text:
User talk:Celestianpower

Hello and welcome to Wikibooks!

Here are some tips to help you get started:
 * You can sign your name on Talk and vote pages using four tildes, like this: ~~~~.
 * Remember to conduct any editing experiments in the sandbox.
 * Check out our help page if you need additional help.
 * Eventually, you might want to read the Manual of Style and Policies and Guidelines.
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 * See list of templates which can save your time
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 * Explore, be bold in editing pages, and have fun!

You will find more resources in Community Portal. If you want to ask a question, visit the Study help desk, the Staff lounge, IRC channel or ask me personally on my talk page.

Good luck! Good to see a familiar name! -- LV (Dark Mark) 02:52, 2 May 2006 (UTC)

cookbook pics
Hi! Photos for the cookbook should go on commons, provided the licensing is kosher. You should also take a look at Cookbook:Policy and Cookbook:Policy/Recipe template to see what sort of formatting/organizational systems we have going. Yay! Kellen T 10:24, 25 August 2006 (UTC)

RC meanderings!
OK - I tend to keep an eye on RC here & I'm nosy!! Impressive work on the Spanish, hope you don't mind - regards -- Herby talk thyme 10:20, 21 December 2006 (UTC)
 * I'm a wanderer from another place too! It really is different here - stick around & in a week you will meet everyone!  There are some good people here but their ways are not like WP I promise you. BTW I "delivered" our attempt at community spirit too - input welcome.  Point me to the existing Spanish page (unless it floats past RC you'll be quicker) - equally ask in the Staff lounge (almost everything happens there).  I'll certainly help if I can - it is possible to make a difference here (IMO) -- Herby  talk thyme 13:45, 21 December 2006 (UTC)
 * OK - feeling slightly silly - just realised how long you've been here - but stick around for break anyway  -- Herby talk thyme 14:03, 21 December 2006 (UTC)

Wikibooks Newsletter, Volume 1
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The staff at Wikibooks 13:19, 21 December 2006 (UTC)

Spanish
Hum - definite content tho (IMO) not as good as yours. I'd try User Talk:Whiteknight probably for an opinion or the staff lounge. Sorry not to be more helpful but feel free to get back to me if I can help in the future. Regards -- Herby talk thyme

 * Hi - happy boxing day (if appropriate) and let me know if you want the redirects from the moves deleted - regards -- Herby talk thyme 14:51, 26 December 2006 (UTC)

 * No problem, I'll clear them now. I have had my additional rights for a very short time compared to you but you do get used to them quite quickly - to be honest I really do see quite why there is a much fuss over them as there is sometimes (tho I am not an admin for  life person, if people use them fine, if not they should be easily removed, now in a perfect world ...!). I do like the "takeover" on Spanish - very neatly done. -- Herby  talk thyme 15:21, 26 December 2006 (UTC)

 * BTW I've left the redirect from the contents page move - more relevant?? -- Herby talk thyme 15:25, 26 December 2006 (UTC)

 * Mind you I always find "Sir" a worrying honourific (well when I use it anyway!). Enjoy the break if you have more to go - sadly work calls tomorrow -- Herby  talk thyme 16:07, 26 December 2006 (UTC)

 * One of the few certainties in life is that I am male! Merely the fact when I use it it does tend to be insulting .  Enjoy the break -- Herby  talk thyme 16:12, 26 December 2006 (UTC)

Add all my "bads" together and you would have worthwhile collection. IRC - yeah I keep getting nudged, part of the problem is that some of the time I am online at work and while a bit of vandalism is not that bad a chat with all the people there are might take an embarrassing amount of time. BTW I agree with much of your user page (wp) - the rant particularly but some other stuff too -- Herby talk thyme 18:22, 26 December 2006 (UTC)
 * reset

BTW I have been known to be on IM -- Herby talk thyme 18:23, 26 December 2006 (UTC)

 * AOL, yahoo, msn (via trillian - which is how I really found wp) (yeah I know I could use IRC on that as well - I have some good reasons and some bad ones ) -- Herby talk thyme 18:32, 26 December 2006 (UTC)

IM
Sorry I couldn't stick around - hope to catch you for a chat soon - cheers -- Herby talk thyme 08:33, 27 December 2006 (UTC)

Things & the world in general!
Hey - good to hear from you - I hope all is well with you - I haven't seen you around for a while either.

 * 1) Good book status - are you MAD?  Your book is so much better than much of the other content of Wikibooks (I know - I watch RC!).  Honestly I think it should be in "good book" status.
 * 2) Completeness.  Now there is a puzzle.  With fiction (in most cases) there is a beginning, a middle and an end.  For textbooks I think it is unlikely that even a print version will be truly complete in the eyes of the author (or indeed other knowledgeable parties - you study a book, it tells you everything, you pick the next one and it tells you something that was missing from the 1st one??!).  For Wikibooks I would risk criticism and say none of them will ever be complete.  Again your's is far more complete than many other offerings on Wikibooks (many are more notes on the subject than a coherent book).
 * 3) Fragments.  Yes awkward.  Handled fine though, it is clear what they are.  I guess my only thought would be to make "Fragmentos para fusionar" a link to a subpage which had links to the fragment.  Not sure if that gains you much?
 * 4) Interaction - well yes, Wikibooks is a little like that at times.  If you will pardon the obvious flaw, it is driven by inertia at times!  I confess I spend some time on Commons & Meta as well these days (I cannot find it in me to get involved in WP).

I hope the world continues to revolve in a reasonable way for you - there are days when I wonder & days when I doubt it . Slugs are my current enemy (I said in a mail to someone earlier - not quite as low as politicians and armament suppliers but when they eat my asparagus!). Take care -- Herby talk thyme 13:57, 17 April 2007 (UTC)

RFA
Hello celestianpower. I just wanted to drop you a line about your RFA request. A few things: Anyway, let me know if you have any questions. --Whiteknight (talk) 22:02, 8 May 2007 (UTC)
 * 1) They never go quickly, so don't despair! A decision will be made eventually, and nobody has forgotten about it.
 * 2) User:Withinfocus' comments are not meant to be insulting, although I know that anything that isnt a "support" vote can feel a little like a personal insult. However, it isn't a negative, it's a positive: an invitation for you to be more active on our discussion pages. We can all see the wonderful work you've done on the spanish book, and we want you to share your wisdom with others. As a good suggestion, try adding the various staff lounge pages, the VFD page, and the bulletin board, so that you can add your two cents when a topic comes up.
 * 3) There are only 4 or 5 votes now, we typically like to promote admins when they have closer to 7-10 votes. Of course, there is no firm limit, it really depends on alot of issues.

 * When I was nominated for adminship, a long long time ago it seems, It was because I was highly active on the VfD page. I hadn't written a single line of policy, and I had read about that much. All people want to see is that you are a "community member", and there are plenty of ways to go about being one. --Whiteknight (talk) 22:27, 8 May 2007 (UTC)

You have a message on your WP talk, please reply.-- SB_Johnny | talk 20:55, 13 May 2007 (UTC)

Congratulations...
You are now an administrator on English Wikibooks. If you're not sure about a policy, just ask me or one of the other admins! -- SB_Johnny | talk 00:38, 15 May 2007 (UTC)
 * And from me - all the best -- Herby talk thyme 07:05, 15 May 2007 (UTC)

Congrats on becoming a moderator! I've seen your work on the Spanish wikibook, and I have to say, you might be the reason that the book reached featured status. Hoogli 21:24, 16 May 2007 (UTC)

Re:Featured Books
There are not alot of things that need to be done to make a book "featured". There is no set number of votes, but i've been typically willing to feature a book if it has about 5 support votes and no oppose votes (more oppose votes typically mean we require more support votes to compensate). But there is no firm number needed, it's all up to the judgement of the person who is willing to say "this is enough".

Once the voting is declared, you need to do a few things:
 * 1) List the book title at Featured books alphabetically
 * 2) Create a Featured book template at Featured books/Templates at the top of the page.
 * 3) Once the template has an image and a suitable description, it can be moved to the bottom of the page, alphabetically.
 * 4) After a while, the main page templates can be expanded to include the new book (we typically wait for a few new books, so we can just include a new round into the main page).

