an exception is thrown from the application to the JVM. Classes are loaded to memory and compiled as needed, either from the file system or from a *.jar file, by the JVM.
 * Invocation of Java programs distributed in this manner requires usage of the command line. Once the user has all the class files, he needs to launch the application by the following command line (where Main is the name of the class containing the main method.)

 * Java 'jar' class libraries : Utility classes, framework classes, and/or third party classes are usually packaged and distributed in Java ' *.jar' files. These 'jar' files need to be put in the CLASSPATH of the java program from  which these classes are going to be used.
 * If a jar file is executable, it can be run from the command line:

 * Client Server applications : The client server applications consist of a front-end, and a back-end part, each running on a separate computer. The idea is that the business logic would be on the back-end part of the program, which would be reused by all the clients. Here the challenge is to achieve a separation between front-end user interface code, and the back-end business logic code.
 * The communication between the front-end and the back-end can be achieved by two ways.
 * One way is to define a data communication protocol between the two tiers. The back-end part would listen for an incoming request. Based on the protocol it interprets the request and sends back the result in data form.
 * The other way is to use Java Remote Invocation (RMI). With the use of RMI, a remote object can be created and used by the client. In this case Java objects are transmitted across the network.
 * More information can be found about client-server programming, with sample code, at the Client Server Chapter in this book.

 * Web Applications : For applications needed by lots of client installations, the client-server model did not work. Maintaining and upgrading the hundreds or thousands of clients caused a problem. It was not practical. The solution to this problem was to create a unified, standard client, for all applications, and that is the Browser.
 * Having a standard client, it makes sense to create a unified, standard back-end service as well, and that is the Application Server.
 * Web Application is an application that is running in the Application Server, and it can be accessed and used by the Browser client.
 * There are three main area of interest in Web Applications, those are:
 * The Web Browser. This is the container of rendering HTML text, and running client scripts
 * The HTTP protocol. Text data are sent back and forth between Browser and the Server
 * The Web server to serve static content, Application server to serve dynamic content and host EJBs.
 * Wikipedia also has an article about Web application.

J2EE code execution
As the focus was shifting from reaching GUI clients to thin client applications, with Java version 2, Sun introduced J2EE (Java 2 Extended Edition). J2EE added : With J2EE the following Java component executions are possible:
 * Components Base Architecture, (Servlet, JSP, EJB Containers)

 * Java Servlet code : (Figure 2) Java got its popularity with server side programming, more specifically with J2EE servlets. Servlets are running in a simple J2EE framework to handle client HTTP requests. They are meant to replace CGI programming for web pages rendering dynamic content.
 * The servlet is running in a so called servlet-container/web container. The servlet's responsibility is to:
 * Handle the request by doing the business logic computation,
 * Connecting to a database if needed,
 * Create HTML to present to the user through the browser
 * The HTML output represents both the presention logic and the results of the business computations. This represents a huge problem, and there is no real application relying only on servlets to handle the presention part of the responsibility. There are two main solutions to this:
 * Use a template tool (Store the presentation part in an HTML file, marking the areas that need to be replaced after business logic computations).
 * Use JSP (See next section)
 * Wikipedia also has an article about Servlets.

 * Java Server Pages (JSP) code : (Figure 3) JSP is an HTML file with embedded Java code inside. The first time the JSP is accessed, the JSP is converted to a Java Servlet. This servlet outputs HTML which has inside the result of the business logic computation. There are special JSP tags that helps to add data dynamically to the HTML. Also JSP technology allows to create custom tags.
 * Using the JSP technology correctly, business logic computations should not be in the embedded Java part of the JSP. JSP should be used to render the presentation of the static and dynamic data. Depending on the complexity of the data, 100% separation is not easy to achieve. Using custom tags, however may help to get closer to 100%. This is advocated also in MVC architecture (see below).

 * EJB code : (Figure 4) In the 1990s, with the client server computing, a trend started, that is to move away from Mainframe computing. That resulted in many small separate applications in a Company/Enterprise. Many times the same data was used in different applications. A new philosophy, "Enterprise Computing", was created to address these issues. The idea was to create components that can be reused throughout the Enterprise. The Enterprise Java Beans (EJBs) were supposed to address this.
 * An EJB is an application component that runs in an EJB container. The client accesses the EJB modules through the container, never directly. The container manages the life cycle of the EJB modules, and handles all the issues that arise from network/enterpise computing. Some of those are security/access control, object pooling, transaction management, ....
 * EJBs have the same problems as any reusable code: they need to be generic enough to be able to be reused and the changes or maintenance of EJBs can affect existing clients. Many times EJBs are used unnecessarily when they are not really needed. An EJB should be designed as a separate application in the enterprise, fulfilling one function.

 * Combine J2EE components to create an MVC architecture : This leads us to the three layers/tiers as shown in (Figure 5).
 * In modern web applications, with lots of static data and nice graphics, how the data is presented to the user became very important and usually needs the help of a graphic artist.
 * To help programmers and graphic artists to work together, the separation between data, code, and how it is presented became crucial.
 * The view (User Interface Logic) contains the logic that is necessary to construct the presentation. This could be handled by JSP technology.
 * The servlet acts as the controller and contains the logic that is necessary to process user events and to select an appropriate response.
 * The business logic (model) actually accomplishes the goal of the interaction. This might be a query or an update to a database. This could be handled by EJB technology.
 * For more information about MVC, please see MVC.
 * For more information about MVC, please see MVC.

Jini
After J2EE Sun had a vision about the next step of network computing. That is Jini. The main idea is that in a network environment, there would be many independent services and consumers. Jini would allow these services/consumers to interact dynamically with each other in a robust way. The basic features of Jini are:
 * No user intervention is needed when services are brought on or offline. (In contrast to EJBs where the client program has to know the server and port number where the EJB is deployed, in Jini the client is supposed to find, to discover, the service in the network.)
 * Self healing by adapting when services (consumers of services) come and go. (Services periodically need to renew a lease to indicate that they are still available.)
 * Consumers of JINI services do not need prior knowledge of the service's implementation. The implementation is downloaded dynamically and run on the consumer JVM, without configuration and user intervention. (For example, the end user may be presented with a slightly different user interface depending upon which service is being used at the time. The implementation of the user interface code would be provided by the service being used.)

A minimal Jini network environment consists of:
 * One or more services
 * A lookup-service keeping a list of registered services
 * One or more consumers

Jini is not widely used at the current writing (2006). There are two possible reasons for it. One is Jini a bit complicated to understand and to set it up. The other reason is that Microsoft pulled out from Java, which caused the industry to turn to the use of proprietary solutions.

title: Java Programming/Execution


text:
Handbook of Genetic Counseling/Autism-1

Autisim

What is autism?

