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LaTeX/Q&A

 If you have a question when dealing with LaTeX and are in need of some help, please refer to How to get help. Please do not add a new section here.

Who?
Who wrote this? It seems a rather phenomenal piece of work! We'd love to publish an article or a notice about it in one of the TeX journals. I looked at the history of a couple pages, but the answer was not apparent ... anyway, thanks, whoever you are! --karl@tug.org

 * well, there is the authors section for this :-) I wrote lots of parts of the book. As you can see, we have the permission to include several existing books on LaTeX here. I have added most of the "not so short introduction...", but I still have to finish. As soon as I have a lot of free time (July I guess), I'll work on introducing all of them and this will be a very good book, (hopefully) having the best of all the others. The main good point is that LaTeX changes quite quickly, while most of the existing guides are really old and mostly outdated. This Wikibook gets updated continuously thanks to lots of contributors. I have seen lots of anonymous users fixing some smaller mistakes. Alessio Damato 08:31, 21 May 2007 (UTC)

Cyrillic letters
How can I write a text in Cyrillic using "math" command? Is it possible?

>> According to Tobias Oetiker's "The Not So Short Introduction to LaTex2e", you need to add the  package before the   package. Here is what might go at the top of the document:

When you are in math mode, remember that to show regular text you use the  command. I added extra braces because there are certain cases where you need them.

 * See also: LaTeX/Internationalization

splitting a project into files (\includeonly)
I've been using \includeonly{} and \include{} as described under the advanced topics section of the wikibook, but am not sure the output is what it should be:  If I put a \label{marker} command in a file foo.1, and then put a \ref{marker} command in a file foo.2, then even though I use \includeonly{foo.1,foo.2} in the rootfile preamble and \include{foo.2} (and no other \include{} command) in the rootfile body, I'm told that the reference was undefined. I thought that \includeonly{} allowed one to preserve cross-references without having to process more than one wants to see. Can anyone tell me what I'm doing wrong? Thanks. -- 132.161.33.86 18:01, 31 January 2007 (UTC)

Using LaTeX on a website
Is it possible to use LaTeX on a personal website in much the same way it is used in Wikipedia, i. e. when LaTeX commands immediately appear as automatically generated picture files?

 * no you can't. Wikipedia stores the sources (containing LaTeX parts as well) and converts them to HTML and images before sending it to user's browser. You should use a software doing the same (or you can use WikiMedia, too), but you need to set up the server properly... Alessio Damato 16:29, 20 August 2007 (UTC)

Thank you. 86.100.3.253 19:44, 22 August 2007 (UTC)

 * yes, it do is possible, using the right CGI-scripts

 * One easy way to do this is to use MathJax: . You just put

 in the document head. Then in the body just use $...$, $$...$$ or \(...\), \[...\] to enclose mathematical formulas. Ashaio (discuss • contribs) 09:19, 8 June 2011 (UTC)

Multi-line title
Hi, I'm quite new to latex and there's something I'd need to do but I'm not able to, nor i could find any hint over the net. What i need is to create a multi-line document main title - it seems easy but i couldn't work it. If someone could help me i would really appreciate it.

[EDIT] OK, I'm ever newer to wikis and i can't create a new topic. Sorry for the mess.

Thank you in advance Antonio

 * Use \\ at the end of each line. Ashaio (discuss • contribs) 09:19, 8 June 2011 (UTC)

Can anyone please tell me what does the command ``punt'' does?

book-writing
~October 4, 2008 how do i write a book using latex? is there an available template?

 * What do you mean by 'book'? A textbook/manual? A novel? Anyway, you should start by specifying document class book and know how to start chapter. There's more about creating table of contents and index. --Derbeth talk 17:06, 8 October 2008 (UTC)

Is there a powerful way for add chemical structures in my papers using Latex? Now i've to add images created with a graphic design software, but it's a really slow way to write them. Nothing like a text definition of chemical structures in Latex with subsequent graphical output? Thank you.

 * Ok. Let me google that for you. --24.113.3.173 (discuss) 00:19, 29 March 2012 (UTC)

address labels
I'm trying to output an address list (home addresses, telephone numbers, email addresses, etc.) in a standard address label-like format. In other words, I'd like, say, 3 labels across, and N labels down (whatever will fit on the page). I've looked at (and used) the labels package, but I don't like one aspect of its formatting. Each of the labels is centered in its "cell". This means that if one label is 3 lines long and another is 6 lines long, the tops of the address labels don't line up horizontally. This is probably considered a "feature", but what I'd like to achieve is that all the "first lines" line up while each address label having possibly different numbers of lines.

Does anyone know how to do this? I'd like output that looks like this:

Address 1/Line 1          Address 2/Line 1            Address 3/Line 1 Address 1/Line 2          Address 2/Line 2            Address 3/Line 2 Address 1/Line 3          Address 2/Line 3            Address 3/Line 3 Address 2/Line 4           Address 3/Line 4 Address 2/Line 5

Address 4/Line 1          etc. Address 4/Line 2 Address 4/Line 3 Address 4/Line 4

Clearly, the size of each "box" should be large enough for the label with the greatest number of lines.

If you have any suggestions, please let me know. If possible, I'd like to have each address label be defined in the same way as in the labels package -- blank lines separate addresses, but other representations would be ok too.

Thanks. 12.107.176.254 (talk) 02:35, 4 November 2008 (UTC) Eric

Section numbering in the PDF version?
Dear Contributors! The LaTeX wikibook is a really impressive and valuable piece of work, thanks a lot! Would it be possible to include [[[sub]sub]sub]section numbering in the PDF version? It would enhance its usability even further!

\renewcommand for section doesn't work
Hello! I wanted to have every section in a new page. So I thought I could renewcommand section to newpage and then section, like: \renewcommand{section}{\newpage \section} However, this freezes my compiler (I am using xelatex). Is it a problem of recursion? Does it not like recursive calls to the same function when renewing it?

Anyway, thinking that could be a problem of recursion, I tried an other way: \newcommand{\oldsection}{\section} \renewcommand{\section}{\newpage \oldsection} This should avoid recursion, but it freezes my compiler anyway. Any idea? Thanks a lot! -- 93.97.73.141 (talk) 23:58, 8 February 2009 (UTC)

 * You need to take a snapshot of \section using let:

\let\oldsection\section \renewcommand{\section}{\newpage \oldsection}
 * --134.169.135.176 (talk) 12:45, 1 April 2009 (UTC)

Chemistry in LaTeX?
As the question already asked above was ignored, I'll try it again. Is there an acceptable way to write chemical formulas? -84.59.3.240 (talk) 14:46, 19 March 2009 (UTC)

 * If you just wish to write formulas, then there is a package mentioned in the formatting section (search for chemical). If you wanted to produce graphical structures, then you could try searching for a package at the CTAN website, see the installing packages section.

If you mean chemical structures, ochem probably is what you are looking for. You can find it here.

chemfig can also be used to draw 2D chemical structures. Unlike ochem, chemfig does not require Perl.

mhchem is fantastic for making entry of formulas and their associated subscripts etc. easier.

More chemistry
What about drawing larger molecular structures, such as CNTs, fullerenes, micelles and reverse micelles?

format arguments in newcommand
In the following newcommand, (how) can the argument be centered, *on the same line* as the labelenumi in the marginpar?

\newcommand{\answer}[1]{\leavevmode\marginpar{\labelenumi\hspace{5pt} #1}}

(Inserting the centering environment between \hspace{5pt} and the argument #1 creates a line space in the marginpar--at least in pdflatex.)

A modified box may be required, but is there a different solution? Thanks --66.31.140.209 (talk) 14:18, 17 May 2009 (UTC)

How can I write latex online & see my letter? May,30.09

Sir, I want to learn latex and writing a book in latex. I have seen the pdf version of this Latex book which is very beautifull and worth reading. Can i get the latex script of the book i.e. .tex file (Latex.pdf-> Latex.tex )? kindly e-mail me on msohaibayub@yahoo.com. i will be waiting eagerly for your reply. Muhammad Sohaib Ayub Bachelors of Information Technology National University Of Science And Technology Pakistan.

Citations -- DOI
How does one include the DOI in citations?

figure and table position within page
I have three questions about how to manage the table and figure within a page: 1)although I have used \newpage in front of every \begin{figure}[H] or \begin{table}[H], sometimes LaTex still put 2 items on one page.

2)For those did appear separately on each page, I can not let the figure located close enough to the caption.

3)Below is the code for two figures I put in. They appear separately on two pages as I wanted. Only that the title of the first one appear in the middle of the page so it is not too far away from the graphic. And for the second one, the title appear at the top of the page, which is what I need, but the graphic stays in the middle of the page. Could anyone tell me how to fix the title at the top of page and let the graphic start right after the caption and any text?