If you need anything else, let me know. --Whiteknight (talk) 14:03, 21 May 2007 (UTC)

Many thanks
& regards -- Herby talk thyme 08:02, 24 June 2007 (UTC)

User:Celestianpower/Spanish table
User:Celestianpower/Spanish table probably belongs at Template:Spanish table header, right? Rodasmith 03:01, 3 November 2007 (UTC)

"Buenas mañanas"?
Is there some region that actually says "Buenas mañanas"? Where? Rodasmith 03:30, 3 November 2007 (UTC)

Need es translator
Hey celestianpower, how are you? I'm in need of a spanish translator to post a message on es.wikibooks about the new logo discussions: Wikibooks/Logo and Wikijunior/Logo. The message would only need to be short, an announcement that we are in the process of selecting new logos, we are looking for submissions, and we are trying to get more wikibookians involved. Let me know if you can help with this. --Whiteknight (Page) (Talk) 16:12, 27 November 2007 (UTC)

 * Thanks for the quick reply! Frankly, so long as the message gets out, I don't care how readable it is. I just want to make sure that we get wikibookians involved. Here is a basic rundown of what the message should say:
 * Discussion is starting to select a new logo for Wikibooks and Wikijunior on meta. All Wikibookians are encouraged to participate.
 * Basically, it's just a short announcement about the discussion, and the links to the discussion pages. We are probably going to get complaints that the discussion pages themselves aren't spanish-friendly, but there isn't much we can do about that. Thanks again! --Whiteknight (Page) (Talk) 20:33, 27 November 2007 (UTC)

Perfect! Thanks Celestianpower! Barnstars for you! --Whiteknight (Page) (Talk) 21:00, 27 November 2007 (UTC)

This user needs a block
His only edits so far I reverted because they were vandalism. Could you please act and do something? Thanks, Laleena (talk) 14:04, 12 January 2008 (UTC)

 * I got it already. blocked for 1 week. --Whiteknight (Page) (Talk) 15:23, 12 January 2008 (UTC)

Spanish wikibook
Check out my new vocabulary page at Spanish/Vocabulary/People. What do you think of structuring the vocabulary pages this way? Cilantrohead (talk) 00:57, 2 March 2008 (UTC)
 * It might be hard to get the words small enough to fit them next to the pictures. I based this on the structure of the Oxford Picture Dictionaries (the 1970's, 1980's and 1990's versions).
 * And yes, I did do the pictures myself. Know any artists who are good with the mouse who can help us? I have new artwork up at Spanish/Vocabulary/Food. Cilantrohead (talk) 00:27, 17 March 2008 (UTC)

Spanish Answers

 * The same with Spanish/Exercises/Introducción a la gramática. Akhram (talk) 15:11, 13 April 2008 (UTC).

 * Hi, Celestianpower. I'm very interesting in the Spanish wikibook because now I'm working in the Spanish Language Division at wikiversity. I can revised the format and the translations (I'm Spanish), but as I am not teacher, I cannot add new chapters or so, only new exercises or some vocabulary. If you are improving the wikibook, you can count on me. Akhram (talk) 13:02, 13 April 2008 (UTC).

Hi, again. I added another template, ES-grammar, for verbs-tables. If you have any idea or improvement, go. Akhram (talk) 14:30, 13 April 2008 (UTC).

Inactivity
So you're aware, you're up for removal of your adminship due to inactivity. The request will be placed at Meta in one month's time. Thanks for your service; you're welcome to request adminship again if you return to Wikibooks. — Mike.lifeguard | talk 21:48, 9 October 2008 (UTC)

title: User talk:Celestianpower


text:
TI-Basic Z80 Programming/Menus

Menu( ( CTL D) is useful for allowing the user to select an option. By using Menu(, you can list several choices which the user can pick; each choice jumping to a different label.

Syntax
The basic syntax for Menu(:

When a user selects an option in the menu by pressing, the program will jump to the Lbl with the same name defined in the Menu( statement.

If the Menu( statement references a Lbl that does not exist, a <tt>LABEL</tt> error will be returned.

Example
To create a simple menu with several options:

Displays the following when executed:

Advanced Menus
The <tt>Menu(</tt> function allows for great use of static menus, but when more choices are needed or when more interactive, dynamic menus are needed. The following method uses <tt>getKey</tt> to achieve this.

''Note: The following example uses the <tt>Text</tt> command, which draws text to the graph screen. This is covered with more detail in later chapters.''

You try it!
Try these examples to practice using the <tt>Menu(</tt> command.

Physics Calculations
The potential energy of an object is defined by $$PE=mgh$$, where m is the mass in kilograms, g is the gravity, and h is the height in meters. The kinetic energy of an object is defined by $$KE=\frac{1}{2}mv^2$$, where m is the mass in kilograms and v is the velocity in meters per second. The apparent weight of an object is defined by $$W=mg$$, where m is the mass in kilograms and g is the gravity. Use the <tt>Menu(</tt> command to write a simple program that the user can select from each of the previously defined formulas, enter known values, and receive an output.

It is important to use the <tt>Stop</tt> command so that when statements under <tt>Lbl A</tt> and <tt>B</tt> are done executing, the succeeding labels do not execute. However, it is not necessary for a <tt>Stop</tt> command after <tt>Lbl C</tt> statements, since it is the end of the program.

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

title: TI-Basic Z80 Programming/Menus


text:
User:Sandycx

Refer to this English Wikipedia user page for my information.

title: User:Sandycx


text:
Radiation Oncology/Fatigue

Fatigue

 * Most frequent symptom in advanced cancer patients
 * No data exist about frequency of fatigue in different tumors
 * Etiology is unclear; autonomic failure has been implicated
 * Management includes treatment of reversible causes (e.g. mood disorders, anemia)
 * No pharmacologic trials have shown improvement in cancer-related fatigue

Anti-cholinergics
Donepezil (Aricept)
 * MD Anderson; 2007 PMID 17687152 -- "Donepezil for cancer fatigue: a double-blind, randomized, placebo-controlled trial." (Bruera E, J Clin Oncol. 2007 Aug 10;25(23):3475-81.)
 * Randomized. 103/142 patients with fatigue score >=4 (scale 0-10) for more than 1 week. Treated with 1) donepezil 5mg x 7days vs. 2) placebo. Everyone donepezil open label second week
 * Outcome: No difference by FACIT-F or ESAS
 * Conclusion: No difference from placebo

Psychostimulants
Methylphenidate (Ritalin)
 * MD Anderson; 2006 - PMID 16648508 — "Patient-Controlled Methylphenidate for Cancer Fatigue: A Double-Blind, Randomized, Placebo-Controlled Trial." Bruera E et al. JCO May 1 2006: 2073–2078.
 * Randomized to 5 mg methylphenidate q2h as needed (patient controlled) vs placebo.
 * No significant difference from placebo.

Antidepresants
Paroxetine (Paxil)
 * Rochester; 2003 PMID 14673053 -- "Differential effects of paroxetine on fatigue and depression: a randomized, double-blind trial from the University of Rochester Cancer Center Community Clinical Oncology Program." (Morrow GR, J Clin Oncol. 2003 Dec 15;21(24):4635-41.)
 * Randomized. 479/549 patients undergoing chemo for the first time, and reported fatigue at their 2nd cycle. Treated with 1) oral paroxetine 20mg qd x8 weeks vs. 2) placebo
 * Outcome: No difference in fatigue between groups; but benefit in depression score
 * Conclusion: No impact on fatigue

title: Radiation Oncology/Fatigue


text:
Radiation Oncology/Dyspnea

Dyspnea and Pneumonitis

Supplemental oxygen

 * MDACC, 2003 - PMID 14694916 — "A randomized controlled trial of supplemental oxygen versus air in cancer patients with dyspnea." Bruera E et al. Palliat Med. 2003 Dec;17(8):659-63.
 * Randomized pts with advanced cancer without severe hypoxemia (SaO2 > 90%) at rest with dyspnea. Randomized to supplemental oxygen or air (5 L/min) by nasal cannula.
 * No significant difference in dyspnea, fatigue, or distance walked.

Pneumonitis

 * Management
 * From University of Pennsylvania Oncolink
 * Oral steroid therapy titrated over several weeks (Prednisone 60 mg/day x2 weeks, very slow taper over 3-12 weeks)
 * Pentoxifylilne could be considered to decrease progression to radiation fibrosis
 * May take 3-18 months for symptoms to fully resolve and/or stabilize. Any further significant improvement after 18 months is rare, due to progression to radiation fibrosis

title: Radiation Oncology/Dyspnea


text:
Organic Chemistry/Alkenes/The pi bond

π Bonding
In General Chemistry, pi bonds (π bonds) are covalent electron bonds where two lobes of one involved electron orbital overlap two lobes of the other involved electron orbital. What this means is, when two atoms are sufficiently close and when they each have one electron that is not being shared, the two electron orbits can essentially "overlap" causing a new bond between the atoms. Any atom capable of forming more than one electron can form pi bonds, so it is relatively common to find pi bonds in molecules containing two or more nitrogen or carbon atoms, but one would never find (in nature) pi bonding between hydrogens, halogens or other atoms which prefer to share only one electron.

The Greek letter π in the name refers to p orbitals, since the orbital symmetry of the pi bond is the same as that of the p orbital when seen down the bond axis. P orbitals most often engage in this sort of bonding, however, d orbitals can also engage in the formation of pi bonds.

Pi bonds are usually weaker than sigma bonds (σ bonds) because pi bond orbitals extend further from the positive charge of the atomic nucleus, which therefore requires additional energy. From the perspective of quantum mechanics, this bond weakness is explained by significantly less overlap between what were previously p orbitals due to the parallel orientation of the orbitals. The pi bond by itself is weaker than a sigma bond, but pi bonds are only found in combination with sigma bonds, so the combination of the two bonds is 'stronger (and shorter in length) than either bond would be by itself.