 * Disorder of brain function that appears early in life -- before the age of 3
 * Autism belongs to a family of related brain conditions affecting behavior early in life, which are often referred to as pervasive developmental disorder
 * Cause of autism is unknown

Traits associated with autism

 * social detachment, e.g., failure to smile at parents and an unawareness of events around them
 * abnormal language development, such as repeating phrases in a mechanical voice
 * unusual repetitive movements, e.g., rocking and flicking fingers
 * mental retardation (usually in more severe cases)
 * Traits vary in severity and persist into adulthood
 * Some individuals with autism have amazing skills (e.g. Rainman)

Incidence

 * Savant syndrome is quite rare (only about 200 cases ever recorded)
 * childhood autism is more common, affecting about one in 700 children
 * Boys are affected four times more often than girls

Can autism "run in families"?

 * If a child has autism, each of the parent's later children has a 3% to 9% chance of having autism.
 * This is 100 to 200 times greater than in the general population.
 * Believed to be multifactorial inheritance
 * Genetic component supported by twin studies

 * The second study used the same twins, but changed the definition of autism
 * new definition was looser -- people with milder behavioral problems were counted as autistic

Genes involved in autism

 * no gene found yet
 * Several candidate regions on chromosomes have been identified through linkage studies

Differential Diagnosis
(known genetic conditions that may share some symptoms of autism)
 * Fragile X syndrome (the FMR1 gene on the X chromosome).
 * Tuberous sclerosis (the TSC1 gene on chromosome 9).
 * Duplications of part of the long arm of chromosome 15.
 * Untreated phenylketonuria (the PAH gene on chromosome 12)

Environmental factors

 * UNKNOWN
 * Autism was thought to result from certain events before or shortly after birth
 * Infection of the brain with herpes virus and infection of the pregnant mother with rubella virus
 * Problems with brain structure are associated with autism, including hydrocephalus and, very rarely, a brain tumor
 * 1993 British study was reviewed by both the Medical Research Council in Great Britain and the Centers for Disease Control in the United States
 * The Centers for Disease Control concluded that: "to date there is no conclusive evidence that any vaccine can cause autism"

Web sites resources

 * The autism page at the National Institute for Neurological Disorders and Stroke:
 * The MedlinePlus web site for autism:
 * The February 2000 issue of Scientific American has an article entitled "The Early Origins of Autism" (full text not on-line).
 * More about autism from the National Immunization Program at the Centers for Disease Control:
 * Diagnosis, assessment and interventions for Autistic Spectrum Disorders:

title: Handbook of Genetic Counseling/Autism-1


text:
Handbook of Genetic Counseling/Autism-2

Autism

What is autism?

 * Autism is considered an organic neurodevelopmental disorder characterized by social, communication, and intellectual developmental disturbance.
 * It was first described in 1943, and was thought at the time that parents were not giving their children enough love and attention. It is now realized that the parents are in no way to blame for the condition.
 * It is generally diagnosed by age three. Based on age of onset, it may be called infantile autism or childhood-onset autism (also called pervasive developmental disorder). These have not been proven to be different disorders, although infantile autism is usually more severe.
 * Characterized by a state of self-absorbance, delayed communication, and a need to maintain routine and repetitive bizarre motor patterns.
 * Associated with fragile X syndrome, tuberous sclerosis, PKU, and Tourette's syndrome.
 * There are not medical tests for autism. Diagnosis is based on observations of the child's behavior. Speech, hearing, and psychological tests are often done.
 * An EEG (electroencephalogram) is often done to look at brain wave abnormalities, which indicate epilepsy. Children with autism sometimes develop epilepsy as they get older.
 * Severity of autism is highly variable.

Symptoms

 * Usually, parents first notice that their baby does not respond to them. The baby may not look at the parents or may not want to be picked up and held.
 * Slow development or lack of physical, social, and learning skills.
 * Development may appear to be uneven. For example, motor development may be normal, but talking is delayed. Also, the child may show a talent for music or drawing but be unable to go to a regular school.
 * Immature rhythms of speech, limited understanding of ideas, use of words without attaching the usual meaning to them.
 * Unresponsive to what is said to them. May appear to be deaf, but really they do not learn the meaning of words. Often seem to be talking to themselves instead of to people around them.
 * Sometimes indicate their needs by gesturing, but usually scream, cry, or have temper tantrums.
 * Abnormal responses to sensations. Sight, hearing, touch, pain, balance, smell, taste, may be affected.
 * Abnormal ways of relating to people, objects, and events. Typically, children with autism do not respond appropriately to adults and other children. Objects and toys are not used as normally intended.
 * Normal relationships with others do not develop. They have difficulty playing with other children. May be withdrawn and inactive.
 * Repetition of actions, words, or body movements such as twirling objects or flapping their hands. Seem to want their lives to be patterns and may become upset by a change in routine.

Quick List of Common Behaviors

 * No cuddling
 * Resistance to change in routine
 * No eye contact
 * Difficulty mixing with other children
 * Gesturing to show needs
 * No fear of real dangers
 * Acting as if deaf
 * Standoffish manner
 * Resistance to learning
 * Sustained odd play
 * Marked physical overactivity
 * Inappropriate attachment to objects
 * Inappropriate laughing and giggling
 * Spinning of objects
 * Rocking movements or hand flapping
 * Sparse, meaningless, or echo speech

Prevalence

 * Incidence is estimated at 4-5/10,000
 * Affects all race, ethnicities, and social classes equally
 * More common in males (3 or 4 to 1), but females are more severely affected
 * About 75% are mentally retarded (IQ below 70)

Causes of Autism

 * Research suggests it is caused by a defect in brain functioning.
 * Multifactorial inheritance with a strong clustering in families.

Prognosis

 * Variable, but at least 2/3 remain severely handicapped as adults.
 * There is no cure.
 * Normal life expectancy.
 * 1/3 of children develop epilepsy or seizures.
 * Many often improve as they grow older, but will continue to have problems relating to others. Adolescence may worsen behavior problems in some

Management

 * Treatment consists of educational and behavioral methods aimed at decreasing behavioral symptoms and aiding in the development of language and self-help skills.
 * Psychopharmacotherapy is often helpful.

Inheritance

 * A couple with one autistic child has a 1/50 chance of having another. This is higher is the couple has an affected female child.
 * The brothers and sisters and close relatives of children with autism have more problems such as epilepsy, learning disabilities, and mental retardation.

Patient Resources

 * National Society for Autistic Children (NSAC)
 * Autism Society of America

title: Handbook of Genetic Counseling/Autism-2


text:
Handbook of Genetic Counseling/Autism-3

Autism (and/or Asperger Disorder)

Contracting

 * Introductions, acknowledge any prior contact
 * Assess main concerns of patient
 * Why are they visiting Genetics today?
 * What do they hope to gain from the session?
 * Assess knowledge of diagnosis
 * Overview of today's session
 * Restate patient's concerns
 * Medical history, family history, diagnosis, genetics, recurrence risk, testing options and limitations

Pediatric Intake

 * Pregnancy and Medical History
 * focus on possible rubella during pregnancy, PKU, infantile spasms, seizures, balance problems, fragile X testing?
 * Developmental History
 * Social skills? (delay in play ~ 2 years old? Prefers to spend time alone? Friendship group? Eye contact?)
 * Communication skills? (Attaches usual meanings to words? Communicates more with gestures? Short attention span?)
 * Behaviors? (Overactive? Passive? Aggressive? Obsession with a certain subject matter? Repetitive routines?)
 * I.E.P. at school?
 * Family History
 * Any relatives with diagnosed autism or Aspergers, Fragile X, Tuberous Sclerosis, mental retardation, learning disabilities, developmental delay (speech problems), seizures, PKU, balance problems, infant deaths, miscarriages?