Many thanks!

\newpage \begin{figure}[H]\footnotesize \caption{\textbf{Impulse Response Function}} \label{fig:IRF} This figure presents the IRF (Impulse Response Function) of the three auto process estimations.\\

\leavevmode \includegraphics[width=1\textwidth]{IRF.pdf} \end{figure}

%\newpage \begin{figure}[H]\footnotesize \caption{\textbf{AR(2) Estimation of Yearly Drifts}} \label{fig: AR2Est} This figure presents the fitted yearly drifts of rating transitions and the AR(2) estimation of the drifts from the third year onwards of the entire sample period.\\

\includegraphics[width=1\textwidth]{AR2Estimates.pdf} \end{figure}

LaTeX PDF Version with external links
I find this book impressive and downloaded the PDF version to be able to use it offline. Unfortunately, all links (e.g. from the glossary) direct me to the web version and not to the local PDF copy. Can this be amended?

Thomas Fischer

This issue seems to be resolved now.--Dirk Hünniger (discuss • contribs) 16:14, 23 June 2013 (UTC)

Page format
Dear, When i prepare a document, it leaves margins of width more then one inch. But i need only less. How can i reduce the page margins in an article?
 * Use the  package.  This package allows you to specify the 4 margins. The values are relative to the edge of paper (0in) and go inward it. It may be implemented as follows:

 * (See more in LaTeX/Page_Layout). Ashaio (discuss • contribs) 09:45, 8 June 2011 (UTC)

How to format many variables? Can I use a wildcard in a new command?
There are many vectors in my file and I hope to show them in the form of boldsymbol. So I did as follow:

\newcommand{\vect}[1]{\boldsymbol{#1}} \newcommand{\va}{\vect{a}} % vector a  \newcommand{\vb}{\vect{b}}  % vector b  \newcommand{\vc}{\vect{c}}  % vector c    ....                      %vector d,e,f ...

I don't hope to repeat these similar commands, so I hope to edit them in two options as follow:

1. Create group of these variables which can be shown in particular form, as look like \vectgroup{a, b, c, ...} % vector a,b,c,... 2. Using a wildcard in a new command: \newcommand{\v*}{\vect{*}} % * can be specialized to a,b,c,...

I believe the Latex have this function, but I cannot implement that. Anyone can give me suggestion? Thousands of thanks.

latex code for cauchy's integral formula

This very book: LaTeX to wiki or wiki to LaTeX?
Was this very book created in LaTeX and then converted to a wiki or visa versa?

 * The PDF version was created with MediaWiki to LaTeX, which, as you may guess, converts the whole wikibook source to LaTeX. --Ambrevar (discuss • contribs) 13:31, 23 June 2013 (UTC)

Furthermore the LaTeX source is attached to the PDF version of this book. --Dirk Hünniger (discuss • contribs) 16:04, 23 June 2013 (UTC)

Sorting a table alphabetically
Hi, Does anybody know how can I sort a table with respect to first column in latex alphabetically? Thanks a lot.

Developing a book in A5
Hello everyone,

I wrote my dissertation in A4 with LaTex. Now I wonder what changes should be done so that the dissertation fits into a A5 book for publication?

Two options seem to be feasible:

1. to define the document as a5paper in \documentclass. However, the output file in Pdf viewer is displayed in A4, which makes the format checking difficult.

2. An alternative is using landscape to fit 2 pages of the document into 1 A4 paper. Thus, each A4 page forms 2 successive pages of A5.

Does anyone have a better idea of converting A4 to A5, in preparation for book pulication？ Thank you in advance!

Sincerely, Nicole

As above, A5
I would love to know how to do this as well. To be precise, entering

\documentclass[10pt,a5paper]{article} \special{papersize=148mm,210mm}

\usepackage[a5paper]{geometry}

will produce an A5 'page', but what you type in will appear as A4 still, and will be chopped off if it is not within your A5 'page'

Brian Daugherty

title: LaTeX/Q&A


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User talk:Person11111~enwikibooks

Thanks for experimenting with Wikibooks. Your test worked, and has now been removed. Please use Sandbox for any other tests you want to do, since testing material in modules will normally be removed quickly. Please see the welcome page if you would like to learn more about contributing to our project. Thanks. --hagindaz 05:14, 20 July 2006 (UTC)

Your account will be renamed
Hello,

The developer team at Wikimedia is making some changes to how accounts work, as part of our on-going efforts to provide new and better tools for our users like cross-wiki notifications. These changes will mean you have the same account name everywhere. This will let us give you new features that will help you edit and discuss better, and allow more flexible user permissions for tools. One of the side-effects of this is that user accounts will now have to be unique across all 900 Wikimedia wikis. See the announcement for more information.

Unfortunately, your account clashes with another account also called Person11111. To make sure that both of you can use all Wikimedia projects in future, we have reserved the name Person11111~enwikibooks that only you will have. If you like it, you don't have to do anything. If you do not like it, you can pick out a different name.

Your account will still work as before, and you will be credited for all your edits made so far, but you will have to use the new account name when you log in.

Sorry for the inconvenience.

Yours, Keegan Peterzell Community Liaison, Wikimedia Foundation 23:34, 17 March 2015 (UTC)

Renamed
 This account has been renamed as part of single-user login finalisation. If you own this account you can |log in using your previous username and password for more information. If you do not like this account's new name, you can choose your own using this form after logging in: . -- Keegan (WMF) (talk) 05:22, 19 April 2015 (UTC)

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

title: User talk:Person11111~enwikibooks


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User talk:1337 U23R

Thanks for experimenting with Wikibooks. Your test worked, and has now been removed. Please use Sandbox for any other tests you want to do, since testing material in modules will normally be removed quickly. Please see the welcome page if you would like to learn more about contributing to our project. Thanks. --hagindaz 05:15, 20 July 2006 (UTC)

title: User talk:1337 U23R


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User:SnapJag

My name is Greg Wright. I am a Software Engineer currently specializing in Database and Systems Architecture. With over 15 years of experience in many areas of Information Technology I am looking forward to contributing in these areas. There are many more years I have "dabbled" with my Atari 400, Atari 2600, Kaypro, and Everex computers. Since then, computers have been the main stay of my work and life.

Additional hobbies and areas of contribution are photography, soccer, and travel. I have served a two year mission in Spain from July 1988 to July 2000 for The Church of Jesus Christ of Latter-day Saints or commonly known as The Mormons although the former is the preferred name. The cities I served were Cordoba (2 mo), Granada (7 mo), Dos Hermanas (3 mo), Alcala de Guadaira (4 mo), Merida (3 mo), Marbella (2 mo). While there I learned, studied, and practiced conversational spanish in the homes and on the streets of the Spanish. An experience to never forget and would advise any young man to do.

title: User:SnapJag


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Talk:Philosophy of Religion

Religion is, necessarily, a very personal enterprise in human experience. It's subjective content is as important as the objective; therefore, I see the Discussion pages as an integral part of the Theology textbook series. I encourage discussion, debate, even exploration of emotions experienced about topics.

Especially, I encourage contributors to the main text to present a short biography in the Discussion pages. We all have biases and they are, perhaps, more relevant to a discussion of religion than to most fields of discourse. I hope to invite people from various religions to critique my content so that an accurate presentation of various schools of religious thought may be obtained. I would like to be kept "honest".

My name is Payton Wolf Bailey VanZandt. I am a Christian fundamentalist, in the old sense of the word. I hold that the Bible is fundamental to the Christian religion - that it is inerrant, primal, intensive, and extensive in respect to the Christian faith; that it is an effective agent in the salvation of Humanity and a positive agent of social change; and that its interpretation, although many leveled, is literal except where it itself indicates otherwise. In practice, I am an evangelist and have studied the scriptures for about 30 years and have made it a point to have some familiarity with other religions that I may come in contact with.

By secular vocation, I am a vocational evaluator and am trained in the sciences and especially in the areas of sociology and psychology with an emphasis on research and statistics.

By culture and, perhaps, by nature, I am a Wolf Therian and have a shamanic viewpoint of the world. This month, at the inception of this work, I am 53 years old and a resident of the Southeastern United States. WolfVanZandt 05:27, 20 July 2006 (UTC)

title: Talk:Philosophy of Religion


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Talk:Online OsiriX Documentation/Customizing OsiriX windows

Are there any ways to create F-Key settings for window leveling? also, as there any ways to sort images status by SEEN, UNSEEN?