Two or More p-Orbitals Can Form a π-Bond
Atoms with double bonds or triple bonds as found in nature always have one sigma-type bond and the rest pi-type bonds. Pi bonds result from parallel orbital overlap: the two combined orbitals meet lengthwise and create more diffuse bonds than the sigma bonds. No commonly-occurring natural substance has more than three bonds to another atom, and if there are three bonds it is safe to assume that the three bonds consist of one sigma bond and two pi bonds.

It is important to note that atoms will not generally form more bonds than predicted by their place in the Periodic Table of Elements. Electrons in pi bonds are also often referred to as "pi electrons".

title: Organic Chemistry/Alkenes/The pi bond


text:
User:Masterofhogets

I'm a New Zealander who contributes to the Wikimedia projects with the same user name. For mor detail see my wikipedia user page.

title: User:Masterofhogets


text:
User:Spoonypirate

Rawr.

title: User:Spoonypirate


text: User:Hagindaz/Sandbox

title: User:Hagindaz/Sandbox


text:
User talk:4836.03

Hello there

I'm afraid Wikibooks is geared towards textbooks rather than novels. Unfortunately, this means that your wikinovel will need to be removed. Hopefully you will be able to find an alternative wiki for it.

So that you are able to fully preserve your work, I'll hold off deleting it for a week, which should give you ample time to create your own copy if you do not already have one.

If you wish to contribute towards writing textbooks in the future, or would like to consult a free online textbook in the future, then we'd be more than happy to see you here.

All the best, Jguk 11:48, 2 May 2006 (UTC)

title: User talk:4836.03


text: Ancient History/Celtic Europe

title: Ancient History/Celtic Europe


text:
Proteomics/Protein Chips/Types

Types:

Types
The two main types of protein chips are analytical and functional. With analytical protein chips, the proteins being studied are in the solution that is washed over the chip. Analytical chips are primarily used to identify the contents of an analyte. With functional protein chips, the proteins being studied are attached to the chip. Functional chips are primarily used to study interactions between the protein of interest and other molecules.

Analytical
Analytical chips are classified according to the capture molecule that is affixed to the chip. The molecule can be very specific as to the types of proteins it binds to. Examples of these specific molecules include antibodies, antigens, enzymatic substrates, nucleotides and other proteins. Analytical chips can also contain molecules that bind to a range of proteins. These molecules are similar to the ones used in liquid chromatography. The techniques include reverse phase, cation exchange and anion exchange.

Reverse phase protein chips, also known as reverse phase protein arrays (RPA), are related to analytical microarrays and are used to identify different levels of expression of proteins. RPAs have become well used to the point where they may even be considered a separate type of protein chip all together. RPAs are high-throughput technology that involves the use of two pre-existing technologies known as laser capture microdissection (LCM) and microarray fabrication. LCM visualizes stained tissue cells of interest under a microscope in real time. Once visualized, the cells are then isolated and lysed and placed into the spots of the microarray. An antibody that can be detected by a fluorescent is used to probe the slides. RPA allows for the protein to be immobilized in order to be analyzed instead of the typical protein microarrays which immobilizes the antibody probe. This is how it got the name ‘reverse phase’. This process allows that the protein need not be labeled since the protein lysate has already been denatured.

Advantages of RPAs over other types include the ability to run different test samples in each individual array spot and only require a single antibody to probe an entire array slide. This use of a single antibody eliminates the need to run multiple analytes, and instead, a single one is measured and then compared to the different test samples that were applied to the individual spots. Use of Reverse Phase Protein Microarrays and Reference Standard Development for Molecular Network Analysis of metastatic Ovarian Carcinoma. Molecular & Cellular Proteomics, 4(4), 346-355. This process is optimal for cell populations with low cell count due to its ability to run a single analyte for a greater number of spots in the array, for example, all of the proteins present in the cell.

A major use of RPAs is to view the different stages of progressing cancer along with studying signaling transduction pathways. They can be used to determine different activation statuses of proteins over a set amount of time or due to certain treatment conditions.

Functional
Unlike analytical chips, there is only one type of functional chip. Functional chips are used to discover additional information and properties about a particular protein. These properties include binding strength, biochemical functions and protein-protein interactions.

The major methods used to characterize an organism's proteome often result in the denaturing of the sample thus ruling out any functional studies. Current functional analysis methods are mostly in vivo techniques which have inherent variabilities. The benefits of functional analysis using these chips is that proteins can be identified and studied in vitro while they are still biochemically active and in their multimeric complexed form.

There are many challenges when developing a functional protein array including creating an expression clone library, actual protein production which includes isolation and purification, adaptation of microarray technology, stabilizing the proteins on the array, and keeping the concentrations of the protein constant between slides as well as between spots on the same slide.

Functional arrays have many uses including the complete characterization of an organism's whole proteome. A study by Zhu et al. developed a yeast proteome array that contained proteins from 93% of the organism's 6280 protein-coding genes. Other experiments include large scale screenings of proteomes for phospholipid-binding and calmodulin-binding specificities.

Protein chips enable us to study biochemical interactions on an unprecedented scale. Thousands of proteins can be screened for protein-protein, protein-nucleic acid, and protein-small molecule interactions simultaneously. The in vitro nature of the method ensures that it has advantages over current functional assay methods, and its parallel, quantitative format propels it above many other techniques in the field.

title: Proteomics/Protein Chips/Types


text:
Proteomics/Protein Chips/Analysis

Analysis:

Analysis
Within the realm of protein chip analysis, there are several hurdles presently being cleared by scientists experimenting at the fringe of this technology. Several of the main challenges facing scientists include: dynamic protein concentrations, almost overwhelming numbers of unique proteins, and creation of specific probes for each protein.

Dynamic protein concentration refers to the reality that the exact number of any given protein within a cell can be drastically different than the exact number of another protein within the same cell. In fact, there are current estimates that place the difference in protein numbers between those expressed at the lowest levels and those expressed at the highest levels at an order of magnitude of roughly 1012. In other words, a million million fold difference can exists between the rarest and the most abundant proteins.

To further complicate the issue of dynamic protein concentrations, the exact number of any given protein will fluctuate based on which type of cell is being considered. Of course, there are some proteins, known as housekeeping proteins, that are highly expressed in every cell. These proteins are needed for the basic structure and functions that keep the cell alive. Housekeeping proteins aside, cells of different tissues will often have varying protein concentration profiles. For example, proteins that are expressed at high concentrations in heart tissue will most likely be expressed at different concentrations in liver tissue. Therefore, methods that detect a protein in one cell type may not work for a different cell type.

Unfortunately, scientists are often interested in those proteins that are rare and present in low concentrations. One method devised in order to overcome this limitation has been the removal of abundant proteins. Usually, there are a very small number of proteins that are present in copious quantities. Through the removal of these proteins, scientists can reduce the order of magnitude differences between the lowest and highest expressed proteins. However, protein purification can be a very laborious and time consuming process and many scientists recognize that it may be prudent to run several protein chip experiments, each analyzing a different range of protein concentrations. 1

Another massive challenge exists in determining a specific probe for each protein. Currently, one attempt to solve this problem is in the designing of specific antibodies. In the past, antibodies have been created through the immunization of animals. This method, however, is not high-throughput enough to be considered effient for protein chip experimental design. Instead, methods are being developed in order to create antibody libraries. 1 A few examples from Molecular Station are listed below.
 * Phage antibody display
 * Ribosome display
 * SELEX (Systomatic Evolution of Ligands by Exponential Enrichment)
 * mRNA display
 * Affibody display

Antibody approaches can be narrowed somewhat by creating antibodies that bind specific protein groups and not specific proteins. An alternative to antibody usage exists in aptamers, or short oligonucleotides which are much easier to create, but can be difficult to select for a specific protein. 1

In order to analyze the results of the protein chip it is necessary to determine the types or numbers of proteins that were bound to the capture agents (for analytical chips) or the number of interactions the proteins had (for functional chips). Analysis of protein chips can be broken into two categories: Labeled and Label-Free. Analysis of protein chips can be a difficult and tricky process. Many intuitive methods have been developed, but each has its own limitations. Short descriptions of these methods and their limitations exists below.

Labeled
This type of analysis involves labeling either with radioactivity or fluorescence. 2 The label can be attached directly to the protein or capture agent (such as an enzyme or substrate) and detected immediately. The label can also be attached to a different molecule (such as an antibody, antigen or substrate) that is washed over the chip as part of a second step. This prevents the label from altering the conformation of the proteins being studied.

However there are several issues that arise with labeled protein chips. Although methods exist to prevent a label from altering protein conformation, a probability of interference with protein interactions still exists. 1 Label influence on binding properties, along with a knack for having a lack of reproducability 1, provide for a couple of significant issues which can be seen as sufficient reasoning for using a label-free approach.

ELISA (Enzyme-Linked Immunosorbent Assay)
ELISA assays are useful tool in the detection of antigens or proteins. A specific antibody is used to target the desired antigen or protein. The complex that forms from the antibody-antigen binding is bound by another antibody which recognizes such complexes. The latter antibody is attached to an enzyme thus 'enzyme-linked' is part of the acronym, ELISA. The binding of the antigen will usually trigger a reaction that can be observed and qualified or quantified.