What is "Asperger Disorder" or "Asperger's Syndrome"?

 * A type of autism that involves a developmental disorder of brain function
 * Autism in general involves three areas:
 * communication (verbal and non-verbal)
 * socialization (interactions with others)
 * behavior
 * diagnosis of a type of autism depends on differences in language development, severity of symptoms, age of onset, and clinical features
 * Symptoms
 * severity is highly variable
 * repetitive movements (i.e., rocking) and routines
 * reduced pain sensitivity
 * aggressive behavior
 * can injure themselves (i.e., biting, head-banging)
 * inability to form emotional bonds with people
 * social and communication skills impaired
 * unusual responses to stimuli (sensitive to sound, light, touch)
 * clumsy movements
 * seizures (1/3 of people with autism will have them)
 * children with "Asperger Disorder" or "Asperger's Syndrome" do not show a history of language delay
 * intelligence is usually normal
 * Etiology
 * caused by abnormalities in brain structure or function, sometimes combined with environmental factors
 * brain cells may migrate to the wrong place in the brain
 * parts of the communication network may fail to form due to problems with neural pathways
 * coordination of thoughts, feelings, and actions may be impaired
 * a number of candidate genes that may play a role in causing Asperger Disorder have been identified and are currently being researched

Genes and Chromosomes

 * inheritance is likely multifactorial (genes plus environment)
 * candidate genes found on chromosomes 6,7,9, 15, X
 * Incidence and Carrier Frequency (autism)
 * 1-2 people per 1,000
 * 2,000 to 4,000 children born each year
 * affects all races, ethnicities, and social classes at equal rates
 * 3X to 4X more common in boys that in girls
 * often associated with other genetic disorders
 * Fragile X (found in 10% of people with autism)
 * Tuberous Sclerosis (1/4 of those affected have autism)

Recurrence risks

 * overall = up to 8.5%
 * affected male = 7%
 * affected female = 14.5%

Natural History

 * symptoms of autism usually appear between 24 and 36 months of age
 * symptoms of Asperger Disorder typically appear later in childhood
 * loss of social skills they may have already developed
 * aggressiveness may increase
 * obsession with a particular subject
 * no cure
 * normal life expectancy

Testing

 * currently, there is no medical test to differentiate between the types of autism (diagnosis must be done clinically)
 * chromosome analysis might detect ~5% of autism (associated with abnormalities on the 6,9, 7, 15, and X chromosomes)

Management

 * ~60% of people with autism will need care throughout adulthood
 * Education
 * Special educational services?
 * I.E.P? Use of visual aids, structured schedule, teacher-to-student ratio? Positive reinforcement? Step-related tasks?
 * Behavior-based interventions at school?
 * Routine; clear consequences?
 * Behavior
 * Behavior Management Specialist
 * reinforcement of routine/rules both at home and at school
 * regular positive reinforcement and rewards
 * Support system for parents?
 * coping mechanisms may include planning for time away from the child, joining support groups, becoming an active advocate for people with autism, planning for the future once they are gone

Treatment

 * some drugs are available to treat symptoms and behavioral problems
 * please note that none of these drugs has been specifically approved for use with people with autism by the F.D.A. and should be taken only under close consultation with a physician *
 * drugs used to treat anxiety and depression (Prozac, Luvox, Zoloft, Anafranil) may relieve some symptoms
 * Anafranil (clomipramine) may reduce obsessive, repetitive behaviors
 * Ritalin may reduce hyperactivity (has been shown to be more effective in those who are higher-functioning and do not have seizures)
 * Vitamin B6 may stimulate brain activity

Psychosocial Issues

 * impending adolescence will likely bring a new awareness that the person is somehow different from their peers
 * may result in feelings of social isolation, loneliness, anxiety, sadness
 * lowering of self-confidence and withdrawal may occur
 * stress levels of caregivers may be high due to:
 * expectations
 * desire for a "normal" child (feelings of guilt, denial, anger)
 * too high or too low for the child?
 * frustration, shame, or disappointment that they are not met
 * pressure to socialize with others? (denial)
 * feeling like other parents don't know what you are dealing with or going through
 * sadness at loss of hopes and dreams for the child
 * frustration with possible changing diagnosis?
 * dealing with challenging behaviors of children (anger, frustration, helplessness)
 * coordinating services (time and energy commitment)
 * maintaining continuity/routine
 * communicating child's needs to the school
 * financial strain
 * does insurance cover any therapy?
 * lack of personal support system (partner, family, church, friends?)
 * lack of or inability to attend community support groups

"Asperger Disorder" or "Asperger's Syndrome" Support Groups and Resources

 * Asperger's related general support site, with forum.
 * Asperger's related forum for anyone having a child with behaviour described in this article
 * Asperger's related site with various features that are described on the site

Autism Support Groups and Resources

 * Autism Society of America
 * provides information and education to assist parents and educators
 * information packages, phone line for questions
 * focuses on the importance of individualizing the management and treatment programs for each person with autism
 * provides information on a range of available intervention options
 * local chapters arrange meetings and may publish a newsletter
 * 7910 Woodmont Ave, #650
 * Bethesda, MD 20814-3015
 * (301) 657-0881
 * 1-800-3-AUTISM (toll-free line)

 * Exploring Autism
 * good overview of the genetics of autism
 * includes frequently asked questions, family stories, a history of autism, and related links
 * Society for Autistic Children of Greater Cincinnati
 * contact number = 948 -1142

 * Indiana Resource Center on Autism
 * Institute for the Study of Developmental Disabilities, Indiana University
 * 2853 East Tenth Street
 * Bloomington, IN 47408-2601
 * (812) 855-6508

 * offers publications, films and videocassettes on a range of topics related to autism

title: Handbook of Genetic Counseling/Autism-3


text:
Handbook of Genetic Counseling/Balanced Robertsonian Translocation

Balanced Robertsonian Translocation

Contracting

 * Why were you referred here today?
 * What are you most concerned about?
 * Outline goals of session namely talking about causes of developmental delay, explaining the results of lab test - balanced robertsonian translocation, and examination

Elicit Medical History

 * Ask about history of delays and developmental milestones.
 * Ask about any perinatal infections.
 * Ask after past and current interventions.
 * Get pregnancy history of the mother including any infections or exposures to possible teratogens.
 * Ask about history of miscarriages or stillbirths.

Family History

 * Ask specifically about occurrence of miscarriage or stillbirth on mother and father's side of family.
 * Also ask about history of delays in family members and mental retardation.