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User:Paul Lynch/Core Topics

 * Principles of Microeconomics
 * Principles of Macroeconomics
 * Biology I(?)
 * General Chemistry (Chemistry 1&2?)
 * Calculus (1, 2, and 3)
 * US History (pre and post Civil War)
 * European History
 * World History
 * (Annotated texts for books usually used in western philosophy classes?)
 * Physics I
 * German
 * Spanish
 * French

title: User:Paul Lynch/Core Topics


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Basic Computer Security/Introduction

Computer security is a wide range topic which has only increased over the last few decades. Previously, security was locking data behind closed doors, but since the ARPANET and now creation of the internet and world wide web, this has significantly changed. The ability to use and access data is now what is driving computing and data locked away and inaccessible is considered useless the majority of the time.

With the increased connectivity of computers, this has additionally allowed malicious actors to take advantage of various weakness in computing as a while, ranging from exploiting vulnerabilities in software to brute forcing passwords.

The sheer number of vulnerabilities in software and hardware has made it a game of catch up as more and more exploits and vulnerabilities continue to be found. It is not a question of if people are trying to crack your security to compromise your machine, it is how easy will it be for them. By taking the proper security measures, it will be much harder and quite often, not worth their time and effort, unless you are specifically targeted.

From passive to active measures, there is a lot which can be done to make being compromised a difficult task.

About this Book
Welcome to Basic Computer Security. The aim of this book is to instruct the reader on numerous topics of computer security such as passwords, privacy, encryption, and networking. This book is written for a reader with little to no previous knowledge of security issues, but one who is familiar with the basic functionality of his or her computer's operating system. The language used in this book should be easily understood by someone with the reading level of a college freshman. We will make our best attempt to define security-related terms and other jargon in a concise, coherent manner. Reading this book should give you a basic understanding of the processes needed to secure your home computer and home network, as well as protect your privacy and data on the web.

As a handy tool, you may click the padlock icon at any time to return to the book's main page. (Also visible on the top right of the page.) This feature will facilitate returning to the index to move on to the next section, to return to this introduction, or to re-orient yourself if you click on a link and find yourself lost.

A short word of warning before we begin: Any book on the subject of security is likely to enlighten the reader on a variety of nasty things that could potentially happen to him or her. It is not our intention to make the reader paranoid or fearful of computers or the Internet; we believe that the primary cause of fear is a lack of understanding. It is our hope that by reading this book you will learn more about the world around you and gain valuable knowledge and understanding that will help you protect yourself, your privacy, and your information. It is better to know how to protect oneself and know how to deal with a situation when it arises than to be an oblivious victim. As our good friend Joe would say, "Knowing is half the battle!"

Below you will find various section headings which reflect the general categories which this book will address. Under each heading you will find a short description of the contents of that section, which may assist you in determining which parts of the book are relevant to your needs.

General Security and Passwords
General Security and Passwords will introduce basic security concepts which apply to most of the other sections in this book. It will also explain some of the key concepts in computer security that may not come up in other areas of security, such as passwords.

Malware
Malware will introduce you to and describe the main malware (malicious software) threats that your computer will be subject to, and will then teach you how to safely and effectively eliminate them. Topic areas include viruses, trojan horses, spyware etc...

Web Security
Web Security will introduce concepts which apply specifically to the world-wide-web. This will include information on Internet browsers, e-mail, and an explanation of some concepts which are integral to the understanding of security on the web. You may not be familiar with some topics or terms discussed in this section. Fear not! We will do our best to make the concepts as easy to understand as possible, as well as make their importance immediately relevant.

PC Security
PC Security will discuss topics which are immediately relevant to the security of your personal computer, whether at home or at work or in transit. These topics include the encryption of data, setting user account controls and ensuring your computer is physically secure, to prevent theft of your important or sentimental data.

Network Security
Network Security will introduce useful topics relevant to home networking. Many people have multiple computers in their home and use a router to connect all of them to the Internet simultaneously. This section will discuss methods of securing your router, your network, and each of your computers from external interference.

Where to Go from Here
The Where to Go from Here section will mention some more advanced concepts of security and will provide links to articles on Wikipedia, other Wikibooks, and external links that discuss security. While these are probably not the best place to start learning about security, you may find them useful or interesting after you have become more familiar with some of the basics.

Return to the Main Page

title: Basic Computer Security/Introduction


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Basic Computer Security/Working

Welcome, Contributors
This page is a workspace for contributors. It will include notes on formatting, templates, and other conventions used in this wikibook. Please feel free to add your name to the contributors' list!

Templates
Each page should contain the navigation template. to correctly insert this template into a page, add: to the very beginning of the page.

Doing this will ensure that each page has the appropriate links for the other pages in its chapter as well as links to the other chapters.

Contributors

 * Anonymous - Many users have contributed anonymously. Thanks to those of you who have done so.  =)
 * banzaimonkey - Oversight and development of post-merge book and expanded layout.
 * Ryan524 - Original inceptions of this book, including the Virii and Spyware pages.
 * TheJC - Further work on the original Spyware page.
 * Chachu207 - Original work on the Passwords page.
 * RohitUpadhyay - Further work on the original Virii page.
 * Wesley Gray- General editing. Contributions to the anti-virus and browser pages.

title: Basic Computer Security/Working


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Template:Basic Computer Security

This navigation bar should be included at the very top of every page in Basic Computer Security.

New style templates:
 * Template:Basic_Computer_Security/Introduction
 * Template:Basic_Computer_Security/General_Security_and_Passwords
 * Template:Basic_Computer_Security/Malware
 * Template:Basic_Computer_Security/Web_Security
 * Template:Basic_Computer_Security/PC_Security
 * Template:Basic_Computer_Security/Privacy
 * Template:Basic_Computer_Security/Network_Security
 * Template:Basic_Computer_Security/Further_Reading

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User:Ervinn/JNDI

Introduction
During programming, many times we'd like to access a resource in a standard way, regardless how the resource is stored or implemented.

In a networking environment sometimes we'd like to share objects among the programs running in the network. In this case, we'd like to map names to objects. For this Java has JNDI, that stands for Java Naming and Directory Interface.

 * Maming Services : Name Services are for to help share a resource among programs. For example a File System is a Naming Service, mapping a file name to physical file. In JNDI, names are associated with objects and objects are found based on their names.

 * Directory Services : Many naming services are extended with a directory service. A directory service associates names with objects and also allows such objects to have attributes. Thus, you not only can look up an object by its name but also get the object's attributes or search for the object based on its attributes. JNDI as the name implies, is also a Directory Service.

 * Atributes : A directory object can have attributes. An attribute has an attribute identifier and a set of attribute values. An attribute identifier is a token that identifies an attribute independent of its values.

 * Directories : A directory is a connected set of directory objects. A directory service is a service that provides operations for creating, adding, removing, and modifying the attributes associated with objects in a directory.

 * Binding : The association of a name with an object is called a binding. For example, a file name is bound to a file. In JNDI, a name is bound to a Java object.

 * References and Addresses : Depending on the naming service, some objects cannot be stored directly; that is, a copy of the object cannot be placed inside the naming service. Instead, they must be stored by reference; that is, a pointer or reference to the object is placed inside the naming service. A reference is information about how to access an object.
 * Although in general a reference can contain any arbitrary information, it is useful to refer to its contents as addresses.

 * In JNDI, objects are stored in naming and directory services in different ways. A service that supports storing Java objects might support storing an object in its serialized form, it depends on the service provider. Some naming and directory services do not support the storing of Java objects.
 * The JNDI defines a 'Reference' class to represent a reference. A reference contains information on how to construct a copy of the object. JNDI will attempt to turn references looked up from the directory into the Java objects.

 * Context : Context is a set of Name to Object binding. It defines a set of naming conventions. It also provide a lookup operations, such as binding name, unbiding name, ....
 * A name in one context object can be bound to another context object (called a subcontext) that has the same naming convention.

 * Initial Context : In the JNDI, all naming and directory operations are performed relative to a context. There are no absolute roots. Therefore the JNDI defines an initial context, InitialContext, which provides a starting point for naming and directory operations. Once you have an initial context, you can use it to look up other contexts and objects.

 * Naming Systems : A naming system provides a naming service to its customers for performing naming-related operations. A naming service is accessed through its own interface.

 * JNDI: Java Naming and Directory Interface.

 * The Java Naming and Directory Interface is an application programming interface (API) that provides naming and directory functionality to applications written using the Java programming language. It is defined to be independent of any specific directory service implementation. Thus a variety of directories--new, emerging, and already deployed--can be accessed in a common way.

 * The JNDI is included in the Java 2 SDK, v1.3 and later releases.