A very useful animation of both a positive and negative ELISA reaction can be found here.

Useful as ELISA assays may be, they are unfortunately prone to false positives as many non-specific protein-antibody interactions can occur. 1

Sandwich Immunoassay
Sandwich immunoassays, a version of an ELISA assy, use fluorescently labeled antibodies for the probe and laser scanning for collecting the data. 2

Isotopic labeling
Isotopic labeling involves using a radio isotope-labeled analyte for the probe and X-ray film for collecting the data. 2 The attachment of unusual isotypes provides the information needed to identify specific markers, or in this case, proteins.

Molecules containing these isotopes can be distinguished by either mass spectrometry or infrared spectroscopy. 3  There are various isotopes and each has a different mass therefore leading to the utilizaion of  mass spectrometry. Infrared spectroscopy can be used because the various isotopes have different vibrational modes.

Planar Waveguide
Planar waveguides involve using fluorescently labeled antibodies for the probe and a charge-coupled device for collecting the data. 2 Waveguides typically involve the detection of electromagnetic waves. The term planar simply refers to the geometry of the system resembling a plane.

Planar waveguides may offer the exciting ability to analyze systems in real-time thus enabling the study of protein interaction kinetics. 1

Electro-Chemical
Electro-chemical detection involves using metal-coupled analyte for the probe and a conductivity measurement for collecting the data. 2

Data
Like DNA microarrays, protein chip experiments using fluorescent labeling provide data in the form of images with spots of varying intensities. These images are then analyzed using software packages similar to those used for DNA microarray analysis. Two examples of the types of analysis performed are the quantification of spot intensities and the comparison of intensities between control and experimental conditions.

Software
Software packages used for analysis of labeled protein chips include:
 * Protein Microarray Analysis Tool (ProMAT) is a freely available software package used to evaluate the intensity of the spots. ProMAT was developed at Pacific Northwest National Laboratory.
 * ZeptoVIEW PRO is a commercially available software package from Zeptosens that allows quantification of spot intensity and is used with their protein chips.

Label-Free
This type of analysis takes advantage of the properties of the proteins and includes mass spectrometry, surface plasmon resonance (SPR) and atomic force microscopy (AFM). 2

Mass Spectrometry
Certain chips, such as the ProteinChips by Ciphergen, can be coupled to a MALDI-TOF mass spectrometer. 2 Improved resolution can be obtained by using SELDI mass spectrometry. 2  Data collection and analysis are performed in the same manner as mass spectrometry performed after protein separation techniques such as liquid chromatography.

Surface Plasmon Resonance (SPR)
Surface plasmon resonance is an optical effect produced when polarized light is shone on a specially designed protein chip. 2 The chip needs to contain a thin metal film that will cause the light to refract. 2  The angle of refraction depends on the mass of the molecule bound to the chip so a protein with a substrate bound to it will cause the light to refract at a different angle than a protein with no substrate. 2  The different angles can be measured by a photodiode array. 2  Additionally, surface plasmon resonance can be coupled to mass spectrometry for protein identification using microrecovery from the chip surface. 2

Surface plasmon resonance has the ability to provide real-time analysis. The consequences of such are that it becomes possible to study the kinetics of protein interactions. Detection resolution, a challenge discussed previously on this page, represents a drawback to SPR analysis. Planar waveguides may provide for a real-time analysis with improved detection resolution. 1

Atomic Force Microscopy (AFM)
Atomic force microscopy uses changes in surface topology to detect protein interactions. 2 It is a high resolution technique and the data is collected in the form of topographical maps. 4

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 * Term 1: definition ( http://notreal.sourceurl.sample/where_your_definition_came_from )
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 * How is this applicable to the proteomics class?

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 * Term 2: definition ( http://notreal.sourceurl.sample/another_example )

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 * How is this applicable to the proteomics class?

Web Site Title
Insert your web site citation here with the format Author1 AB, Author2 CD, etc. http://notreal.sampleurl.sample/this_is_an_example_of_a_site (date accessed)

Main Focus

One or two statements here

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 * Term 1: definition ( http://notreal.sourceurl.sample/where_your_definition_came_from )
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title: Proteomics/Protein Chips/Analysis


text:
Proteomics/Protein Chips/Online Resources

Online Resources:

Online Resources
There are many online resources available for additional information about protein chips. Below are a few of our favorites.

Databases

 * The NCBI's Protein Database
 * RCSB Protein Data Bank
 * Swiss-Prot

Journals

 * Protein Science
 * Proteomics
 * The Protein Journal

Related to Types
Bertone P, Snyder M. Advances in functional protein microarray technology. FEBS, 2005; 272(5400-5411).
 * The authors discuss the uses and construction of functional protein microarrays
 * Complete Article in FEBS (Free)

Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, Bertone P, Lan N, Jansen R, Bidlingmaier S, Houfek T et al. (2001) Global analysis of protein activities using proteome chips. Science 293, 2101–2105.
 * The authors develop a functional array for the yeast proteome
 * Complete Article in Science (Free)

Related To Analysis
Xu, Qingchai, Lam, Kit S. "Protein and Chemical Microarrays- Powerful Tools for Proteomics." Journal of Biomedicine and Biotechnology (2003) 5:257-266. Download the paper.

Related to Applications
LaBaer, Joshua & Ramachandran, Niroshan. "Protein Microarrays as Tools for Functional Proteomics." Current Opinion in Chemical Biology (2..05) 9:14-19. View the paper.

Duan L, Wang Y, Li SS, Wan Z, Zhai J. Rapid and simultaneous detection of human hepatitis B virus and hepatitis C virus antibodies based on a protein chip assay using nano-gold immunological amplification and silver staining method. BMC Infectious Diseases, 5 (2005).
 * An antigen-coated protein chip was used to detect the presence of hepatitis B and hepatitis C antibodies in human serum samples.
 * Article Abstract in PubMed
 * Complete Article in BMC Infectious Diseases

Ge H. UPA, a universal protein array system for quantitative detection of protein–protein, protein–DNA, protein–RNA and protein–ligand interactions. Nucleic Acids Research, 28 (2000).
 * The author created a functional type of protein chip to simultaneously study the interaction of proteins, DNA, RNA and ligand.
 * Article Abstract in PubMed
 * Complete Article in Nucleic Acids Research

Kozak KR, Amneus MW, Pusey SM, Su F, Luong MN, Luong SA, Reddy ST, Farias-Eisner R. Identification of biomarkers for ovarian cancer using strong anion-exchange ProteinChips: Potential use in diagnosis and prognosis. Proceedings of the National Academy of Sciences of the United States of America 100:12343–12348 (2003).
 * The authors combined strong anion-exchange protein chips with SELDI-TOF mass spectrometry to identify potential biomarkers for ovarian cancer.
 * Article Abstract in PubMed
 * Complete Article in Proceedings of the National Academy of Sciences of the United States of America

Related to Introduction/History
MacBeath G, Schreiber SL. Printing proteins as microarrays for high-throughput function determination. Science, 289: 1760-3 (2000).
 * The authors developed a way to rapidly create protein chips
 * Article Abstract in PubMed
 * Complete Article in Science (Subscription Required)

Related to Types
Jona G, Snyder M. Recent developments in analytical and functional protein microarrays. Curr Opin Mol Ther., 2003; 5(271-277).
 * The authors discuss the uses and construction of both analytical and functional protein microarrays
 * Abstract in Pubmed (Free)
 * Complete Article in Curr Opin Mol Ther. (Subscription)

Related to Analysis
Ferracci G, Seagar M, Joel C, Miquelis R, Leveque C. Real time analysis of intact organelles using surface plasmon resonance. Analytical Biochemistry, 334: 367-375 (2004).
 * The authors used Surface Plasmon Resonance to study organelles on a protein chip.
 * Article Abstract in PubMed
 * Complete Article in Analytical Biochemistry (Subscription Required)

Kim TJ, Cho HS, Park NY, Lee JI. Serodiagnostic comparison between two methods, ELISA and surface plasmon resonance for the detection of antibody titres of Mycoplasma hyopneumoniae. Journal of Veterinary Medicine Series B, 53: 87-90 (2006).
 * The authors compare the results of two analysis methods: surface plasmon resonance and ELISA
 * Article Abstract in PubMed

Zhu H, Snyder M. Protein Chip Technology. Current Opinion in Chemical Biology, 7: 55-63 (2003).
 * An excellent review article that contains a summary of detection methods used with protein chips
 * Article Abstract in PubMed
 * Complete Article in Current Opinion in Chemical Biology (Subscription Required)

Related to Applications
Fan G, Molstad M, Braziel RM, Standley M, Huang J, Rodgers W, Nagalla S. Proteomic profiling of mature CD10+ B-cell lymphomas. American Journal of Clinical Pathology, 124: 920-29 (2005).
 * The authors used protein chips coupled to SELDI-TOF mass spectrometry to classify different types of B-cell lymphomas.
 * Article Abstract in PubMed
 * Complete Article in American Journal of Clinical Pathology (Subscription Required)