Genes and Chromosomes

 * Use Greenwood book and karyotype in explanation.
 * Cells make up the body; each cell contains chromosomes which are made of a chemical called DNA which in turn contains genes.
 * Genes are like recipes that are instructions to make proteins such as skin, muscle and organs.
 * In the lab, technicians break open the cell and these are what chromosomes look like.
 * There are 46 chromosomes total in humans, 23 come from mom in her egg and 23 from dad in his sperm. So one chromosome 1 comes from mom and the other from dad to form the 23 pairs.
 * The 23rd pair are called the sex chromosomes. Women have two XXs and Men have an X and Y. The Y chromosomes is not really shaped like a Y, but is named that to distinguish it from the X.
 * Chromosomes are able to exchange DNA with each other. Sometimes this happens with two different chromosomes of different pairs such as number 13 and 15. Also, an arm of one chromosome can become attached to the arm of another. These are called translocations.
 * Certain chromosomes with one very short arm and one very long arm are involved in a Robertsonian translocation. The short arms become detached from the long arms and are lost, but the long arms attach to each other forming one large chromosome from two smaller ones. The small arms of these chromosomes do not contain genes, so no significant information is lost. This is called a balanced Robertsonian translocation.
 * Your lab results show that this happened between one chromosome 13 and a one 15. Because the two chromosomes essentially joined together into one, the lab report shows you have 45 chromosomes instead of 46.

Robertsonian Translocations

 * Can occur de novo or can be inherited.
 * Cytogenetic testing of blood relatives can be done to detect de novo or familial translocation.
 * Are one of most common types of translocation and is detected in 1/1000 fetuses by amniocentesis.
 * Occurs in a germ cell before meiosis and involves the acrocentric chromosomes 13, 14, 15 (D), and 21, 22 (G).
 * The short arms of two chromosomes are lost and the long arms joined end to end at the centromeres. They may be homologous or non-homologous chromosomes that are joined, e.g. t21;21 or t13;15 respectively.
 * D/D translocations occur between chr. 13-15. D/G occurs between one of 13-15 and one 21-22. G/G occurs between 21-22.

Balanced and Unbalanced Translocations

 * Balanced translocations normally do not cause any abnormal phenotype.
 * Unbalanced translocations can cause miscarriage, stillbirth, or a birth of a baby with multiple malformations, developmental delay, and mental retardation (Maternal-Fetal Medicine: Principles and Practices, 1994).
 * Unbalanced translocations occur when a diploid germ cell with a translocation goes through meiosis. Abnormal segregation of the chromosomes in which only a portion or more than 1 copy of any part of either chromosome involved in the translocation can result in a fetus with an unbalanced translocation upon fertilization.

Risks Associated with Balanced Translocation Carriers

 * If a familial translocation has been detected through an individual with an unbalanced translocation, then the recurrence risk of having another child with an unbalanced translocation is 15%.
 * If not biased by the presence of an individual with an unbalanced translocation, then the recurrence risk is 1-2%.
 * Risk for both situations for spontaneous miscarriage is 25%.
 * Couples with a D/D translocation are at decreased risk (1-2%) of having a child with an unbalanced translocation since loss or gain of genetic information in these chromosomes is lethal.
 * Maternal carriers of balanced translocations have greater likelihood than paternal carriers of having children with unbalanced translocations.

Developmental Delay

 * Unknown cause in 50% of cases.
 * Result of environmental and/or genetic factors.
 * Approximately 2000 genetic causes are known which include chromosomal abnormalities, metabolic or endocrine disorders, hereditary degenerative disorders, hormonal deficiency, hereditary syndromes.
 * Environmental causes are infection, irradiation, or exposure to certain toxins during prenatal development. Peri or postnatal causes are prematurity, anoxia, cerebral damage, infection, toxins, hormone deficiencies, metabolic disorders, epilepsy.
 * Prevalence of people with some form of mental retardation is 1-3% in US.
 * Intervention services are available very early and reach into adulthood. Assessment of development done at CCDD. School system provides services in the form of Individualized Education Plan (IEP) and focuses on special services like speech therapy. Adults can be provided with job training and many live in group homes.

Clinical Features of Mental Retardation

 * Affects developmental and cognitive abilities.
 * IQ score lower than 70.
 * Ranges are: Mild, 50-55 to 70; Moderate, 35-40 to 50-55; Severe, 20-25 to 35-40; Profound, below 20-25.
 * Most individuals with MR range between 55-69.
 * People with MR may have limits in the following: communication, work, self-care, social skills, self-direction, and academic skills, living alone.
 * Onset is before 18 years.

Recurrence Risks

 * Difficult to calculate risk if cause is unknown.
 * Empiric risk around 10%

Psychosocial Issues

 * Provision of adequate intervention
 * Burden of taking care of individual with MR
 * Affects sibling and other family relationships.
 * Uncertainty as to cause of MR and recurrence risks.


text:
Handbook of Genetic Counseling/Balanced Translocation

Balanced Translocation

Introduction and Contracting

 * Can you explain in your own words what you understand about why you were referred to genetics?
 * What are your main concerns for ______ at this time?
 * Do you have any specific questions you would like us to make sure we try to answer?

Outline session

 * Take medical and family history
 * Review the chromosome results with you
 * Explain more about why we want to do chromosome testing on you (parents)
 * Dr Viskochil will examine him
 * We will then make sure to discuss any further questions or concerns

Medical/Developmental History

 * follow form that I started filling out and confirm info

Family History

 * 3 generation pedigree
 * include standard questions don't forget miscarriages as they occur more frequently in people with balanced translocation

Explain Chromosomes and Genes (using sample karyotype)

 * When the lab looked at _____ 's cells under a microscope they found a change in the chromosomes
 * The change they found was called a translocation

What is a translocation?

 * Transfer of chromosomal material between chromosomes

Why do translocations happen?

 * We do not really know why - (Sort of. It happens because it is possible. And its possible because of the inherent nature of the genetic material.)
 * Estimated that about 1 person in 500 has a chromosome translocation
 * We know that our chromosomes seem to break and rejoin quite often, and it is only sometimes that it leads to problems
 * These changes are out of our control, and nearly always translocations happen in either the egg or sperm cell before they join together
 * Therefore they are not likely to be caused by anything during the pregnancy

How Translocations Occur

 * Sometimes the chromosomes break during cell division and are usually repaired
 * Sometimes two fragments may break off from two different chromosomes, and "swap" places
 * This is called a reciprocal translocation (this is the type of translocation he has)

Show Karyotype and Explain Specific Break Points

 * Sometimes helps to see the actual karyotype
 * 46 means that the usual number of chromosomes is present
 * Y chromosome is what makes him male
 * T stands for translocation, where a piece of chromosome 2 and 21 exchanged places
 * The rest just tells us more exactly where the chromosomes broke
 * So arrows are pointing to where the chromosomal material exchanged places

Balanced Translocations

 * In most cases, there is no loss or gain of chromosomal material during the exchange process
 * When the lab looked they didn't see any missing or extra pieces of chromosomes and they therefore think that this might be a balanced translocation