JNDI/Java Naming and Directory Interface

 * Architecture : The JNDI architecture consists of an API and a service provider interface (SPI). Java applications use the JNDI API to access a variety of naming and directory services. The SPI enables a variety of naming and directory services to be plugged in transparently, thereby allowing the Java application using the JNDI API to access their services.

 * Initial Context:

// Identify service provider to use Hashtable env = new Hashtable(11); env.put(Context.INITIAL_CONTEXT_FACTORY,    	    "com.sun.jndi.fscontext.RefFSContextFactory"); try { // Create the initial context Context ctx = new InitialContext(env); // Look up an object Object obj = ctx.lookup(name); // Print it out System.out.println(name + " is bound to: " + obj); // Close the context when we're done ctx.close; } catch (NamingException e) { System.err.println("Problem looking up " + name + ": " + e); }

java.util.Properties p = new java.util.Properties; p.put(Context.PROVIDER_URL, "IIOP:///"); p.put(Context.INITIAL_CONTEXT_FACTORY, "com.ibm.websphere.naming.WsnInitialContextFactory"); InitialContext initContext = new InitialContext(p); // Look up a transaction userTran = (UserTransaction)initContext.lookup("jta/usertransaction"); userTran.begin; // Call the finder // Assume that employeeHome has already been found, and has a method defined findAll Enumeration enum = employeeHome.findAll; while (enum.hasMoreElements) { // Process the enumeration } userTran.commit;

title: User:Ervinn/JNDI


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English in Use/Apostrophes

An apostrophe can be used to form possessives for nouns, indicate the omission of letters in a word for stylistic purposes or as a colloquial form of a word, and be used to indicate plurality.

The term is derived from the Latin word apostrophus itself derived from the Greek words αποστροφος meaning accident of elision αποστρεφειν meaning a turning away.

The apostrophe usually denotes either the possessive case of a noun, or the elision of one or more letters of a word: as,

 * "The girl's regard to her parents' advice;"

'Gan, lov'd, e'en, thro'; for began, loved, even, through.

It is sometimes used in pluralizing a mere letter or sign: as,

 * "Two a's—three 6's."

Apostrophe is also a figure of speech in which an absent person, a personified inanimate being, or an abstraction, is addressed as though present.

This sense is maintained when a narrative or dramatic thread is broken in order to digress by speaking directly to someone not there, e.g.,

 * “Envy, be silent and attend!”—Alexander Pope.
 * “On a Certain Lady at Court.”

title: English in Use/Apostrophes


text: Category:Book:PyGTK For GUI Programming

title: Category:Book:PyGTK For GUI Programming


text: Category:Book:Radiation Oncology

title: Category:Book:Radiation Oncology


text: Category:Book:Radmind

title: Category:Book:Radmind


text: Category:Book:Reaktor

title: Category:Book:Reaktor


text:
User:Chazz

Chazz here. I signed up here because I found the Muggles' Guide listed as Collaboration of the Month (July '06) and figured I could help. I'm located on the west coast of British Columbia, in Canada, a little north of Seattle.

Muggles' Guide to Harry Potter
The question has come up in the past about the sources people are working from. For what it's worth: the sources I have are all Bloomsbury Press / Raincoast Press (UK / Canada) – although my books are all Raincoast Press, as I am in Canada, the text is identical with the Bloomsbury books.

Philosopher's Stone (US edition is called Sorcerer's Stone): 1997, the earlier edition with "1 wand" listed twice in the book list

Chamber of Secrets: 1998

Prisoner of Azkaban: 1999

Goblet of Fire: 2000

Order of the Phoenix: 2003, First Canadian Edition

Half-Blood Prince: 2005

Deathly Hallows: 2007

When withinfocus trimmed back his participation in this project, I took over a lot of the editing work on the Muggles' Guide; however, I have become tired also of the job, and am electing to cut back my editing significantly. We are extremely lucky to have some very enthusiastic writers still on this project, after so very many years; and in particular, PNW Raven, still going strong, is likely your best bet for guidance if you are interested in helping out.

As of August 2019, I am completely out. Goodbye, good luck.

title: User:Chazz


text:
Human Physiology/Genetics and inheritance

Introduction
Genetics is the science of the way traits are passed from parent to offspring. For all forms of life, continuity of the species depends upon the genetic code being passed from parent to offspring. Evolution by natural selection is dependent on traits being heritable. Genetics is very important in human physiology because all attributes of the human body are affected by a person’s genetic code. It can be as simple as eye color, height, or hair color. Or it can be as complex as how well your liver processes toxins, whether you will be prone to heart disease or breast cancer, and whether you will be color blind. Defects in the genetic code can be tragic. For example: Down Syndrome, Turner Syndrome, and Klinefelter's Syndrome are diseases caused by chromosomal abnormalities. Cystic fibrosis is caused by a single change in the genetic sequence. Genetic inheritance begins at the time of conception. You inherited 23 chromosomes from your mother and 23 from your father. Together they form 22 pairs of autosomal chromosomes and a pair of sex chromosomes (either XX if you are female, or XY if you are male). Homologous chromosomes have the same genes in the same positions, but may have different alleles (varieties) of those genes. There can be many alleles of a gene within a population, but an individual within that population only has two copies, and can be homozygous (both copies the same) or heterozygous (the two copies are different) for any given gene.

Genetics is important to medicine. As more is understood about how genetics affects certain defects and diseases, cures and treatments can be more readily developed for these disorders. The sequence of the human genome (approximately 3 billion base pairs in a human haploid genome with an estimated 20,000-25,000 protein-coding genes) was completed in 2003, but we are far from understanding the functions and regulations of all the genes. In some ways medicine is moving from diagnosis based on symptoms towards diagnosis based on genetics, and we are moving into what many are calling the age of personalized medicine.

DNA
Deoxyribonucleic acid (DNA) is the macromolecule that stores the information necessary to build structural and functional cellular components. It also provides the basis for inheritance when DNA is passed from parent to offspring. The union of these concepts about DNA allows us to devise a working definition of a gene. A gene is a segment of DNA that codes for the synthesis of a protein and acts as a unit of inheritance that can be transmitted from generation to generation. The external appearance (phenotype) of an organism is determined to a large extent by the genes it inherits (genotype). Thus, one can begin to see how variation at the DNA level can cause variation at the level of the entire organism. These concepts form the basis of genetics and evolutionary theory.

Gene
A gene is made up of short sections of DNA which are contained on a chromosome within the nucleus of a cell. Genes control the development and function of all organs and all working systems in the body. A gene has a certain influence on how the cell works; the same gene in many different cells determines a certain physical or biochemical feature of the whole body (e.g. eye color or reproductive functions). All human cells hold approximately 30,000 different genes. Even though each cell has identical copies of all of the same genes, different cells express or repress different genes. This is what accounts for the differences between, let's say, a liver cell and a brain cell. Genotype is the actual pair of genes that a person has for a trait of interest. For example, a woman could be a carrier for hemophilia by having one normal copy of the gene for a particular clotting protein and one defective copy. A Phenotype is the organism’s physical appearance as it relates to a certain trait. In the case of the woman carrier, her phenotype is normal (because the normal copy of the gene is dominant to the defective copy). The phenotype can be for any measurable trait, such as eye color, finger length, height, physiological traits like the ability to pump calcium ions from mucosal cells, behavioral traits like smiles, and biochemical traits like blood types and cholesterol levels. Genotype cannot always be predicted by phenotype (we would not know the woman was a carrier of hemophilia just based on her appearance), but can be determined through pedigree charts or direct genetic testing. Even though genotype is a strong predictor of phenotype, environmental factors can also play a strong role in determining phenotype. Identical twins, for example, are genetic clones resulting from the early splitting of an embryo, but they can be quite different in personality, body mass, and even fingerprints.

Genetics
Genetics (from the Greek genno = give birth) is the science of genes, heredity, and the variation of organisms. The word "genetics" was first suggested to describe the study of inheritance and the science of variation by prominent British scientist William Bateson in a personal letter to Adam Sedgwick, dated April 18, 1905. Bateson first used the term "genetics" publicly at the Third International Conference on Genetics (London, England) in 1906.

Heredity and variations form the basis of genetics. Humans apply knowledge of genetics in prehistory with the domestication and breeding of plants and animals. In modern research, genetics provide important tools for the investigation of the function of a particular gene, e.g., analysis of genetic interactions. Within organisms, genetic information is generally carried in chromosomes, where it is represented in the chemical structure of particular DNA molecules.