Huelseweh B, Ehricht R, Marschall HJ. A simple and rapid protein array based method for the simultaneous detection of biowarfare agents. Proteomics, April 18, 2006.
 * The authors developed antibody coated protein chips to detect the presence of biowarfare agents. Their careful antibody selection allows them to use one chip to test for the presence of multiple agents.
 * Article Abstract in PubMed
 * Complete Article in Proteomics (Subscription Required)

Warren EN, Jiang J, Parker CE, Borchers CH. Absolute quantitation of cancer-related proteins using an MS-based peptide chip. Biotechniques, 38:S7-11 (2005).
 * The authors combined a protein chip with mass spectrometry to detect, identify and quantify proteins related to cancer.
 * Article Abstract in PubMed
 * Complete Article in Biotechniques (Subscription Required)

Tutorials and Information

 * A comparison of the types of manufacturing methods
 * Informational videos and animations provided by Ciphergen. Ciphergen is a protein chip manufacturer.  They have an online video showing the role of protein chips in clinical proteomics and an online animation about how protein chips are analyzed.
 * Protein Arrays Resource Page - Additional information and links provided by Genomic Solutions
 * Protein Chip Wikipedia entry
 * Latest news releases - covered by Laboratorytalk
 * A good example of a protein chip experiment. Zhu, H. et al. (2001) performed a protein chip experiment in order to analyze yeast protein kinases.

Next chapter: Proteomics/Proteomics and Drug Discovery


text:
Talk:Parkour

Lets share some info about parkour.
Also finally Knuxus I read your note on "parkour, not pure parkour." I disagree, i think this is a black and white issue, either it is the fastest way to cross something or it isn't. No contest. - Ukemi

Okay, ive done some basic edits but i have to go now, exams tomorrow. You may have to touch up spelling (abbreviated?) and layout/style stuff, since i don't know how to do that properly in wikipedia. Also considering adding more to the origins sections, such as herbetism, and david belles original goals and opinions, there is a wikiquote article with le parkour quotations. The exercises section should also be redone, i have no idea how good hindu squats are but if your taking this off Matt Furey rewrite now, and also i have heard they can damage your knees because your knee hangs over your toes. APK has the WOD, and parkour.net has a full workout posted there, so steal or link to that. Apart from that, good work on this, its a work in progress but it has the makings of a good article. - Ukemi

Hey Knuxus, M2 (love APK btw, and im in Australia :), you guys have awesome articles). Im just gonna skim through this and change some stuff, I saw the parkour (also called Freerunning) thing on the heading and cringed, so if you don't mind im just gonna go through this. If you want some really good articles on this stuff go to www.aparkour.com, an Australian traceur started this to provide insurance for his friends to begin volunteer schools, both for just general traceurs but also specifically for disadvantaged groups and those in youth prisions, a la Yamakasi and some of Urban Freeflows PK events. Lots of good stuff there, especially on spirit. - Ukemi

Please help me improving this book with photos, texts, videos and other stuff that might improve it.--Knuxus 16:01, 2 May 2006 (UTC)

Requesting for someone to interlink this article with a portuguese wikibooks page by the same name(Parkour). --Knuxus 20:47, 2 May 2006 (UTC)

I'll happily lend a hand with writing the book but unfortunatley I'm rather busy currently. Anyhow, just a quick pointer, you may want to scrap the picture of David Belle on the front page, it shows him doing a backflip which is not parkour, it's tricking. There are plenty of other better pictures of Belle out there. I'd love to see this finished though, it could become a great resource. Aj* 21:08, 2 May 2006 (UTC)

Thank you Aj, your comment is truly useful, the photo will be changed to something more Parkourish --Knuxus 21:54, 2 May 2006 (UTC) Changes done, but I think there is a lot of better images which could be more illustrative, like from the movie, or even real photos, I just couldn´t find them, if someone has something, please feel free to change...--Knuxus 22:07, 2 May 2006 (UTC)

I'll be happy to help, I need to see what proper ettiquette is for these pages. for example, american parkour.com (my website) has some good tutorials for these moves which I'd be happy to contribute, but they must remain the property of american parkour (properly credited). please feel free to email me m2rock@yahoo.com to discuss. Thanks! M2 17:19, 12 May 2006 (UTC)

I really have nothing to discuss about, just put your content and then we will see, if you want credits you may put it, i dont have any problems with pub, as long as it remains in the subject.

I am moving "360 Underbar" to "Parkour Moves" and renaming to "Reverse Underbar". This move is useful anytime you need to go under a bar and must go head first instead of feet first. M2 16:08, 28 June 2006 (UTC)

Please put any info you want, with all of your copyrights and references to your site, if you want to put your pictures and videos you may do it also, you can put as many as you want, as long as it stays on topic. This is not my projects, I only initiated it, it is yours, and fully yours, you may do whatever you want, well, it still has to remain legal... --Knuxus 10:07, 7 July

Why include Aesthetic moves since they're not Parkour?

Answering that question: often many aestethic moves are used in parkour, they are parkour, but not pure parkour... and since there is no tricking wikibook i think they should remain here...--Knuxus 13:35, 24 July 2006 (UTC)

 * Um, no. Aesthetic moves, or moves that will not aid you in overcoming an obstacle efficiently are not parkour and never will be, see Free Running. There is no such thing as pure parkour and this guide is very misinformed. I recommend reading Wikipedia's entry on Parkour and simply linking to that or pulling that content for the "What is" and "History" sections. --Undaunted 21:41, 29 August 2006 (UTC)

watch this video

http://youtube.com/watch?v=IVQFOAZNSWo

Images used
I think we should add more images to Commons instead of linking to external picture sites. That way we won't have so many 404 errors, and can display them here. --Explodicle (talk) 22:01, 4 May 2009 (UTC)

Other
At the beginning of the text, "Le Parkour (also called Parkour, and abbreviated PK)". Parkour is said twice. I think that the original writer meant that the first of the two to be written parcours. --Darren-Jaguar (talk) 11:09, 17 May 2009 (UTC)

title: Talk:Parkour


text:
Proteomics/Protein Chips/History

 * 1) Introduction
 * 2) History
 * 3) Manufacture
 * 4) Types
 * 5) Analysis
 * 6) Reproducibility
 * 7) Applications
 * 8) Algorithms
 * 9) Online Resources

Nucleic Acid Microarrays
The use of microarrays for gene expression profiling was first published in 1995. This technology allowed scientists to analyze thousands of mRNAs in a single experiment to determine whether expression is different in disease states. Unfortunately, mRNA levels within a cell are often poorly correlated with actual protein abundance. This can be due to many factors including degradation rate of mRNA versus proteins and post-transcriptional controls and modifications. Measuring the amount of protein directly would bypass any mRNA inconsistencies and give a true level of gene function, however traditional protein characterization methods were slow and cumbersome. These combined factors were the impetus behind the creation of protein chips.

Deficiency of Traditional Protein Characterization Methods

Before the advent of protein chips, protein measuring and characterization was done using two different methods: 2D gel electrophoresis coupled with mass spectrometry, and liquid chromatography. These methods can separate and visualize a large number of proteins per experiment, however they are time consuming when compared to protein chips. Their process is very low-throughput because of lack of automation. Reproducibility is also a factor because of the large amount of sample handling. A better, more standardized, higher-throughput method needed to be invented for protein measuring and characterization.

Protein Chip Precursors to Modern Day

Immunoassays, the precursor to protein chips available since the 1980s, exploit the interactions between antibodies and antigens in order to detect their concentrations in biological samples. Their creation, however, is tedious and expensive. As a response to this, researchers at Harvard University combined the technologies of immunoassays and DNA microarrays to develop the protein chip. In their landmark paper, published in 2000, "Printing Proteins as Microarrays for High-Throughput Function Determination," Gavin MacBeath and Stuart Schreiber described how to create protein chips and demonstrated three types of applications that would benefit from this new technology. The strengths of their approach were the use of readily available materials (i.e. glass slides, polyacrylamide gel), the relative ease of implementation (robotic microarray printers), and compatibility with standard instrumentation.

Within the past five years, many companies, including Biacore, Invitrogen, and Sigma-Aldrich, have begun production of industrial level protein array systems that can be used for drug discovery and basic biological research. Commercial entities have made protein chip research a streamlined and standardized process on the same level as DNA microarrays compared to its inception in 2000.

Academic research plays a huge role in the development and improvement of these technologies. The collaboration of academic research with systems such as the Affymetrix GeneChip and the Human Genome Initiative has allowed for friendly competition, resulting in the advancement of technologies. With more develops come a better understanding and encourages even more research towards these fields.

Affymetrix is a company that has been manufactures microarrays, named GeneChip, since 1992. They have 13 locations across the world with headquarters located in the US (California), UK, Japan, and China.