What Are the Effects

 * Often people will have a balanced translocation and not even know because they don't experience any problems (this occurs in majority of cases of new balanced rearrangements Warburton 1991)
 * Sometimes, apparently balanced translocation carriers show some characteristics or symptoms (Warburton showed that frequency of abnormality was 6.1% but confidence interval includes 3% in apparently balanced translocations)
 * One explanation for this finding is that the break may have occurred in the middle of a gene that is important in growth or development and the gene no longer provides correct instructions because it is disrupted
 * We do not know if this translocation is the explanation for the characteristics and health problems in ______

What will results from parental chromosomes tell us

 * In order to determine what the translocation might mean it is important to do chromosomes on all parents of children with a translocation
 * If a parent has the same translocation and they do not have any of the same symptoms or characteristics as the child then we cannot conclude that the translocation is the cause
 * If neither parent has the translocation than it may explain some or all of the characteristics and health problems in ______, but would be difficult to know for certain
 * Parental chromosomes will also be important because it will help us determine what risks might be to future offspring

What can happen in offspring of people with balanced translocation

 * If one of the parents carries a balanced translocation, it is possible for a child of theirs to acquire a bit of extra chromosome material or a bit missing
 * Either of these would be known as an UNBALANCED translocation
 * This extra and or missing pieces of chromosome can unfortunately cause serious mental, physical and medical challenges in the child who inherits them
 * Sometimes they cause a miscarriage, but not always
 * However, it is also possible for these same parents to have a child with normal chromosomes, or a child with the same balanced rearrangement of their chromosomes as the parent
 * Having a balanced translocation of your chromosomes does not mean you cannot have normal healthy children
 * Factors that influence risks (not applicable in this case)
 * Ascertainment - A family ascertained as a result of a previously affected child is seen to be at increased risk of recurrence since the imbalance has been proved viable.
 * Risk of having an affected child is lower when a family is ascertained following for example repeated spontaneous miscarriage since in these cases the imbalance is more likely to be inviable
 * Each time they have a child, there are several possibilities.
 * they may have a child with normal chromosomes
 * they may have a child with the same balanced rearrangement of the chromosomes as the parent
 * they may have a child with an unbalanced rearrangement of the chromosomes which may cause mental and physical challenges
 * the pregnancy may end in a miscarriage

What sort of problems do unbalanced translocations cause?

 * Can be difficult to predict because it depends on:
 * Which parts of chromosomes are missing or duplicated (aneuploidy for 4p, distal 4q and 9p for example all have a high degree of viability therefore relatively high risk)
 * how large of pieces they are (if large less likely to be viable due to more extra or missing information)
 * There are not usually the same breaking points for each translocation because it is random so we don't have any other children to compare this exact translocation to
 * Nearly always have learning problems though if translocation is unbalanced

Tests in Pregnancy for Translocation Carriers

 * amniocentesis This is usually done from 14 weeks in the pregnancy and the result normally takes about 2 weeks.
 * Chorionic villus sampling (CVS) usually done between 10-12 weeks in the pregnancy, and the results take about 2 weeks.

Psychosocial Considerations

 * Information can be difficult to understand because translocations are not an easy concept
 * Don't expect them to remember everything, we will provide a summary in a letter we will write
 * People who have a balanced translocation of their chromosomes do not have a disease that can be "caught" by other people
 * Guilt about possibly passing this on (not under our control can't cause or prevent)
 * What do other family members know and do you plan on telling them
 * Either parent considering having more children because this may alter their plans or could be upsetting to think they may have a recurrence risk if they didn't think so before

References and Patient Resources

 * patient literature about translocations
 * Chromosome deletion outreach support site
 * Unique a UK rare chromosome disorder support group (similar to chromosome deletion outreach)
 * information on translocations more advanced
 * Dorothy


text:
Handbook of Genetic Counseling/Bardet-Biedl Syndrome-1

Bardet-Biedl Syndrome

Introduction

 * How have thing been going since we saw you last?

Contracting

 * Are there some major issues that you want to make sure are addressed today?
 * We will gather medical information, any changes in the family, physical exam

Interim History

 * Hospitalizations?
 * Surgeries?
 * Illnesses?
 * Any doctor visits?
 * Ophthalmology visit?
 * How's the eating schedule been going?
 * Regular meal times?
 * Modified meals?
 * Scheduled snack times?
 * Restricted to one helping at meals?
 * Is involved in any school-type programs?
 * EI preschool referral
 * Behavior issues
 * Developmental issues
 * speech difficulties?
 * Motor issues (walking, running)
 * Know colors/body parts
 * Potty trained

Establish Plan

 * Reiterate plan that was agreed upon in case (i.e. hospitalization in two weeks time? Vs. continue with strenuous weight loss plan)
 * Reassess parents' state of mind and emotional level
 * Make sure parents understand importance and necessity of 1) eye appointment & 2) weight loss


text:
Blender 3D: Noob to Pro/Advanced Tutorials/Advanced Animation/Guided tour/Const/cl

Copy Location

The Copy Location constraint does as the name states: it will copy the location of the target to the source (constrained object). Less Influence will drag the constrained object less and less to the target.

If it's an armature, a new field will appear to let you tell which bone will be the target. Don't forget TABKEY completion while writing the name of your object/bone!

You can tell Blender to work only on the selected axis. Many uses are possible :)

The Constraint Panel

 * The Target field will let you select which Object the constraint holder will follow.

Where To Use It
Most of the time this little constraint is useful to stick objects to one another. By playing with the Influence you can tell when it will work, when it will remain motionless.

A good use of it is to ask a character to pick up something. By having a bone or empty for each side of the relationship (hand <-> glass), as the hand approaches the glass, you can align the two empties and fire the constraint up (1.00) to stick them together. You add another child-bone in the middle of the hand to tell where the glass will be. Thus moving the hand will move the glass. On the side of the glass just add an empty and make it parent of the glass. Add a copy location to the empty pointing to the bone in the hand we just did. There you go. Of course when the hand rotates the glass will not. For that you will need to add a Copy Rotation Constraint.

Before Blender 2.40, the above method was a good way of faking parent relationship without rotation. But now we have the hinge option which does the same.

Create this kind of tracking device using the X Y Z toggle button


text:
Handbook of Genetic Counseling/Bardet-Biedl Syndrome-2

Bardet-Biedl Syndrome

Genetic Etiology
Incidence and Carrier Frequency
 * Mode of inheritance: Autosomal Recessive. It requires a recessive mutation in one of six loci plus an additional mutation in a second locus, known as triallelic inheritance.
 * Chromosome locations: This syndrome is linked to 6 different loci-BBS1 on 11q13, BBS2 on 16q21, BBS3 on 3p13, BBS4 on 15q22.3, BBS5 on 2q31, and BBS6 on 20p12
 * Incidence is 1 in 100,000, with an increased prevalence in Arab and Bedouin populations (1 in 13,500). Carrier frequency is 1 in 179.