Genes encode the information necessary for synthesizing the amino-acid sequences in proteins, which in turn play a large role in determining the final phenotype, or physical appearance of the organism., or in case case sun energized protein In diploid organisms, a dominant allele on one chromosome will mask the expression of a recessive allele on the other. While most genes are dominant/recessive, others may be codominant or show different patterns of expression. The phrase "to code for" is often used to mean a gene contains the instructions about a particular protein, (as in the gene codes for the protein). The "one gene, one protein" concept is now known to be the simplistic. For example, a single gene may produce multiple products, depending on how its transcription is regulated. Genes code for the nucleotide sequence in mRNA and rRNA, required for protein synthesis.

Gregor Mendel researched principals of heredity in plants. He soon realized that these principals also apply to people and animals and are the same for all living animals.

Gregor Mendel experimented with common pea plants. Over generations of the pea plants, he noticed that certain traits can show up in offspring with out blending any of the parent's characteristics. This is a very important observation because at this point the theory was that inherited traits blend from one generation to another.

Pea plant reproduction is easily manipulated. They have both male and female parts and can easily be grown in large numbers. For this reason, pea plants can either self-pollinate or cross-pollinate with other pea plants.

In cross pollinating two true-breeding plants, for example one that came from a long line of yellow peas and the other that came from a long line of green peas, the first generation of offspring always came out with all yellow peas. The following generations had a ratio of 3:1 yellow to green. In this and in all of the other pea plant traits Mendel observed, one form was dominant over another so it masked the presence of the other allele. Even if the phenotype (presence) is covered up, the genotype (allele) can be passed on to other generations.

Time line of notable discoveries

1859 Charles Darwin publishes "The Origin of Species"

1865 Gregor Mendel's paper, Experiments on Plant Hybridization

1903 Chromosomes are discovered to be hereditary units

1906 The term "genetics" is first introduced publicly by the British biologist William Bateson at the Third International Conference on Genetics in London, England

1910 Thomas Hunt Morgan shows that genes reside on chromosomes, and discovered linked genes on chromosomes that do NOT follow Mendel's law of independent allele segregation

1913 Alfred Sturtevant makes the first genetic map of a chromosome

1913 Gene maps show chromosomes contain linear arranged genes

1918 Ronald Fisher publishes On the correlation between relatives on the supposition of Mendelian inheritance - the modern synthesis starts.

1927 Physical changes in genes are called mutations

1928 Fredrick Griffith discovers a hereditary molecule that is transmissible between bacteria

1931 Crossing over is the cause of recombination

1941 Edward Lawrie Tatum and George Wells Beadle show that genes code for proteins

1944 Oswald Theodore Avery, Colin McLeod and Maclyn McCarty isolate DNA as the genetic material (at that time called transforming principle)

1950 Erwin Chargaff shows that the four nucleotides are not present in nucleic acid in stable proportions, but that some general rules appear to hold. (e.g., the nucleotide bases Adenine-Thymine and Cytosine-guanine always remain in equal proportions)

1950 Barbra McClintock discovers transposons in maize

1952 The Hershey-Chase experiment proves the genetic information of phages (and all other organisms) to be DNA

1953 DNA structure is resolved to be a double helix by James D. Watson and Francis Crick, with help from Rosalind Franklin

1956 Jo Hin Tjio and Albert Levan established the correct chromosome number in humans to be 46

1958 The Meselson-Stahl experiment demonstrates that DNA is semi-conservatively replicated

1961 The genetic code is arranged in triplets

1964 Howard Temin showed using RNA viruses that Watson's central dogma is not always true

1970 Restriction enzymes were discovered in studies of a bacterium Haemophilus influenzae, enabling scientists to cut and paste DNA

1977 DNA is sequenced for the first time by Fred Sangr, Walter Gilbert, and Allan Maxam working independently. Sanger's lab complete the entire genome of sequence of Bacteriophage

1983 Kary Banks Mullis discovers the polymerase chain reaction (PCR) enabling the easy amplification of DNA

1985 Alec Jeffreys discovers genetic finger printing

1989 The first human gene is sequenced by Francis Collin and Lap-Chee Tsui. It encodes the CFTR protein. Defect in this gene causes Cystic Fibrosis

1995 The genome of Haemophilus influenza is the first genome of a free living organism to be sequenced.

1996 Saccharomyces cerevisiae is the first eukaryote genome sequence to be released.

1998 The first genome sequence for a multicellular eukaryote, C. elegans is released.

2001 First draft sequences of the human genome are released simultaneously by the Human Genome Project and Celera Genomic

2003 (14 April) Successful completion of Human Genome Project with 99% of the genome sequenced to a 99.99% accuracy

2006 Marcus Pembrey and Olov Bygren publish Sex-specifics, male line trans-generational responses in humans, a proof of epigenetics

Transcription and Translation
Transcription is the process of making RNA. In response to an enzyme RNA polymerase breaks the hydrogen bonds of the gene. A gene is a segment of DNA which contains the information for making a protein. As it breaks the hydrogen bonds it begins to move down the gene. Next the RNA polymerase will line up the nucleotides so they are complementary. Some types of RNA will leave the nucleus and perform a specific function.

Translation is the synthesis of the protein on the ribosome as the mRNA moves across the ribosome. There are eleven basic steps to translation.

 * 1) The mRNA base sequence determines the order of assembling of the amino acids to form specific proteins.
 * 2) Transcription occurs in the nucleus, and once you have completed transcription the mRNA will leave the nuecleus, and go into the cytoplasm where the mRNA will bind to a free floating ribosome, where it will attach to a small ribosomal subunit.
 * 3) Methionine-tRNA binds to the nucleotides AUG. AUG is known as the start codon and is found at the beginning of each mRNA.
 * 4) The complex then binds to a large ribosomal subunit. Methionine-tRNA is bound to the P site of the ribosome.
 * 5) Another tRNA containing a second amino acid (lysine) binds to the second amino acid. Binding to the second codon of mRNA (on the A-site of the ribosome).
 * 6) Peptidyl transferase, forms a peptide3 bond between the two amino acids (methionine and lysine).
 * 7) The first amino tRNA is released and mRNA is translocated one codon carrying the second tRNA (still carrying the two amino acids) to the P site.
 * 8) Another tRNA with attached amino acid (glutamine) moves into the A site and binds to that codon.
 * 9) It will now form a peptide bond with lysine and glutamine.
 * 10) Now the tRNA in the P site will be let go, and mRNA is translocated one codon, (the tRNA with three amino acids) to the P site.
 * 11) This will continue going until it reaches the stop codon (UAG) on the mRNA. Then this codon will tell it to release the polypeptide chain.

These are some good sites to visit
 * A http://www.studiodaily.com/main/technique/tprojects/6850.html
 * B http://multimedia.mcb.harvard.edu/media.html

Select A the video of the Inner Life of a Cell. If you want to hear the descriptions in this process go to B web site and select the Inner Life: view the animation.

Inheritance
Children inherit traits, disorders, and characteristics from their parents. Children tend to resemble their parents especially in physical appearance. However they may also have the same mannerisms, personality, and a lot of the time the same mental abilities or disabilities. Many negatives and positives tend to "run in the family". A lot of the time people will use the excuse "It runs in the family" for things that have alternative reasons, such as a whole family may be overweight, yes it may "run in the family" but it could also be because of all the hamburgers and extra mayo that they all eat. Or the fact that after they eat the hamburgers they all sit on the couch and don't move for the rest of the evening. Children may have the same habits (good or bad) as their parents, like biting their nails or enjoying reading books. These things aren't inherited they are happening because children imitate their parents, they want to be like mom or dad. Good examples are just as important as good genes.

Mechanisms of inheritance
A person's cells hold the exact genes that originated from the sperm and egg of his parents at the time of conception. The genes of a cell are formed into long strands of DNA. Most of the genes that control characteristic are in pairs, one gene from mom and one gene from dad. Everybody has 22 pairs of chromosomes (autosomes) and two more genes called sex-linked chromosomes. Females have two X (XX) chromosomes and males have an X and a Y (XY) chromosome. Inherited traits and disorders can be divided into three categories: unifactorial inheritance, sex-linked inheritance, and multifactor inheritance.

Unifactorial Inheritance

Traits such as blood type, eye color, hair color, and taste are each thought to be controlled by a single pair of genes. The Austrian monk Gregor Mendel was the first to discover this phenomenon, and it is now referred to as the laws of Mendelian inheritance. The genes deciding a single trait may have several forms (alleles). For example, the gene responsible for hair color has two main alleles: red and brown. The four possibilities are thus

Brown/red, which would result in brown hair, Red/red, resulting in red hair, Brown/brown, resulting in brown hair, or Red/brown, resulting in red hair.

The genetic codes for red and brown can be either dominant or recessive. In any case, the dominant gene overrides the recessive.

