OpenLLM-France/wikimedia huggingface dataset:
# Radiation Oncology/Cervix/Preinvasive

* Front Page: Radiation Oncology | RTOG Trials | Randomized Trials
* Cervix: Main Page |
* Overview |
* Micro-invasive |
* Early Stage Non-Bulky |
* Early Stage Bulky |
* Locally Advanced |
* Brachytherapy |
* Cervix Randomized |
* GOG Trials |
* RTOG Cervix

## Overview

* Typically managed with close surveillance / cytology / HPV testing / LEEP / colposcopy
* Hysterectomy if repeat colposcopy / LEEP not feasible
* Role of radiation is somewhat controversial, particularly as older literature used "carcinoma in situ", which is no longer in the cytologic classification vocabulary

## Radiation

* Yonsei University, Korea; 2012 (1868-2005) PMID 22901420 -- "High-dose-rate intracavitary radiotherapy in the management of cervical intraepithelial neoplasia 3 and carcinoma in situ presenting with poor histologic factors after undergoing excisional procedures." (Kim YB, Int J Radiat Oncol Biol Phys. 2012 Sep 1;84(1):e19-22. doi: 10.1016/j.ijrobp.2012.02.045.)
** Retrospective. 166 patients with CIN3 (n=15) or CIS (n=151), diagnosed by conization or biopsy. Endocervical gland involvement (81%), positive margin (44%), ECC positive (31%). Treated with HDR tandem & ovoids. Point A. Dose 30/6 fxs (range 30-52). Median F/U 12.7 years
** Outcome: recurrence 2/166 patients
** Toxicity: 1 rectal bleeding, managed with conservative management
** Conclusion: HDR effective for CIN3/CIS, in patients with poor histologic features after excision
# Radiation Oncology/Cervix/RTOG Cervix

* Front Page: Radiation Oncology | RTOG Trials | Randomized Trials
* Cervix: Main Page |
* Overview |
* Micro-invasive |
* Early Stage Non-Bulky |
* Early Stage Bulky |
* Locally Advanced |
* Brachytherapy |
* Cervix Randomized |
* GOG Trials |
* RTOG Cervix
* RTOG Website
* Wikibooks list of RTOG trials
CERVICAL CANCER: RTOG OPEN TRIALS :
| Number | Title |
| 07-24 | Phase III Randomized Study of Concurrent Chemotherapy and Pelvic Radiation Therapy with or without Adjuvant Chemotherapy in High-Risk Patients with Early-Stage Cervical Carcinoma Following Radical Hysterectomy |
CERVICAL CANCER: RTOG CLOSED TRIALS :
| Number | Title | Publication PMID XXXXXXXXXX |
| 04-18 Clinicaltrials.gov | A Phase II Study of Intensity Modulated Radiation Therapy (IMRT) to the Pelvis +/- Chemotherapy for Post-Operative Patients With Either Endometrial or Cervical Carcinoma | |
| 04-17 Clinicaltrials.gov | A Phase II Study of Bevacizumab in Combination with Definitive Radiotherapy and Cisplatin Chemotherapy in Untreated Patients with Locally Advanced Cervical Carcinoma | |
| 01-28 Clinicaltrials.gov | A Phase I/II Study Of Cox-2 Inhibitor, Celebrex (Celecoxib), and Chemoradiation in Patients with Locally Advanced Cervical Cancer | PMID 17482376 PMID 17084549 PMID 18299147 PMID 19509178 |
| 01-16 Clinicaltrials.gov | A Two-Part Phase I/II Study Of Extended Field External Irradiation And Intracavitary Brachytherapy Combined With Chemotherapy (Weekly Cisplatin-Arm 1) And Amifostine (Weekly Cisplatin And Amifostine-Arm 2) In Carcinoma Of The Cervix With Positive Para-Aortic Or High Common Iliac Lymph Nodes | PMID 17398031 |
| 71-05 | [Split course vs continuous RT] | PMID 6406397 |
Review of RTOG Cervix trials:
# Radiation Oncology/Cervix/Protons

* Front Page: Radiation Oncology | RTOG Trials | Randomized Trials
Proton Therapy in Cervical Cancer