Clinical Features
Testing
 * Obesity
 * Eye Problems: Rod-cone dystrophy (major)
 * Retinitis pigmentosa
 * Strabismus
 * Cataracts
 * Mouth and Tooth Problems: High arched palate
 * Dental crowding
 * Hypodontia
 * Small tooth roots
 * Cardiac Problems: Left ventricular hypertrophy
 * Other congenital heart defects
 * Hypertension
 * Hepatic Fibrosis
 * Hirschsprung disease (less than 10% of patients)
 * Hypogonadism (major)
 * Undescended testes (10%)
 * Hypothyroidism
 * Asthma (27%)
 * Renal Problems (major): Nephrogenic diabetes insipidus
 * Irregular kidney contour (fetal lobulation)
 * Polydipsia and Polyuria (66% of patients)
 * Recurrent urinary tract infections (30% of patients)
 * Polydactyly of hands and/or feet (major)
 * Brachydactyly of hands
 * Speech delays
 * Ataxia
 * Developmental delay
 * Learning disabilities (major)
 * Diabetes mellitus (15-45% of patients)
 * A clinical diagnosis is made with the presence of 4 major features or 3 major and 2 minor features
 * Age of onset is usually early childhood.
 * Life span is variable, depending on severity and management of symptoms.
 * Chromosomal testing is available. This can be done prenatally as well as postnatally.

Surveillance, Management, and Treatment Options

 * In the clinic, fundoscopic examination of the eyes should be performed through dilated pupils as well as blood pressure measurement and urinalysis for glucose, protein and leukocytes. Baseline investigations should include ERG/VER, ECG, echocardiogram, ultrasound of the kidneys and urinary tract and either an IVP or DMSA/DPTA scan. The child should be evaluated by cardiology, ophthalmology, urology, nephrology, genetics, speech, endocrinology, and orthopedics. It is not possible to cure this condition, but regular follow-up for symptoms can improve quality of life.

Psychosocial Issues

 * Guilt, fear, anger, anxiety, sadness, desperation, and depression are common feelings associated with this diagnosis. It is important to assess the family situation, support system, financial position, and living environment as well as offer any resources to families that may be helpful

Support Groups

 * Retinitis Pigmentosa International
 * 23241 Ventura Boulevard
 * Woodland Hills CA 91364
 * 8189920500
 * 8003444877
 * e-mail: rpint@pacbell.net
 * Home Page:

 * American Foundation for the Blind
 * 11 Penn Plaza
 * New York NY 10001
 * 2125027600
 * 8002325463
 * e-mail: afbinfo@afb.org
 * Home Page:

 * American Printing House for the Blind
 * 1839 Frankfort Avenue
 * Louisville KY 40206-0085
 * 5028952405
 * 8002231839
 * e-mail: info@aph.org
 * Home Page:

 * National Association for Parents of the Visually Impaired
 * P.O. Box 317
 * Watertown MA 02472
 * 6179727441
 * 8005626265
 * e-mail: napvi@perkins.pvt.k12.ma.us
 * Home Page:

 * Prevent Blindness America
 * 500 East Remington Road
 * Schaumberg IL 60173
 * 8478432020
 * 8003312020
 * e-mail: info@preventblindness.org
 * Home Page:

 * Vision Community Services
 * 23 A Elm St
 * Watertown MA 02472
 * 6179264232
 * 8008523029
 * e-mail: mablind@tiac.net
 * Home Page:

 * Blind Children's Fund
 * 4740 Okemos Road
 * Okemos MI 48864-1637
 * 5173471357
 * n/a
 * e-mail: blindchfnd@aol.com
 * Home Page:

 * Laurence Moon Bardet Biedl Syndrome
 * c/o The Foundation Fighting Blindness
 * Hunt Valley MD 21031
 * 4107851414
 * 8883943937
 * e-mail: randerson@blindness.org
 * Home Page:

 * American Council of the Blind, Inc.
 * 1155 15th Street
 * Washington DC 20005
 * 2024675081
 * 8004248666
 * e-mail: info@acb.org
 * Home Page:

 * National Association for Visually Handicapped
 * 22 West 21st Street
 * New York NY 10010
 * 2128893141
 * n/a
 * e-mail: staff@navh.org
 * Home Page:


text:
Handbook of Genetic Counseling/Beal's Syndrome

Beal's Syndrome

Introduction

 * What do you know about why you're here?

Contracting

 * Get medical information about *Get some pregnancy history
 * Get family history
 * Doctor will examine
 * Discuss findings and answer any questions

Beals Syndrome (Contractural Arachnodactyly Syndrome)

 * Basic features
 * appearance
 * Occasional micrognathia, scaphocephaly, iris coloboma, ASD and VSD
 * Changes as the child grows
 * Gradual improvement in joint movements
 * Genetics
 * Autosomal dominant
 * Linked to fibrillin locus on chrom. 5 (FBN2 gene)
 * National Organization for Rare Disorders, Inc.(NORD)
 * P.O. Box 8923
 * New Fairfield, CT 06812-8923
 * Telephone: (203) 746-6518
 * Fax: (203) 746-6481
 * Toll free: (800) 999-6673
 * TDD: (203) 746-6927
 * e-mail: orphan@rarediseases.org
 * Home Page:


text:
Handbook of Genetic Counseling/Becker Muscular Dystrophy

Becker Muscular Dystrophy

General Information

 * Dystrophinopathies
 * Characterized by a spectrum of muscle disease that ranges from mild to severe
 * Duchenne/Becker muscular dystrophy is severe
 * Skeletal muscle is primarily affected in both
 * DMD is rapidly progressive and presents in early childhood.
 * Patients are often wheelchair-bound by age 12
 * Becker is characterized by later-onset skeletal muscle weakness
 * Patients remain ambulatory into their 20s
 * Despite milder skeletal muscle involvement, heart failure from dilated cardiomyopathy is a common cause of morbidity and the most common cause of death
 * Mean age of death is in the mid-40s
 * Dystrophin gene
 * Xp21.2
 * Encodes protein dystrophin
 * 85% of males with BMC have deletions or duplications involving exons of this gene
 * Molecular genetic testing is available clinically
 * Prevalence
 * 1 in 18,000 live male births

Diagnosis

 * Clinical
 * Family history
 * Compatible with X-linked recessive inheritance
 * Creatine Phosphokinase (CK) concentration
 * Evaluated by blood test
 * Elevated serum CK concentration results from progressive elimination of dystrophic muscle fibers.
 * Can also result from strenuous exercise
 * CK concentration gradually decreases with advancing age due to the progressive elimination of these muscle fibers.
 * 100% of males with BMD have a serum CK concentration >5x normal
 * ~30% of female carriers have a concentration 2-10x normal
 * Some investigations have shown a wide variability in BMD carriers
 * Many have levels within the normal range, so other tests are necessary
 * CPK is not completely reliable
 * Clinical findings
 * Progressive symmetrical muscle weakness and atrophy, proximal greater than distal, often with calf hypertrophy
 * Weakness of quadriceps femoris may be the only sign
 * Activity-induced cramping in some patients
 * Flexion contractus of the elbows may occur late in the course
 * Wheelchari dependency, if present, after 16 years of age
 * Preservation of neck flexor muscle strength in BMD differentiates it from DMD
 * Molecular genetic testing
 * Deletions involving one or more exons of the DMD gene
 * ~85% of males with BMD have deletions
 * Testing is done by PCR or southern blot
 * Available on a clinical basis
 * The remaining ~15% have duplications of one or more exons of the DMD gene or other mutations such as small deletions or insertions, single base changes, or splicing mutations
 * Carrier testing may be performed but requires quantitative analysis for gene dosage which can be difficult to perform and interpret
 * Prenatal testing is available