Next section: Manufacture

Related Journal Articles (Subscription Required)
MacBeath G, Schreiber SL. Printing proteins as microarrays for high-throughput function determination. Science, 289: 1760-3 (2000).
 * The authors developed a way to rapidly create protein chips
 * Article Abstract in PubMed
 * Complete Article in Science (Subscription Required)

title: Proteomics/Protein Chips/History


text:
IB Music/Music History/Modern Period

Tone color

 * 1) Has major role in keeping unity
 * 2) noiselike and percussive sounds used
 * 3) Glissando, flutter tonguing, and pizzicato common
 * 4) Percussion standard, numerous
 * 5) Piano used percussively
 * 6) Transparency: individual lines clear
 * 7) Less emphasis on blended sound

Harmony

 * 1) Consonance and dissonance
 * 2) * Composers began using dissonant chords more
 * 3) * no longer general principle of stability
 * 4) new chord structures
 * 5) * Polychord: one traditional chord on another
 * 6) * Fourth chords used, instead of thirds
 * 7) * Tone cluster: chord of notes only half step apart

Alternatives to the traditional tonal system

 * 1) Church modes revived
 * 2) Polytonality
 * 3) Bitonality

Impressionism and symbolism
Impressionism emerged from France in the late 19th century. There were two main composers, Claude Debussy, and Maurice Ravel.

In reaction to the Romantic period, it used more expression in the atmosphere of the piece rather than the music itself.

Whole tone scales were prominently used, and the songs were usually instrumental. Woodwinds were dominant in the pieces, while strings blended colors instead of making block sounds.

It had indefinite rhythms, and it was more fluid filled with downbeats.

Simplicity and abstraction was explored, and was greatly influenced by non-Western arts and Dadaism. Artists sought fresh concepts in foreign music, such as Africa, Asia, and eastern Europe.

Light, lacy chords develop the shimmery and hazy atmosphere of Impressionistic music. Dissonance was usually left unresolved, creating irregular phrases and concealed cadences.

Rather than using triads and four-note chords as used previously, five-note combinations known as ninth chords (1-3-5-7-9) were brought up. This formed dissonant polychords of 6 and 7 notes.

It was the transition from the Romantic period to the Modern era. Though its duration was fleeting, Debussy and Ravel are considered some of the greatest composers.

Expressionism
Expressionism was the German response to French Impressionism. The Germans dug down to the depths of the soul, whereas the French explored the impressions of the outer world. Some composers influenced by this style was Arnold Schoenberg. The musical characteristics of Expressionism include wide leaps in the melody and the use of instruments in extreme registers.

Avant Garde
→Composers came back with shell shock →They were absolutely terrified and wanted to convey the horrors of war
 * 1) Harsh, experimental music
 * 2) Represents the fury of the world, a defiance
 * 3) It set out to express the unsayable
 * 4) Controversial
 * 5) Starts after World War 2

Characteristics
→Influenced by Russian folk music →He would take fragments of melodies and change them into something new
 * 1) Russian
 * 2) Most popular modernist of all
 * 3) Neoclassical and nationalist for the first half of his career
 * 1) Wanted to surprises his audiences through rhythm
 * 2) In the latter part of his career he began using the 12-tone system (after 1944)

Famous Pieces

 * 1) The Rite of Spring

Expressionism
Expressionism was the German response to French Impressionism. The Germans dug down to the depths of the soul, whereas the French explored the impressions of the outer world. Some composers influenced by this style was Arnold Schoenberg. The musical characteristics of Expressionism include wide leaps in the melody and the use of instruments in extreme registers.

Characteristics
→ The communist version of a modernist → Bound by the policies of Stalinism and the USSR → He tried to push the envelope with these policies and was sometimes criticized → I know it doesn't make any sense that he tried to push it and was still the best but he was
 * 1) Russian
 * 2) Social Realist
 * 1) USSR's star composer
 * 1) Had to be patriotic to Russia and serve the masses
 * 2) New music to reflect the new society (of the Soviet government)
 * 3) Always on the fence with Stalin's government, constantly risking prosecution because of the nature of Stalinism

Famous Pieces
→ It was sexual, about betrayal and murder → Stalin didn't like it → Was to be released while Stalin was on one of his purges → One note out of place would have meant his end → A triumph
 * 1) Lady Macbeth (Opera)
 * 1) 5th Symphony

title: IB Music/Music History/Modern Period


text:
Proteomics/Protein Chips/Applications

Applications:

Applications
Protein chips are a powerful resource which offers high-throughput methodology approaching that of DNA microarrays thus narrowing the gap between genomics and proteomics.

Protein chip experiments, like the field of proteomics itself, can be divided into two types of questions.
 * 1) Qualitative - What is it? What does it do?  Does it interact with anything?
 * 2) Quantitative - How much is there?

Protein chip applications are numerous and span the entire field. They include:
 * Probing a tissue extract for disease markers
 * Investigating protein-protein, protein-nucleic acid, and protein-drug interactions
 * Determining the amount of a protein in a particular sample
 * Identifying antibodies in a particular sample

Some specific examples of protein chip applications are:
 * Looking for hepatitis B antibodies in a human blood sample
 * Identifying biomarkers for ovarian cancer
 * Diagnosing SARS

Example Application
Zhu, H. et al. (2001) utilized protein chips in an effort to study the yeast proteome.1 Protein chips offer a high throughput method of analyzing such data. However, hurtles had to be cleared in order to over express the proteins from the proteome.

Zhu, H. et al. utilized high copy expression vectors and recombinant technology to clone 5800 ORFs from the yeast genome, which translates into approximately 80% of the yeast proteome. The expressed proteins were printed to the protein chips using a microarrayer and two varieties of protein chip surfaces: aldehyde-treated and nickel coated. Although both treatments were successful, the nickel coated chip was superior to the aldehyde-treated chip.

The group then checked the reproducibility of their protein spotting attempts. They found that more than 93% of the proteins were surely attached to the chip, and, in repeating the experiment, found that more than 95% of the proteins were correctly reproduced.

The main goal, or application if you will, of this experiment was to determine protein function. In order to do this, the proteins on the chips were tested for protein-protein and protein-lipid interactions.

The group provides a good example of how the results were interpreted. They probed the proteins on the chip for calmodulin binding functionality and observed both known and novel calmodulin binding proteins. Calmodulin is a calcium binding proteins that is highly conserved and is involved in many cellular processes. Through the analysis of the sequences of these proteins, Zhu, H. et al. were able to develop consensus sequences that identify motifs that should be associated with calmodulin binding.

Limitations of the study include confounding through indirect protein interactions and the possible absence of some post-translational modifications.

The effects of this study were to elucidate the potential of protein chips for observing protein - protein, protein - lipid, and protein - drug interactions within an eukaryotic cell's proteome. The paper for this study can be found here and a website containing supplemental materials can be found here.

Resources
1.Zhu, H. et al. "Global Analysis of Protein Activities Using Proteome Chips." Science 293.5537 (2001): 2101-2105. | View the paper.

title: Proteomics/Protein Chips/Applications


text:
Proteomics/Protein Chips/Manufacture

Manufacture:

Manufacture
Protein chips and DNA microarrays are manufactured in a similar fashion. Both involve spotting a biological component (such as DNA or proteins) onto a coated glass slide or other substrate such as gel pads and microwells. For protein chips, the slide must be coated with a substance that will bind the proteins without denaturing them. There are variety of binding methods available including absorption, cross-linking and hybridization.

Glass Slide Chips

Glass slide chips are advantageous because they can be used with standard microarray equipment and are inexpensive. They are prone, however, to evaporation of samples and cross contamination. The first methods for creating protein chips on glass slides involved placing the proteins in small gel pockets that were attached to the glass surface. The process then evolved to attaching the proteins with a crosslinking agent that coated the glass. This agent would bind to the primary amines on the proteins, while a 40% glycerol solution would prevent dehydration due to evaporation. Most array spotting is now done in a high humidity enviornment to control evaporation.

Well Chips
Using wells instead of coated glass slides reduces the problem of evaporation and cross contamination between spots. However, this method is more expensive and is not compatible with DNA microarray spotting equipment.

3D Matrix Gels
A third method is to use a 3D matrix created by polyacrylamide gel pads. This method limits evaporation and allows the proteins to remain in an aqueous environment. Additionally, this method allows for stronger binding of the proteins. Like the microwell method, this method is more expensive and can't be used with traditional DNA microarray spotting equipment.

Protein Attachment Methods
The surface of the chip must be modified to allow the proteins to bind properly. An attachment layer which usually consists of a sugary gel such as dextran-based hydrogel is coated onto the chip. The noise level for these types of attachment layers is high, however, because of the non-specificity of the medium. Cross-linkers can be used that covalently bind to certain groups on proteins, allowing for much more specific binding. The cross-linkers could, however, effect the conformation or activity of the proteins. It is important to remember that unlike nucleic acids, different proteins will be effected in different ways by the surface chemistry of the chip, i.e. a certain treatment will tightly bind some proteins but may denature others.

Protein Delivery Methods
Many protein chips made currently are spotted using automated technology, with spot densities greater than 30,000 spots per chip, though some low density chips may still be hand spotted. In addition to spotting, peptides can be synthesized on the chip via photolithography.