## Clinical

* Tsukuba; 2003 (1983-1991) PMID 12654436 -- "Long-term results of proton beam therapy for carcinoma of the uterine cervix." (Kagei K, Int J Radiat Oncol Biol Phys. 2003 Apr 1;55(5):1265-71.)
** Retrospective. 25 patients, SCC of cervix, Stage IIB-IVA. EBRT followed by proton boost, median total dose 86 Gy. Median F/U 11.6 years
** Outcome: 10-year OS IIB 89%, IIIB/IVA 40%; 5-year LC IIB 100%, IIIB/IVA 61%
** Toxicity Grade 4+ in 4%
** Conclusion: EBRT + proton boost effective for those not eligible for intracavitary RT

## Dosimetric

* San Diego; 2010 PMID 21081882 -- "Dosimetric comparison study between intensity modulated radiation therapy and three-dimensional conformal proton therapy for pelvic bone marrow sparing in the treatment of cervical cancer." (Song WY, J Appl Clin Med Phys. 2010 Aug 15;11(4):3255.)
** Planning comparison. 6 cervical patients (3 postop and 3 definitive). IMRT vs 3D-CPT
** Outcome: PTV dose conformity slightly better with PT. High dose regions (>V30), IMRT better. Low dose regions (V10, V20), PT better
** Conclusion: Further studies are necessary
# Radiation Oncology/Chemotherapy combinations

* Front Page: Radiation Oncology | RTOG Trials | Randomized Trials
This page is for listing chemotherapy combinations, e.g. CHOP.
    Note: pages may link directly to a particular chemo combination
need to add full info:
* VAMP/COP
* MOPP/ABVD
* MOPP/ABV
* CHOD/BVAM
* EBVP
* COPP (and COPP/ABVD)
* ABV
* AVD
* AV
* EVE
Chemocare.com Acronym list
# Raku Programming/Exceptions and Handlers
## Exceptions

In the most basic sense, exceptions represent errors that are caused by your program. However, instead of crashing your program, exceptions have the opportunity to be caught and handled gracefully. Exceptions are said to be raised or thrown, and special code blocks called handlers can catch them.
# Raku Programming/Grammars
## Grammars

Regular expressions by themselves are useful but limited. It can be difficult to reuse regexes, difficult to group them into logical bunches, and very difficult to inherit regexes from one bunch to another. This is where grammars come in. Grammars are to regexes what classes are to data and code routines. Grammars allow regexes to act like normal first-class components of the programming language and make use of the cool features of the class system. Grammars can be inherited and overloaded like classes. In fact, the Raku grammar itself can be modified to add new features to the language on the fly. We will see examples of that later.

## Rules, Tokens and Protos

Grammars are broken into components called rules, tokens and protos. Tokens are like the regexes we've already seen. Rules are like subroutines because they can call other rules or tokens. Protos are like default multisubs, they define a rule prototype that can be overridden.

### Tokens

Tokens are regex that don't backtrack meaning that if a portion of the expression has been matched, this portion will not be altered even if it prevents a larger portion of the expression from matching. While this sacrifices some of the flexibility of regexes, it allows more complex parsers to be created efficiently.

### Rules

Rules are ways to combine tokens and other rules together. Rules are all given names, and can refer to other rules or tokens in the same grammar using < > angle brackets. Like tokens they do not backtrack but spaces within them are interpreted literally instead of being ignored:
This rule matches a URL string where a protocol name such as "ftp" or "https" is followed by the literal symbol "://" and then a string representing an address. This rule depends on two sub-rules, <protocol> and <address>. These could be defined as either tokens or rules, so long as they are in the same grammar:

### Protos

Protos define a type of rules or tokens. For example, we could define a proto-token <protocol> and then define several tokens representing different protocols. Within one of these tokens, we can refer to its name as <sym>:
This would be equivalent to saying:
but is more extensible, allowing types of protocol to be specified later. For example if we wanted to define a new type of URL which also supported the "spdy" protocol, we could use:

## Matching Grammars

Once we have a grammar like the one defined above, we can match it with the .parse method:

## Match Objects

A match object is a special data type that represents the parse state of a grammar. The current match object is stored in the special variable $/.