Clinical Description

 * Males
 * Characterized by later-onset skeletal muscle weakness (as compared to DMD which presents ~ age 4 years)
 * Patients remain ambulatory into their 20s with BMD
 * Heart failure from dilated cardiomyopathy is a common cause of morbidity and the most common cause of death
 * The mild end of the spectrujm includes men with onset of symptoms after age 30 years who remain ambulatory even into their 60s
 * Cognitive impairment is not as common or as sever as in DMD
 * Females
 * Occasionally have clinical features as the result of X chromosome rearrangements involving the DMD locus (Xp21.2)
 * 81% of BMD carriers have no signs or symptoms
 * 14% have mild to moderate muscle weakness
 * 16% have left ventricle dilation
 * 5% have myalgia or cramps
 * No BMD carrier females have been found to have dilated cardiomyopathy
 * Genotype-Phenotype Correlations
 * In males, phenotypes are best correlated with the degree of expression of dystrophin, which is largely determine by the reading frame of the spliced messaged obtained from the deleted allele
 * The BMD phenotype occurs when there is some dystrophin, usually resulting from:
 * Deletions or duplications that juxtapose "in-frame" exons
 * Some splicing mutations
 * Most non-truncating single base changes that result in translation of a protein product with intact N or C termini
 * A dystrophin protein that retains partial function produces the milder BMD phenotype
 * Management
 * There is no treatment for BMD
 * Appropriate management can prolong survival and improve quality of life
 * Physical therapy to promote mobility
 * Range-of-motion exercises
 * Braces to delay the onset of contractures
 * Monitoring and surgical intervention for orthopedic complications
 * Scoliosis, kyphosis, or lordosis
 * Routine monitoring for evidence of cardiomyopathy
 * All carriers should have a complete cardiac evaluation at least once

Differential Diagnosis

 * Limb-girdle muscular dystrophy
 * A group of disorders clinically similar to DMD
 * Occurs in both sexes
 * Caused by mutations I genes that encode sarcoglycans and other proteins that interact with dystrophin
 * Emery-Dreifuss muscular dystrophy
 * Associated with limb contractures and cardiac arrhythmia
 * X-linked recessive, autosomal dominant, and autosomal recessive forms
 * Caused by mutations in the LMNA gene
 * Spinal muscular atrophy
 * Caused by mutations in the SMN gene
 * Characterized by:
 * Poor muscle tone
 * Symmetric muscle weakness that spares the face and ocular muscles
 * Evidence of anterior horn cell involvement
 * Includes fasciculations of the tongue and absence of deep tendon reflexes
 * Dilated cardiomyopathy
 * Can be sporadic or familial
 * No other phenotypes are associated with mutations in the DMD gene

Inheritance

 * X-linked recessive
 * Carrier females have a 50% chance of transmitting the BMD mutation in each pregnancy
 * With each pregnancy, a carrier has a 25% chance of having an affected child
 * Risk to family members
 * A woman with an affected son and one other affected relative in the maternal line is an obligate heterozygote
 * A woman with more than one affected son and no other family history can have:
 * A germline mutation
 * DMD disease-causing mutation present in every cell
 * Germline mosaicism
 * Mosaicism for a DMD disease-causing mutation which includes the germline
 * The frequency of germline mosaicism in DMD is estimated at 12% to 20%
 * If proband is only affected family member, must determine if mother and other females are carriers
 * The proband may have a de novo DMD disease-causing mutation
 * The mutation could have occurred in the egg at the time of conception
 * The mutation could have occurred after conception and therefore is present in some but not all cells of the proband's body.
 * The likelihood that the mother is a carrier is low
 * The proband's mother may have a de novo mutation
 * 2/3 of mothers of sporadically occurring males with DMD are carriers
 * Could have occurred if:
 * Mutation occurred in the egg or sperm at the time of her conception and is present in every cell of her body (germline mutation)
 * Mutation is present in some but not all cells of her body (somatic mosaicism)
 * Mutation is present only in her egg cells (germline mosaicism) and is not detected in a blood sample.
 * The proband's mother may have inherited a DMD mutation from her mother who is a carrier, her mother or father who has somatic mosaicism, or her mother or father who has germline mosaicism.

Risk Assessment

 * All daughters of a male affected with BMD are carriers; none of the sons will inherit the mutation

Ordering the test

 * Patient must sign consent form for DNA analysis
 * Give the patient a copy
 * Put the original in the chart

Resources

 * Muscular Dystrophy Association
 * 800-572-1717
 *


text:
File:MacOSX Firefox Install Window.png

Summary
Window of Firefox disc image on MacOSX.

Licensing
/Images

title: File:MacOSX Firefox Install Window.png


text:
User:Cronian~enwikibooks

I'm interested in the potential for creating and using more decentralized learning environments, especially for technically oriented subjects. I spend my time trying to figure out how to read more difficult math books.

When I'm feeling more confident, I have attempted to start writing some math books.

title: User:Cronian~enwikibooks


text:
Talk:Evolution of Operating Systems Designs/State of current research

DRM
For those that don't know:

What DRM is trying to do is not at all impossible or futile from a design point of view. Sure, there is an analog hole, but that degrades quality. High-quality digital copies can be very well controlled by DRM.

Consider the next-generation AMD processor in a motherboard with a TPM chip. Here is how it works.

 * 1) A regular OS load happens. This may be compromised of course, but that gets detected later.
 * 2) The OS sets aside 64 kB of physically linear RAM, then loads some code into it.
 * 3) The OS executes a special new CPU instruction (opcode) to enter trusted (evil) mode.
 * 4) The CPU performs a special bus cycle to inform other CPUs and restrict DMA access to the 64 kB chunk.
 * 5) A well-protected chip on the motherboard is granted access to this memory.
 * 6) The well-protected chip verifies a digital signature, then grants access to itself.
 * 7) The CPU begins executing the trusted and protected 64 kB.
 * 8) The CPU is placed into a new hypervisor-like mode, with the 64 kB of code in control. Unlike normal CPUs, these CPUs have 8 protection rings (not just 4) and an enhanced ability to virtualize themselves. The 64 kB of code can do something a bit like VMWare, but with less performance loss.
 * 9) The 64 kB of code checks a digital signature on the regular OS.
 * 10) The regular OS, now somewhat trusted because of the digital signature, can continue execution. The 64 kB of special code remains protected by hardware though, and retains the ability to monitor execution of the regular OS. The regular OS can ask the 64 kB of special code to perform various services in cooperation with the well-protected chip.