Manufacturer's Websites
Biacore - makers of SPR-based protein interaction analysis systems

Bio-Rad Laboratories - makers of the ProteOn XPR36 Protein Interaction Array System

Ciphergen - makers of the ProteinChip® System Series 4000

EMD - makers of the ProteoPlex 16-Well Human Cytokine Array

Invitrogen - makers of ProtoArrayTM

LC Sciences - makers of custom peptide microarrays for kinase profiling, epitope binding and other applications

Plexigen - makers of the geneCubeTM

SCHOTT - Manufacturers of NexterionTM coated slides for protein microarrays

Sigma-Aldrich - makers of the PanoramaTM Ab Microarray Cell Signaling Kit

title: Proteomics/Protein Chips/Manufacture


text:
Proteomics/Proteomics and Drug Discovery/Software Tools

This Section:

=Helpful Links, Resources, and Software=

These tools and databases are examples of the publicly available resources available to drug discovery teams. Private databases often contain the contents of publicly available ones as well.

Protein, Proteomics, and Drug Discovery Resources
Databases
 * NCBI The National Center for Biotechnology Information has databases on protein structure and sequences, nucleotide sequences, dozens of journals, and more.
 * Protein Data Bank (PDB)  The PDB is a repository of biological macromolecular structure data.

Applications
 * ExPASy Proteomics Server It contains many useful tools for protein sequence and structure analysis

Print/Web Resources
 * Drug Design by Landes Bioscience A free-access book on NCBI, this has good information about drug discovery.
 * Drug Discovery News Contains many free articles on current news and trends in drug discovery.
 * Biotechnology Information Directory This is a list of links in genomics, proteomics, and drug discovery.

Virtual Drug and Target Libraries
Free Libraries

 * Human Metabolome Database HMD is a free database with slightly under 2500 metaboites linked to over 5500 protein and DNA sequences that correspond to them.
 * National Cancer Institute (NCI) Database [search for Enhanced NCI Database Browser] This publicly available database contains over 250,000 compounds, along with detailed search features.
 * ZINC ZINC is a free library from UCSF containing an astounding 4.6 million searchable compounds in multiple formats with vendor links for ordering.

Pay-per-use Libraries

 * Available Chemicals Directory (ACD)  The ACD is a proprietary chemical database marketed by Elsevier MDL.  It contains over 480,000 unique chemical compounds; versions are available on a subscription basis for access at a number of academic institutions.
 * Quantum Lead Virtual Screening Services This pay per use library contains 50,000 compounds.  The company also offers other software for compound analysis.
 * Therapeutic Target Database (TTD)  The TTD contains information about known therapeutic protein and nucleic acid targets. Furthermore, it describes the targeted disease conditions and provides pathway information. Currently, the TTD includes 1535 drug targets and 2107 drugs/ligands (Chen).

Docking and Scoring Tools
The search space in a docking problem consists of all possible conformations (the relative positions of atoms in the 3D structure of a molecule, independent of the coordinate system) and configurations /orientations (the positions of atoms of a molecule after undergoing a rotation and translation in a coordinate system of the protein paired with the ligand). With present computing resources, it would be impossible to exhaustively explore the search space for all possible poses (a pose is the name given to the configuration of the conformation of a molecule in a coordinate system). Needless to say, every docking simulation is a trade-off between accuracy and speed and a good docking tool is expected to maintain a reasonably good balance between the two. The success of a docking program can be said to depend on depend on two components: the scoring function and the search algorithm. There are many competitive docking tools available from various sources, ranging from expensive and feature-rich corporate suites to simple yet powerful applications developed by academic/ research institutes.
 * A scoring function discriminates correct (experimentally verified) docking poses from incorrect ones. It estimates the binding affinity between ligand and receptor.
 * A search algorithm finds the best docking pose measured by the scoring function

DOCK
DOCK was developed by the team led by Irwin Kuntz at the University of California, San Francisco (http://dock.compbio.ucsf.edu/). The most recent version, DOCK 6; is written in C++ and is functionally separated into independent components, thereby conferring program flexibility. The Kuntz lab provides source code for all programs and they are available free of charge for academic institutions, however industrial organizations are charged a licensing fee. Following are some of the applications cited by the authors for DOCK: The main DOCK executable is run command line from a standard unix shell and windows users need to run it using a Linux-like environment like Cygwin. DOCK uses an “incremental construction” docking algorithm, which essentially means that the ligands are initially ‘fragmented’: The active site of the protein is identified by the program sphgen, which also generates the sphere centers filling the site. Scoring grids are generated by the program grid. The program DOCK then matches the spheres to the ligand atoms and uses the scoring grids to evaluate ligand orientations and finally minimizes the energy based scores. A comprehensive tutorial for DOCK 6 and the docking process in general can be found here: http://www2.umdnj.edu/~kholodvl/tut/DOCK60_intro_linux.pdf
 * predict binding modes of small molecule-protein complexes
 * search databases of ligands for compounds that inhibit enzyme activity
 * search databases of ligands for compounds that bind a particular protein
 * a base ‘anchor’ is selected
 * the anchor fragment is placed/ anchored to the active site
 * followed by incremental addition of the other fragments

GLIDE
Glide is a commercial product marketed as “A complete solution for ligand-receptor docking” by Schrödinger (http://www.schrodinger.com/). Some of the highlights of the tool include:
 * A range of speed vs accuracy options, from the HTVS (high-throughput virtual screening) mode for millions of compounds, to the SP (standard precision) mode, to the XP (extra precision) mode with advanced scoring.
 * User-friendly interface: Glide automates calculations for large libraries of compounds and organizes docking results in both summary and detailed reports. The ‘Maestro’ user interface provides advanced visualization and analysis tools to examine ligand-receptor interactions.
 * Cross-platform (Linux, SGI, and IBM/AIX) and Parallel processing support.

Glide uses a “Stochastic Search” docking algorithm. The algorithm approximates a complete systematic search over ligand positions, orientations, and conformations in the receptor site. The energy minimization stage utilizes the Monte Carlo simulation algorithm.

The enhanced features and easy-to-use interface of Glide, however comes at a cost that is both financial and computational.

Yucca
Yucca is a very recent and new algorithm specifically for small molecule docking, developed by Vicky Choi at the Department of Computer Science, Virginia Tech. The algorithm (still under active development), is based on an efficient heuristic for local search and has been used in conjunction with the conformer generator OMEGA (Optimized Molecular Ensemble Generation Application) to generate a set of low-energy conformers. Yucca utilizes a “multiconformer” algorithm. The conformers obtained from OMEGA are then rigidly docked and the configurations are coarsely sampled. Each configuration is then improved locally to a local minimum.

Comparative evaluation of Yucca with the other existing algorithms seems to prove it to be a competitive tool, however it is still being developed and tweaked to add and improve features. Among the improvements being made are: the tool’s own conformer generator, a better scoring function, flexible receptor docking and virtual screening.

Other available software tools include: The Binding Affinity Prediction of Protein-Ligand server is a tool which can be used to calculate the binding energy of a non-metallo protein-ligand complex. AutoDOCK, like DOCK, attempts to determine the orientation of a compound in a drug target. AutoDOCK, being a docking and scoring package, also contains scoring functions. AutoDOCK has also been applied to the problem of protein-protein docking. A newer system that claims to use novel docking algorithms. FleXX is another widely used docking program, known for its speed compared to many other applications. Molecular docking server is an internet service that calculates the site, geometry and energy of small molecules interacting with proteins. ZLAB is free academically but requires a paid license through Accelrys commercially. It is a two-stage docking system with ZLAB performing initial FT calculations and RLAB optimizing the highest scoring hits.
 * BAPPL
 * AutoDOCK
 * Docking Study with HyperChem
 * FleXX
 * Molecular Docking Server
 * ZLAB

See the Wikipedia Molecular docking site for links to additional softwares.

Although there are currently, many applications that simulate intermolecular interactions, there is still much room for improvement. Newer applications and algorithms are being developed constantly and the struggle for the perfect balance between accuracy and speed remains one of the critical factors. For instance, Glide, in spite of being among the best performers in terms of accuracy and ease of use, loses out heavily on computational time. Institutionally designed packages such as DOCK and AutoDock also have strengths as they are constantly worked on and updated. Most such academic software, however are command-line based and pose a steep learning curve for most users. Various other problems such as flexible receptor docking (which is, at this point enormously computationally expensive) are still areas of active research.


text:
Parkour/Basic Moves/Parkour Roll

The Parkour Roll is a very important skill to learn properly. The purpose of this roll is to lighten the impact of a fall or landing during your run. Practice safe rolls without much speed or height at first, on grass.