## Parser Actions

A grammar can be turned into an interactive parser by combining it with a class of parser actions. As the grammar matches certain rules, corresponding action methods can be called with the current match object.
# Raku Programming/Introduction

The Raku programming language is the sixth major revision of Perl.
It was designed in order to tackle with the caveats that Perl had accumulated during its now long history. Those caveats were mainly due to a requirement of backward compatibility of successive versions of Perl. That's why Raku is the first version of Perl that is not backward-compatible.
Raku does not replace Perl. It is rather a sister language or, as some like to put it, the R&D branch of Perl. To some degree, Raku is to Perl what C++ is to C. Although C++ is very successful programming language, it has not in any way replaced C.
# Raku Programming/Junctions
## Junctions

Junctions were originally implemented as part of a fancy Perl module to simplify some common operations. Let's say we have a complex condition where we need to test variable $x against one of several discrete values:
This is a huge mess. What we want to do is basically create a list of values and ask "if $x is one of these values". Junctions allow this behavior, but also do so much more. Here's the same statement written as a junction:

## Types of Junctions

There are 4 basic types of junctions: any (logical OR of the components), all (logical AND of all components), one (logical XOR of all components), and none (logical NOR of the components).

### List Operators

List operators construct a junction as a list:

### Infix Operators

Another way to specify a junction is to use infix operators like we have already seen:
Notice that there isn't an infix operator to create none junctions.

## Matching Junctions

Junctions, like any other data type in Raku, can be matched against using the smart match operator ~~. The operator will automatically perform the correct matching algorithm depending on which type of junction is being matched.

### all Junctions

An all junction will only match if all the elements in it match the object $x. If any of the elements do not match, the entire match fails.

### one Junctions

A one junction will only match if exactly one of its elements match. Any more or any less, and the entire match fails.

### any Junctions

An any junction matches so long as at least one element matches. It could be one or any other number but zero. The only way for an any junction to fail is if none of the elements match.

### none Junctions

none junctions only succeed in a match if none of the elements in the junction match. In this way, it's equivalent to the inverse of the any junction. If any succeeds, none fails. If any fails, none succeeds.
# Raku Programming/Meta Operators
## Meta Operators

Operators do things to data. Meta operators do things to operators.

## Reduction Operators

Reduction operators act on a list and return a scalar value. They do this by applying the reduction operator between every pair of elements in the array:
The [ ] square brackets turn any operator that normally acts on scalars into a reduction operator to perform that same operation on a list. Reductions can also be used with relational operators:

## Hyper Operators

Reduction operators apply an operator to all the elements of an array and reduces it to a single scalar value. A hyper operator distributes the operation over all the elements in the list and returns a list of all results. Hyperoperators are constructed using the special "french quotes" symbols: « and ». If your keyboard doesn't support these, you can use the ASCII symbols >> and << instead.
You can also use unary operators with hypers:
Unary hyperoperators always return an array that is exactly the same size as the list it is given. Infix hyperoperators have different behavior depending on the sizes of its operands.
Pointing the hyper symbols in different directions affects how Raku treats the elements. On the sharp side, it extends the array to be as long as the one on the dull side. If both sides are sharp, it will extend whichever is smaller.
Hypers can also be used with assignment operators:

## Cross Operators

The cross is a capital X symbol. As an operator, the cross returns a list of all possible lists made by combining the elements of its operands:
The cross can also be used as a meta operator, applying the operator it's modifying against every possible combination of elements from each operand:
# Spanish/Haber

Verbs

# Haber

"Haber" is an irregular verb that means "to have" in the sense of having done something, or "there is" or "there are". It is used mostly as an auxiliary verb to form the perfect compound tenses (has/had done, etc.)
    Infinitive: haber
    Present Participle: habiendo
    Past Participle: n/a

## Indicative
### Present

(aka Present Perfect)
(hecho is the :Past participle: of hacer, meaning "to make" or "to do". Here, it means "done".)
    Yo he hecho I have done
    tú has hecho You (informal) have done
    él/ella/usted ha hecho He/she has, you (respectful) have done
    nosotros hemos hecho We have done
    (vosotros habéis hecho) You (plural, informal) have done
    ellos/ustedes han hecho They / you (plural, formal) have done
    hay There is / there are (special form)
(Don't know what Yo, tú, él, and so on mean ? They are pronouns.)