Now remember that encryption is happening on the monitor cable, the FireWire cable, etc.

Oh, you want to stop this with a custom driver? Sorry. The obvious problem is that an unsigned driver could be refused, but remember that the 64 kB of special trusted code is running the rest of the OS in a sort of virtual machine. In particular, memory writes can be intercepted via the permission bits in the page tables. There are two sets of page tables. Stuff first gets remapped by the ones the regular OS is handling, then gets remapped by the page tables that the 64 kB of trusted code is handling.

By this mechanism and by control of DMA, the 64 kB can be safely expanded. Whole videos could be decrypted into protected memory, though this isn't really required since the regular OS can be verified and protected.

AlbertCahalan 05:22, 12 November 2005 (UTC)

Yeah, and exactly who the hell is researching DRM hardware? Excepting Intel maybe, nobody. The fact is, you're blatantly misusing language. Everyone OTHER than you understands DRM research to mean DRM software *development*. You mean it in a very narrow non-standard sense, and you never bother to explain what sense it is you do mean it. 24.200.176.92 02:35, 13 November 2005 (UTC)


text:
XML - Managing Data Exchange/Database and XML

Native XML Database
The term Native XML database: has become popular since 1999, after the company Software AG released the first version of its native XML server Tamino, which included a native XML database. A definition of a native databases is that it:

"[d]efines a (logical) model for an XML document and stores and retrieves documents according to that model." (Bourret, 2002)"

To model data in XML, two principle approaches are used: Data-centric documents and Document-centric documents.

 * Data-centric documents (for data transport) have fairly regular structure, order typically does not matter, and little or no mixed content.

 * Document-centric documents (usually for human consumption) have less regular or irregular structure, significant order of the elements, and lots of mixed content.

Examples of Native databases

eXist
eXist is an Open Source effort to develop a native XML database system, tightly integrated with existing XML development tools like Apache's Cocoon. The database may be easily deployed, running either standalone, inside a servlet engine, or directly embedded in an application.

Some features that are available in eXist and that can be found in most Native XML databases are :

 * Schema-less storage - Documents do not have to be associated to schema or document type, meaning they are allowed to be well formed only.

 * Collections - A collection plays a similar role to a directory in a file system. When submitting a query the user can choose a distinct part of the collection hierarchy or even all the documents contained in the database.

 * Query languages - The most popular query languages supported by Native XML databases are XPath (with extensions for queries over multiple documents) and XQuery.

Relational Databases
Database vendors such as IBM, Microsoft, Oracle, and Sybase have developed tools to assist in converting XML documents into relational tables.

Let us look at IBM and Oracle:

IBM Technology
DB2 XML Extender provides access, storage and transformation for XML data through user-defined functions and stored procedure. It offers 2 key storage models: XML Colums and XML Collections.

1. XML Column: stores and retrieves entire XML documents as DB2 column data. Use of XML Columns is recommended when XML   documents already exist and/or when there is a need to store XML documents in their entity.

2. XML Collection: composes XML Documents from a collection of relational tables.

A data access definition (DAD) file is used for both XML Column and XML Collection approaches to define the "mapping" between the database tables and the structure of the XML document.

 Specifies that the XML data is either to be decomposed from XML documents into a collection of relational tables, or to be composed into XML documents from a collection of relational tables.

The DAD file defines the XML document tree structure, using the following kinds of nodes:

 * root_node - Specifies the root element of the document.
 * element_node - Identifies an element, which can be the root element or a child element.
 * text_node - Represents the CDATA text of an element.
 * attribute_node - Represents an attribute of an element.

 * XML for DB2 Information Integration Redbook.

Oracle
Oracle's XML SQL Utility (XSU) uses a schematic mapping that defines how to map tables and views, including object-relational features, to XML documents. Oracle translates the chain of object references from the database into the hierarchical structure of XML elements.

A corresponding XML document generated from the given object-relational model looks like:

XSU can be used for executing queries in a Java environment and retrieve XML from the database.

XPath
../XPath/ is a language for addressing parts of an XML document, and is the common locator used by both XSLT and XPointer. An XPath expression is a series of location steps separated by " / ". Each step selects a set of nodes that become the current node(s) for the next step. The set of nodes selected by the expression are the nodes remaining after processing each step in order.

XQuery
../XQuery/ is a query language under development by the World Wide Web Consortium (W3C). The ambitious task is to develop the first world standard for querying Web documents. XQuery is a versatile markup language, capable of labeling the information content of diverse data sources including structured and semi-structured documents, relational databases, and object repositories.

 * Catalog of XQuery Processors at www.SQLSummit.com.

MySQL 5.1
MySQL has a command line utility for executing queries against a MySQL database; it has an option for using XML as their output format. MySQL also allows convertion to XML; more information can be found in ../Converting MySQL to XML/ MySQL allows users to execute any SQL query. mysqldump allows users to specify which tables to dump and to specify a where clause to restrict the rows that are dumped. In its Beta release of MySQL 5.1, several features have been added including new XML functions.

In order to understand these New functions, we will use the following table:

XML Functions
MySQL version 5.1 has functions for searching and changing XML documents: ExtractValue and UpdateXML.

This function takes 2 string arguments: The first parameter correspond to the XML_document string, and the 2nd Parameter XPath_string (XPath expression / locator). This will result in the return of the string containing a value from the document.
 * EXTRACTVALUE (XML_document, XPath_string);

mysql> SELECT EXTRACTVALUE(doc,'//firstname') FROM Customers;

+--+ +--+ +--+ 3 rows in set (0.01 sec)
 * EXTRACTVALUE(doc,'//firstname')         |
 * John                                    |
 * Aminata                                 |
 * Lamine                                  |

mysql> SELECT ExtractValue(doc,'/person[@id="3"]/firstname') as fname FROM Customers;

+-+ +-+ +-+ 3 rows in set (0.02 sec)
 * fname  |
 * Lamine |
 * Lamine |
 * Lamine |

This function takes 3 string arguments: The first two paramaters are similar to the ones used with extractValue, XML_document and XPath_string. The third parameter is the new value that will replace the one found. This function will then returns the changed XML.
 * UPDATEXML (XML_document, XPath_string, new_value);

mysql> SELECT UpdateXML(doc,'/person[@id="3"]/phoneno', ' 111-2233 ') FROM Customers;

+--- +                                                   | +--- +      John Smith 123-5678         |      Aminata Cisse 123-5679      |      Lamine Smith 111-2233 | +--- + 3 rows in set (0.00 sec)
 * UpdateXML(doc,'/person[@id="3"]/phoneno',' 111-2233 ')

Installation
Currently (04/05/06) MySQL 5.1 does not come with the installer (Beta Version).

Quick Windows installation.

Details information can be found in the online Manual:

 * Windows.

 * Mac OS.

 * Linux.

 * and more in the Manual.