When two people create a child, they each supply their own set of genes. In simplistic cases, such as the red/brown hair, each parent supplies one "code", contributing to the child's hair color. For example, if dad has brown/red he has a 50% chance of passing brown hair to his child and a 50% of passing red hair. When combined with a mom who has brown/brown (who would supply 100% brown), the child has a 75% chance of having brown hair and a 25% chance of having red hair. Similar rules apply to different traits and characteristics, though they are usually far more complex.

Multifactorial inheritance
Some traits are found to be determined by genes and environmental effects. Height for example seems to be controlled by multiple genes, some are "tall" genes and some are "short" genes. A child may inherit all the "tall" genes from both parents and will end up taller than both parents. Or the child my inherit all the "short" genes and be the shortest in the family. More often than not the child inherits both "tall" and "short" genes and ends up about the same height as the rest of the family. Good diet and exercise can help a person with "short" genes end up attaining an average height. Babies born with drug addiction or alcohol addiction are a sad example of environmental inheritance. When mom is doing drugs or drinking, everything that she takes the baby takes. These babies often have developmental problems and learning disabilities. A baby born with Fetal alcohol syndrome is usually abnormally short, has small eyes and a small jaw, may have heart defects, a cleft lip and palate, may suck poorly, sleep poorly, and be irritable. About one fifth of the babies born with fetal alcohol syndrome die within the first weeks of life, those that live are often mentally and physically handicapped.

Sex-linked Inheritance

Sex-linked inheritance is quite obvious, it determines your gender. Male gender is caused by the Y chromosome which is only found in males and is inherited from their fathers. The genes on the Y chromosomes direct the development of the male sex organs. The x chromosome is not as closely related to the female sex because it is contained in both males and females. Males have a single X and females have double XX. The X chromosome is to regulate regular development and it seems that the Y is added just for the male genitalia. When there is a default with the X chromosomes in males it is almost always persistent because there is not the extra X chromosome that females have to counteract the problem. Certain traits like colorblindness and hemophilia are on alleles carried on the X chromosome. For example if a woman is colorblind all of her sons will be colorblind. Whereas all of her daughters will be carriers for colorblindness.

Exceptions to simple inheritance
Our knowledge of the mechanisms of genetic inheritance has grown a lot since Mendel's time. It is now understood, that if you inherit one allele, it can sometimes increase the chance of inheriting another and can affect when or how a trait is expressed in an individuals phenotype. There are levels of dominance and recessiveness with some traits. Mendel's simple rules of inheritance does not always apply in these exceptions.

Polygenic Traits
Polygenic traits are traits determined by the combined effect of more than one pair of genes. Human stature is an example of this trait. The size of all body parts from head to foot combined determines height. The size of each individual body part are determined by numerous genes. Human skin, eyes, and hair are also polygenic genes because they are determined by more than one allele at a different location.

Intermediate Expressions
When there is incomplete dominance, blending can occur resulting in heterozygous individuals. An example of intermediate expression is the pitch of a human male voice. Homozygous men have the lowest and highest voice for this trait (AA and aa). Tay-Sachs, causing death in childhood, is also characterized by incomplete dominance.

Co-dominance
For some traits, two alleles can be co-dominant. Were both alleles are expressed in heterozygous individuals. An example of that would be a person with AB blood. These people have the characteristics of both A and B blood types when tested.

Multiple-Allele Series
There are some traits that are controlled by far more alleles. For example, the human HLA system, which is responsible for accepting or rejecting foreign tissue in our bodies, can have as many as 30,000,000 different genotypes! The HLA system is what causes the rejection of organ transplants. The multiple allele series is very common, as geneticists learn more about genetics, they realize that it is more common than the simple two allele ones.

Modifying and Regulator Genes
Modifying and regulator genes are the two classes of genes that may have an effect on how the other genes function. Modifying Genes alter how other genes are expressed in the phenotype. For example, a dominant cataracts gene may impair vision at various degrees, depending on the presence of a specific allele for a companion modifying gene. However, cataracts can also come from excessive exposure to ultraviolet rays and diabetes. Regulator Genes also known as homoerotic genes, can either initiate or block the expression of other genes. They also control a variety of chemicals in plants and animals. For example, Regulator genes control the time of production of certain proteins that will be new structural parts of our bodies. Regulator genes also work as a master switch starting the development of our body parts right after conception and are also responsible for the changes in our bodies as we get older. They control the aging processes and maturation.

Incomplete penetrates
Some genes are incomplete penetrate. Which means, unless some environmental factors are present, the effect does not occur. For example, you can inherit the gene for diabetes, but never get the disease, unless you were greatly stressed, extremely overweight, or didn't get enough sleep at night.

Inherited Genetic Disease
Some of the most common inherited diseases are hemochromatosis, cystic fibrosis, sickle cell anemia and hemophilia. They are all passed along from the parents and even if the parents don't show signs of the disease they may be carriers which mean that all of the children they have may be born with the disease. There is genetic testing that may be done prenatally to determine if the baby is conflicted with one of these diseases.

Hemochromatosis
Even though most people have never heard of hemochromatosis it is the most common inherited disease. About 1 in 300 are born with hemochromatis and 1 in 9 are carriers. The main characteristic is the intake of too much iron into the inflicted body. Iron is crucial to the workings of hemoglobin but too much iron is just as bad as too little iron. With hemochromatosis deposits of iron form on almost every major organ especially the liver, heart and pancreas, which causes complete organ failure. Hemochromatosis patients usually absorb two or three times the iron that is needed for normal people. Hemochromatosis was first discovered in 1865 and most patients have Celtic ancestry dating back 60 or 70 generations.

Treatments for hemochromatosis
The most common treatment for hemochromatosis is to induce anemia and maintain it until the iron storage is reduced. This is done by therapeutic phlebotomy. Phlebotomy is the removal of a unit of blood (about 500 mls.) This must be done one to two times a week and can take weeks, months, or years to complete. After this treatment some patients will never have to do it again and others will have to do it many times over the course of their life. Patients who undergo their recommended treatments usually go on to live a long and healthy life. Patients who decide against treatment increase their chances of problems such as organ failure -- or even death. Along with phlebotomy treatment, patients should stick to a low iron diet and should not cook with iron cookware.

Cystic Fibrosis (CF)
Cystic fibrosis is a disease that causes thick, sticky mucus to build up in the lungs and digestive tract. It is the most common lung disease in children and young adults and may cause early death. The mucus builds up in the breathing passages of the lungs and in the pancreas. The build up of the mucus results in terrible lung infections and digestion problems. Cystic fibrosis may also cause problem with the sweat gland and a man's reproductive system. There are more than 1,000 mutations of the CF gene, symptoms vary from person to person. The most common symptoms are: No bowel movements for the first 24 to 48 hours of life, stools that are pale or clay colored, foul smelling or that float, infants that have salty-tasting skin, recurrent respiratory infections like pneumonia, coughing or wheezing, weight loss or low weight gain in childhood, diarrhea, delayed growth, and excessive fatigue. Most patients are diagnosed by their first birthday but less severe cases sometimes aren't caught until after 18 years of age. 40% of patients are over 18 years old and the average life span of CF patients is about 35 years old, which is a huge increase over the last 30 years. Patients usually die of lung complications.

Treatment for cystic fibrosis
In 2005 the U.S food and drug administration approved the first DNA based blood test to help detect CF. Other tests to help detect CF include: Sweat chloride test, which is the standard test for CF. High salt levels in the patients sweat is an indication of CF, Fecal fat test, upper GI and small bowel series, and measurements of pancreatic function. After a diagnosis has been made there are a number of treatments available, these include: Antibiotics for respiratory infections, pancreatic enzyme replacement, vitamin supplements (mostly A, D, E, and K), inhalers to open the airways, enzyme replacement therapy which makes it easier to cough up the mucus, pain relievers, and in very severe cases, lung transplants.