Steps

 * Land on the heels of your feet. If your heels fall back on the ground - the roll you need to do is the back roll. You must maintain forward momentum for the front roll to have any purpose.
 * Keep your legs at a ninety degree (right) angle when you land. this will prevent you from injuring your knees, and keep your forward momentum.
 * Your hands should be out in front of you pulling you into this movement. It helps to form a diamond shape with the hands. Place the forearm that corresponds with the shoulder you are most comfortable rolling with on the ground.
 * Upon impact you should move your gaze down to your waist line and tuck your chin in.
 * Pull your shoulder forward with your hands. At the same time push off from your toes.
 * Roll onto your shoulder in a diagonal motion. Keep your legs tucked, so that your body is tense and strong.
 * Now from your shoulder roll onto the muscle surface of your gluteus maximus. If you roll onto your hip or the side of your pelvis, you'll probably end up bruising yourself.
 * Roll up on to one knee, and use the continuing momentum to come up on both feet. This last position will vary from person to person.

Visual Guides and Tutorials

 * Very Informative and Entertaining Beginner Parkour Roll Tutorial

title: Parkour/Basic Moves/Parkour Roll


text:
Cookbook:Chicken Paprikash

Ingredients

 * 1 whole chicken, cut up (skin optional)
 * Bacon grease, lard, or other fat
 * 2 standard-size containers of sour cream
 * Paprika
 * White or yellow onion, finely chopped
 * 2–3 cups (480–700 g) flour
 * 2–3 eggs
 * Water
 * Salt
 * Bacon grease or oil

Equipment

 * Big pot
 * Pan with lid

Chicken

 * 1) Brown the onions in a heavy skillet with some bacon grease until softened and well-colored.
 * 2) Add chicken. Brown rapidly, then season with paprika to taste.
 * 3) Turn heat down, add enough water added to cover the bottom of the pan, and cook on low. Keep covered but with the lid slightly cocked to prevent boiling.
 * 4) Proceed with the dumplings while cooking the chicken.

Dumplings

 * 1) Combine flour, eggs, and a pinch of salt with enough to make a dough. For dumplings to be ‘sticky’ inside, make a wetter dough; for all the way through, make a drier dough.
 * 2) Use a dessert spoon (or a melon baller for smaller dumplings) to drop pieces of dough into boiling salted water. To keep them from sticking to the spoon, let it heat up in the water.
 * 3) Let simmer until the dumplings float. Drain, put in a bowl with a tiny slick of melted fat, and keep them to one side in a warm place.

Assembly

 * 1) Once the chicken is fully cooked (160°F) and your dumplings are all done, stir dumplings and sour cream into the pan of chicken. Mix thoroughly but carefully to coat.
 * 2) Add more paprika until it is more pink (or orange) than white.
 * 3) Taste sauce; it may need more paprika or salt. Sometimes it is easier to remove the chicken, and then pour the dumplings and sour cream over the top to coat (when serving), depending on how big your pan is.

Notes, tips, and variations

 * Use seeded rye bread to sop up the sauce when you're done eating.

title: Cookbook:Chicken Paprikash


text:
Confederate States Government

The Constitution and Government of Dixie

Secession

 * /Election of Lincoln/
 * /Jefferson Davis/
 * /Battle of Galveston/

title: Confederate States Government


text:
Muggles' Guide to Harry Potter/Places/Riddle Manor

General Overview
Riddle Manor is the ancestral home of Tom Marvolo Riddle's Muggle father, Tom Riddle. For much of this story, it stands empty.

Extended Description
In Harry Potter and the Goblet of Fire we read the story of how Tom Riddle Sr. and his parents were found dead one morning fifty years ago, and how the gardener, Frank Bryce, was suspected of their murders until it was found that they apparently had not been murdered by anything, but had simply died... possibly of fright. We also see how Lord Voldemort has moved into that house, and we see him killing Frank. Other clues through the course of the book lead us to believe that Voldemort is using the house as his base of operations; in fact, according to what we are later told by Barty Crouch, he has moved his base of operations to Bartemius Crouch's house, where he and Wormtail take up residence after Mr. Crouch is placed under the Imperius curse. After Crouch's escape, Voldemort and Wormtail do return to Riddle Manor, and remain there until the end of the book.

While no direct mention of the Manor is made in other books, we do see some of its environs in Professor Dumbledore's Pensieve in Harry Potter and the Half-Blood Prince.

Analysis
Riddle Manor is not, strictly speaking, necessary. It is true that a shut-in, poverty-stricken girl like Merope Gaunt is most likely to become infatuated with the local lord of the Manor, as he will have all the appropriate accouterments – attendants, property, jewelery – and financial means to lift our poor peasant out of her downtrodden existence and into the lap of luxury. Though likely any reasonably well-off Muggle would have served the purpose, it is much more romantic if the lord of the manor falls for the peasant girl; and Merope seems to have been preconditioned to be romantic. One must assume that Riddle Manor is created purely to highlight the romance that Merope can force with her phial of love potion.

After the death of the Riddle family, the house, we are told, reverted to some mysterious people in London who tried, unsuccessfully, to rent it out. While we are never told who the people in London are, it is possible that they are, knowingly or otherwise, agents of Tom Marvolo Riddle, who could have assumed that he was the heir, being the late Tom Riddle's son. One wonders, though, whether he would not try to dispose of anything that reminded him of his Muggle father. As the house certainly must remind him of the late Tom Riddle, one must wonder why Tom Marvolo Riddle would choose to live in it.

While evidence in the text does indicate that Tom Riddle and Merope Gaunt did get married (Dumbledore uses the terms "husband" and "wife" to refer to them, and refers to Merope as "Merope Riddle" at least once), one wonders exactly how title to Riddle Manor got transferred. As the manor and lands were purely Muggle property, Tom Marvolo Riddle would have necessarily had to deal with the Muggles he hated, in order to secure his claim to the property and arrange agents to take care of it. One has a rather ludicrous image of Tom Marvolo Riddle, wand concealed up his sleeve, dealing with an army of faceless bureaucrats.

In fact, except for the one night when Frank Bryce was killed, we do not know where Voldemort was living. He could well have chosen to leave Riddle Manor that night for some place with less associations for him. Or he could have chosen to stay there, as a way of spiting his deceased father and grandparents. We do know that he was in the environs of Little Hangleton in June, when the Triwizard Tournament ended.

Greater Picture
It is tempting to believe that Voldemort created a Horcrux, the one embedded in the ring of the Peverells that Voldemort had stolen from his uncle Morfin Gaunt, via the murder of Tom Riddle Sr. Evidence in Harry Potter and the Half-Blood Prince is inconclusive: Riddle's conversation with Professor Slughorn, that we see in the Pensieve, suggests that Riddle did not yet know how to create a Horcrux. During that conversation, Tom asks about Horcruxes, and we see that Tom is wearing the Gaunt ring. It is possible that Tom had already created a Horcrux, in the ring, and his question is designed to put Slughorn more at ease about his abilities and ideas; we can see that the main thrust of his questions is more to do with the possibility of creating multiple Horcruxes. Dumbledore does state that Tom had no longer wanted to wear the ring once it was a Horcrux, and while this must be supposition on Dumbledore's part, he was usually accurate in his guesses. Additionally, we have Tom's look of triumph when he has received the information about Horcruxes from Slughorn; given the author's usual efficiency, we have to think that he has done more here than just hoodwink Slughorn. Tom must have gotten some real information from Slughorn to merit that amount of joy.

The author has stated that it was the death of Tom's father that allowed him to create his first Horcrux; presumably he only chose to hide the Horcrux away, rather than keeping it close to himself, when he had created a second one. This would imply that Dumbledore had made a trivial error; as mentioned, Dumbledore believed at that time that Tom knew how to make a Horcrux, but not that he had done so. Dumbledore likely believed that the ring had only been made into a Horcrux via the death of Moaning Myrtle; at that point, likely, Tom stopped wearing the ring, hiding it in the Gaunt shack, because he now had the Diary as a backup. In this case, Tom's look of triumph at the conclusion of his talk with Slughorn probably relates to his having learned that making multiple Horcruxes was possible.

It is possible that Frank Bryce's murder was used to create the final Horcrux of the set that Voldemort was planning; bringing the circle to closure, by generating the last piece of his "immortality" in the abandoned home of his hated father, would likely have appealed to Voldemort's sense of humour. It is also possible that Bertha Jorkins' death was used to create a Horcrux; at that point, he would have been keen to finish the full set, and would have had no way to know that Frank would so conveniently present himself. The author has stated in an interview that the sixth and final Horcrux was created by means of the death of Bertha Jorkins, which does make it more of a matter of expedience than a plan. This is borne out by the non-snake-like behaviour of Nagini when passing by Frank Bryce in the hallway; Nagini likely would have behaved quite differently if she had not already been carrying a fragment of Voldemort's soul.


text:
Template:GNU C Compiler Internals/Contents

Table of Contents

 * 1) GNU C Compiler Architecture. Compilation of an expression
 * 2) Compilation of a function
 * 3) Function calls
 * 4) Stackguard
 * 5) GEM Framework
 * 6) Function Overloading in C
 * 7) Return Address Defence
 * 8) Adding Syntactic Sugar
 * 9) Improving Code Style
 * 10) Security Enhancements
 * 11) Links
 * 12) Contributors


text: GNU C Compiler Internals/GCC 3.4

title: GNU C Compiler Internals/GCC 3.4


text: GNU C Compiler Internals/GCC 4.1

title: GNU C Compiler Internals/GCC 4.1