Sickle cell anemia
Sickle cell anemia is an inherited disease of the red blood cells which causes abnormally shaped red cells. A typical red blood cell has about 270 million hemoglobin molecules, which bind with oxygen. In a person with sickle cell disease, one amino acid is changed in the hemoglobin molecule, and the end result is misshapen red blood cells. In a patient with sickle cell disease the red blood cells change from the normal round shape to the shape of a sickle or "C" shaped. The abnormal shape causes the cells to get stuck in some blood vessels which causes blockage in the vessel. This causes pain and can destroy organs because of the lack of oxygen. Sickle cells live only 10 to 20 days and a normal cell lives about 120 days. This rapid death of blood cells leads to chronic anemia. Complications can include severe pain, terrible infection, swelling of the feet and hands, stroke, damage to the eyes, and damaged body organs. These effects can vary from person to person depending on the type of sickle cell disease they have. Some patients are mostly healthy and others are in the hospital more than they are out. Thanks to diagnosis and treatment advancements, most children born with sickle cell grow up to have a normal and relatively healthy life. The form of sickle cell is determined by which genes they inherit from the parents. When a child inherits a sickle cell gene (hemoglobin gene) from each parent it is called hemoglobin SS disease ( which is the formal name for sickle cell). When a child inherits a sickle cell gene from one parent and a different abnormal gene from the other parent, it is a form of disease called hemoglobin SC disease or hemoglobin S-thalassemia. If a child inherits a normal gene from one parent and a sickle cell gene from the other, the child will not have sickle cell but will be a carrier and may pass it to their children. Sickle cell affects mostly African Americans and some Latino Americans. A person who is a carrier (has one copy of the gene) is resistant to malaria. This heterozygote advantage explains why the gene is more common in people in equatorial regions, or who are descendants of such people (such as African Americans).

Treatment for Sickle cell anemia
Sickle cell is diagnosed at birth with a simple blood test. If the first blood test is positive then a second test is done just for confirmation. Because of the high risk of infections that occur with sickle cell, early diagnosis is very important. Other than a bone marrow transplant there is no known cure for sickle cell. Bone marrow transplants have a high risk of rejection and aren't an available option for every patient. The patient would need a bone marrow donor match with a low risk of rejection. Even without a cure, with the use of pain medications and antibiotic treatments, children with sickle cell can live a long and happy life. Blood transfusions are sometimes used to treat episodes of severe pain. For adults who have recurrent pain episodes (at least 3 yearly), a cancer drug, hydroxyurea (marketed as Droxia), has been approved to relieve symptoms. It appears to work by increasing the flexibility of sickle cells.

Hemophilia
About two thirds of people who have Hemophilia have inherited it. For the other third, there is no known cause for possessing the disorder. There are two types of hemophilia, Type A and Type B. Both are caused by a low level or a complete absence of protein in the blood. Without this protein, blood is not able to clot.

Some of the symptoms of Hemophilia are bleeding in the joints, knees, and ankles. Stiffness without pain in the joints, stiffness with a lot of warmth,(most ability for movement is lost due to swelling) blood in the urine or stool, excessive bleeding after surgery or loosing a tooth, excessive bruising, abnormal menstrual bleeding, and nose bleeds that last for long periods of time.

Hemophiliacs blood does not coagulate like a normal persons. Coagulation controls bleeding, it changes blood from a liquid to a solid. Within seconds of a cut or scrape, platelets, calcium and other tissue factors start working together to form a clot. Over a short time the clot strengthens and then dissolves as the injury heals. Hemophiliacs are missing the clotting factor, or it isn't working correctly which causes them to bleed for a longer time. The most common myth is that a person with a bleeding disorder will bleed to death from a minor wound or that their blood flows faster than somebody without a bleeding disorder. Some of the risks hemophilia are: Scarring of the joints or joint disease, vision loss from bleeding of the eyes, chronic anemia from blood loss, a neurological or psychiatric problem, death which may occur from large amounts of blood loss or bleeding in the brain or other vital organs. Most cases of hemophilia are caused from inherited disorders but sometimes people can get it from vitamin K deficiency, liver disease, or treatments like prolonged use of antibiotics or anti coagulation drugs. Hemophilia is the best known bleeding disorder and it has had the most research done on it, so hemophiliacs have a slight advantage over people with other bleeding disorders.

Treatment for hemophilia
To treat Hemophilia, a Clotting Factor is needed. It is in the shape of powder kept in a small, sterile glass bottle. It has to be kept in the fridge. When needed, The Clotting Factor is mixed with sterile water, then one minute later it can be injected into a vein. It may also be mixed with a large amount of water and injected through an IV.

There are over 140 centers that specialize in hemophilia. Most of these centers are "Comprehensive Care Facilities". Comprehensive care facilities provide all the services needed by a hemophiliac and their family. Services provided include: Primary physician, nurse coordinator, physiotherapist, and dentist. Hemophiliacs require a special dentist because of the higher risk of bleeding. It is recommended that hemophiliacs go to the treatment centers twice a year for a complete check-up.

The basic and most common treatment for patients with hemophilia A and B is factor replacement therapy. Factor replacement therapy is the IV injection of Factor VIII and IX concentrates which help control bleeding. This concentrate comes from two sources: human plasma and genetically engineered cells made by DNA technology. This concentrate is what the hemophiliac is lacking in their own genes. After the injection is given the patients blood becomes "normal" for a couple of hours which gives time for a clot to from at the site of a damaged blood vessel. This treatment is not a permanent cure, within about 3 days there is no trace left in the system. Today's Factor treatments are much more concentrated than they were in the past so very little is required even if the patient is going in for major surgery or has a major injury. Treatments are also very convenient, they can be stored at home in the fridge for up to 6 months. So if the patient is injured they don't need to go to the hospital they can give themself an injection at home. After the injection it only takes about 15-20 minutes for the clotting process to begin. There is a risk of contracting other disease such as AIDS from Factor VIII that is made from human plasma, but as technology gets better the cases of AIDS has dropped. There is no possibility of contracting diseases from genetic engineering Factor VIII.

Hemophiliacs can live a long life. The most common reason for early death among patients has been from AIDS related complications.

Non-heritable Genetic Disorders

Any disorder caused totally or in part by a fault (or faults) of the genetic material passed from parent to child is considered a genetic disorder. The genes for many of these disorders are passed from one generation to the next, and children born with a heritable genetic disorder often have one or more extended family members with the same disorder. There are also genetic disorders that appear due to spontaneous faults in the genetic material, in which case a child is born with a disorder with no apparent family history.

Down Syndrome, also known as Trisomy 21, is a chromosome abnormality that effects one out of every 800-1000 newborn babies. During anaphase II of meiosis the sister chromatids of chromosome 21 fail to separate, resulting in an egg with an extra chromosome, and a fetus with three copies (trisomy) of this chromosome. At birth this defect is recognizable because of the physical features such as almond shaped eyes, a flattened face, and less muscle tone than a normal newborn baby. During pregnancy, it is possible to detect the Down Syndrome defect by doing amniocentesis testing. There is a risk to the unborn baby and it is not recommended unless the pregnant mother is over the age of thirty-five. Other non-lethal chromosomal abnormalities include additional osex chromosome abnormalities which is when a baby girl (about 1 in 2,500)is born with one x instead of two (xx) this can cause physical abnormalities and defective reproduction systems. Boys can also be born with extra X's (XXY or XXXY) which will cause reproductive problems and sometimes mental retardation.

Chromosomal Abnormalities In most cases with a chromosomal abnormality all the cells are affected. Defects can have anywhere from little effect to a lethal effect depending on the type of abnormality. Of the 1 in 200 babies born having some sort of chromosomal abnormality, about 1/3 of these results in spontaneous abortion. Abnormalities usually form shortly after fertilization and mom or dad usually has the same abnormality. There is no cure for these abnormalities. Tests are possible early in pregnancy and if a problem is detected the parents can choose to abort the fetus.

Mutant Genes
Mutation is a permanent change in a segment of DNA.

Mutations are changes in the genetic material of the cell. Substances that can cause genetic mutations are called mutagen agents. Mutagen agents can be anything from radiation from x-rays, the sun, toxins in the earth, air, and water viruses. Many gene mutations are completely harmless since they do not change the amino acid sequence of the protein the gene codes for.

Mutations can be good, bad, or indifferent. They can be good for you because their mutation can be better and stronger than the original. They can be bad because it might take away the survival of the organism. However, most of the time, they are indifferent because the mutation is no different than the original.

The not so harmless ones can lead to cancer, birth defects, and inherited diseases. Mutations usually happen at the time of cell division. When the cell divides, one cell contracts a defect, which is then passed down to each cell as they continue to divide.

Teratogens refers to any environmental agent that causes damage during the prenatal period. Examples of Common Teratogens:
 * drugs: prescription, non-prescription, and illegal drugs
 * tobacco, alcohol,
 * radiation,
 * environmental pollution,
 * infectious disease,
 * STD's,
 * Aids,
 * Parasites,

Sensitive period to teratogen exposure, in the embryonic period is most vital. Fetal damage is minor.

Genetic Engineering
Genetic engineering is where the DNA or gene gets changed by a scientist to make a gene with the characteristics that they want it to have, and to get rid of the characteristics that they don't want the gene to have. This process can be applied towards any plant, animal, or person.

The main reason for genetic engineering is to "mass produce" a certain protein. Each cell is responsible for producing a certain protein and these proteins can be used for medical treatment and diagnosis. The job of each gene is to control the production of a particular protein in a living cell. If the gene responsible for synthesizing an important or useful protein can be found, and if that gene can be inserted into another cell that can be made to reproduce, then a colony of cells containing that gene can be grown and the protein will be manufactured in large quantities. This process is responsible for insulin and growth hormones and it is also used in vaccines to help prevent hepatitis and a treatment to help prevent viral infections. It also helps in genetically engineering Factor VIII which is a treatment for hemophilia.

The first step is to find the gene in the DNA of a cell that is responsible for the manufacturing of the desired protein. Then that gene is either extracted or the exact chemical structure is figures out to be synthesized. The last step is to insert the DNA into the recipient which is done by using special enzymes to split a molecule of the recipients cell and inserting the new gene.

There have been many steps taken to bring technology closer to being able to fix genetically inherited diseases. Hopefully someday there will be many fewer babies born with genetic diseases and disorders.

Gene Therapy
Gene therapy is a way to correct the defective genes that are the cause of disease development. When the genes are altered proteins are not able to function normally and as a result of this, defects can occur. Current gene therapy is still being experimented with, but in some cases it is very effective.

Genes are carried on chromosomes and are the basic physical and functional parts of hereditary. When there is a genetic disorder, gene therapy can help fix the problem either permanently or at least temporarily. The most common form of gene therapy is to insert a gene into a nonspecific place to replace a malfunctioning gene. Another method is gene swapping, where an abnormal gene is replaced by a normal gene. Genes could also be repaired through "selective reverse mutation" which returns the gene to it's original function. The degree to which a gene is turned on or off can also be altered.

Gene therapy works on the principle belief that a virus genome can be manipulated to remove disease causing genes and new therapeutic genes can be inserted in their place. These new genes are called gene therapy vectors. (The virus container is the vector and the new gene is the payload.)

A few of the different viruses used as gene therapy vectors are: Retroviruses - A class of viruses that can create double-stranded DNA copies of their original RNA genomes. Theses copies of its genomes can be mixed into the chromosomes of "host" cells. HIV is a type of retrovirus. Adenoviruses - A class of viruses with double-stranded DNA genome that cause respiratory, intestinal, and eye infections in humans. The common cold is an adenovirus. Adeno-associated viruses - A class of small, single-stranded DNA viruses that can insert their genetic material at a specific site on chromosome 19. (chromosome 19 represents about 2% of the human genome and contains about 1,500 genes. Some of the genes included are genes that code for insulin-dependent diabetes, myotonic dystrophy, migraines, and inherited high blood cholesterol). A class of double-stranded DNA viruses that infect a particular cell type, neurons, called Herpes simplex viruses is another common virus used in gene therapy. It is the virus that causes cold sores.

Major advancements have been made in gene therapy. There are many new discoveries in helping cure and treat diseases that claim millions of lives. Some of the disease that have cures or treatments because of gene therapy include: Parkinson's, Huntington's, Cystic Fibrosis, Some cancers, "Bubble Boy" syndrome and sickle cell. With technology jumping ahead, maybe someday there will be a cure for every life threatening disease.

Genetic Regulation of Development and Homeostasis
It is very easy to think of genetics as why I have blue eyes while both of my parents have brown eyes. Or how hemophilia is passed down from mother to son, and not mother to daughter. But Genetics is more in depth than that. At conception you started as a single cell. That cell started to divide. You didn’t increase in mass just in the number of cells. Once the bundle of cells reached a certain number, things changed. You started gaining mass by acquiring new resources (from your mother) and increasing in cell number. Your cells specialized. Some cells became the liver. Others became heart, lungs, brain, and so forth. Why is this? How did that little bundle of cells "know" when it was time to specialize? It is because your DNA has regulatory control over your entire system. If it didn’t, that bundle of cells would just keep dividing as undifferentiated cells and never specialize, never gain form or function. Thanks to the genetic regulatory control over your system, your anatomy forms correctly with everything in its proper place. Even after fetal development gene regulation still controls what each cell produces and how it functions. Puberty just doesn’t happen at the age of twelve. Puberty happens because genes in your genetic code are triggered by your growth and development, causing your endocrine system to start producing the proper hormones, thus causing you to mature sexually. Even aging is genetically controlled. The mechanisms of genetic regulation are not discussed here, but it is worth noting that any step of gene expression may be modulated, from the DNA-RNA transcription step to post-translational modification of a protein. Gene regulation gives the cell control over structure and function, and is the basis for cellular differentiation. A cell can also respond to changes in its environment by altering gene expression. For example, a pancreatic cell exposed to high glucose levels releases pre-formed insulin that it was storing. Yet, if the high levels of glucose continue, the cell will transcribe additional copies of the gene for making insulin and thus increase insulin production to meet demand. This is homeostasis in action.

Glossary
Allele: one member of a pair of genes that occupy a specific position on a specific chromosome

Autosome: chromosome that is not a sex chromosome

Chromosome: threadlike strand of DNA and associated proteins in the nucleus of cells that carries the genes and functions in the transmission of heredity information

Cystic Fibrosis: recessive genetic disorder affecting the mucus lining of the lungs, leading to breathing problems and other difficulties

Fetal Alcohol Syndrome: combination of birth defects resulting form high (sometimes low) alcohol consumption by the mother during pregnancy

Gene: is a segment of nucleic acid that contains the information necessary to produce a functional product, usually a protein.

Genetics: is the science of genes, heredity, and the variation of organisms.

Genome: complete set of genetic information of an organism including DNA and RNA

Genotype: actual set of genes an organism has. It is the blue print of gentic material.

Hemochromatosis: metabolic disorder that causes increased absorption of iron, which is deposited in the body tissues and organs; the iron accumulates in the body where it may become toxic and causes damage

Hemoglobin: component of red blood cells that carries oxygen

Hemophilia: group of heredity disorders in which affected individuals fail to make enough of certain proteins needed to form blood clots

Inheritance: characteristics given to a child by a parent

Modifying Gene: alters how other genes are expressed in the phenotype

Multifactorial Inheritance: trait or disorder determined by multiple genes and/or environmental effects

Phenotype: organisms physical appearance

Polygenic: trait whose expression is influenced by more than one gene

Regulator Genes: initiate or block the expression of other genes.

Sex-linked: pertaining to a trait of a disorder determined by the sex chromosome in a persons cells or by the genes carried on those chromosomes

Sickle Cell Anemia: recessive disorder in which red blood cells take on an unusual shape, leading to other problems with the blood

Synthesize: to make using biochemical processes

Unifactorial Inheritance: trait or disorder determined by a single pair of genes

Zygote: cell formed by the union of male and female gametes. A Zygote is a cell that is the result of fertilization.

Review questions

 * Answers for these questions can be found here

1. DNA is found on
 * A) endoplasmic reticulum
 * B) ribosomes
 * C) chromosomes
 * D) cytoplasm

2. Even though each cell has identical copies of all of the same genes, different cells __________ or ___________ different genes
 * A) express, repress
 * B) genotype, phenotype
 * C) dominant, recessive

3. In diploid organisms, a dominant allele on one chromosome will
 * A) show the expression of a recessive allele
 * B) mask the expression of a recessive allele
 * C) show that there are dominant alleles on both chromosomes
 * D) none of the above

4. Transcription occurs in the
 * A) cytoplasm
 * B) golgi apparatus
 * C) mitochondria
 * D) nucleus

5. This is the start codon and is found at the beginning of each mRNA
 * A) AGU
 * B) GAU
 * C) UAG
 * D) GUA
 * E) AUG

6. Sara was born with cystic fibrosis, from this we could assume that
 * A) all of her siblings also have cystic fibrosis
 * B) only her dad is a carrier
 * C) only her mom is a carrier
 * D) both of her parents are carriers

7. Jesse was born with a flattened face, almond eyes and less muscle tone; it could be assumed that he has
 * A) a chromosome abnormality on chromosome 21
 * B) a chromosome abnormality on chromosome 19
 * C) a chromosome abnormality on chromosome 20
 * D) a chromosome abnormality on chromosome 22
 * E) No chromosome abnormality, these are his inherited traits

8. The most common inherited disease is
 * A) hemochromatosis
 * B) cystic fibrosis
 * C) sickle cell anemia
 * D) hemophilia
 * E) all of the above

9. Being a carrier of sickle cell anemia means that the person will
 * A) also be a carrier of hemophilia
 * B) be resistant to malaria
 * C) have children that all have sickle cell anemia
 * D) have children that all have malaria
 * E) none of the above

10. Hemophilia is
 * A) a Y linked disease
 * B) an XY linked disease
 * C) an X linked disease


text: Category:Book:Relationships

title: Category:Book:Relationships