### Imperfect

(aka Pluperfect)
    Yo había hecho I had done
    tú habías hecho
    él/ella/usted había hecho
    nosotros habíamos hecho
    (vosotros habíais hecho)
    ellos/ustedes habían hecho
    había There was / There were (Special form)

### Preterite

Haber is used in the preterite exceedingly rarely. Mostly it is used as a literary tense.
    Yo hube hecho I had done
    tú hubiste hecho
    él/ella/usted hubo hecho
    nosotros hubimos hecho
    (vosotros hubisteis hecho)
    ellos/ustedes hubieron hecho
    hubo There was / There were

### Future (Perfect)

(aka Future Perfect)
    Yo habré hecho I will have done
    tú habrás hecho
    él/ella/usted habrá hecho
    nosotros habremos hecho
    (vosotros habréis hecho )
    ellos/ustedes habrán hecho
    habrá There will be
— or —
    Yo voy a haber hecho I will have done / I'm going to have done
    tú vas a haber hecho
    él/ella/usted va a haber hecho
    nosotros vamos a haber hecho
    (vosotros vais a haber hecho)
    ellos/ustedes van a haber hecho

## Subjunctive
### Subjunctive

    Yo haya hecho I may have done or (if) I have done etc.
    tú hayas hecho
    él/ella/usted haya hecho
    nosotros háyamos hecho
    (vosotros hayáis hecho)
    ellos/ustedes hayan hecho
    haya There may be

### Imperfect Subjunctive

    Yo hubiera hecho I might have done or (if) I had done
    tú hubieras hecho
    él/ella/usted hubiera hecho
    nosotros hubiéramos hecho
    (vosotros hubierais hecho)
    ellos/ustedes hubieran hecho
    hubiera There might have been
— or —
    Yo hubiese hecho I might have done or (if) I had done
    tú hubieses hecho
    él/ella/usted hubiese hecho
    nosotros hubiésemos hecho
    (vosotros hubiesein hecho)
    ellos/ustedes hubiesen hecho
    hubiese There might have been

## Conditional

    Yo habría hecho I would have done
    tú habrías hecho
    él/ella/usted habría hecho
    nosotros habríamos hecho
    (vosotros habríais hecho)
    ellos/ustedes habrían hecho
    habría There would be
# Spanish/History

Here is a little history about the development of this Wikibook, detailing milestones since the beginning of the project.

### 1 Jun 2006

* 109 pages under Spanish namespace
* 29 pages outside of Spanish namespace
* 31 pages linked to from main page
   * 1 entry page
   * 10 lessons
   * 3 vocabulary
   * 3 grammar
   * 4 verbs
   * 4 learning tools
   * 3 "and more" pages
   * 1 history of the project
   * 1 list of contributors
   * 1 requests page
* 10 lessons complete (one more linked to but as of yet unedited)
* 2 stubs
* Index of sound files (but all links are broken)
* 14 exercises
* 8 external links
* 8 users listed as main contributors

### 03 Oct 2003

* 6 lessons complete with vocabulary, grammar, and exercises
* about 10 exercises (all of which are "fill in the blank" type of exercises)

### 25 Aug 2003

* Most titles now in both Spanish and English
* Index of soundfiles
* First exercise (regular verbs)

### 16 Aug 2003

* Introduction
* 8 Lessons (3 lesson with more than just mere vocabulary)
* 4 Appendices (Characters, Slang, Verb Tenses, Web Resources)
* A handful of images and sound files
* A total of about 10 users have contributed to the book
* Talk page contains a huge number of potential topics

### 09 Aug 2003

* Introduction
* 6 Lessons (1 lesson with more than just mere vocabulary)
* 1 Appendix (Slang)

### 02 Aug 2003

* Spanish took off as the first Wikibook on a foreign language
# Spanish/Future

Spanish/Verbs
I will think, he will shout, you will die, ...
Pensaré, gritará, morirás, ...
— or —
Voy a pensar, va a gritar, vas a morir, ...
There are two ways to communicate future events in Spanish. In the first one, add an ending to the unchanged infinitive form of the verb. These same endings are used for all three types of verbs (-AR, -ER and -IR), which makes learning them easier:
-é
-ás
-á
-emos
-án
Pensaré: I will think
Pensarás: you will think
Pensará: it will think
Pensaremos: we will think
Pensarán: they will think
Iré: I will go
Irás: you will go
Irá: she will go
Iremos: we will go
Irán: y'all will go
There are 12 verbs which change their infinitives before adding the ending, and they can be classified into 3 catigories: First, the "drop 'e's" are "querer," "poder," "caber," "haber," and "saber." Each of these loses the 'e' before the final 'r' when forming the future tense. These can be remembered by the mnemonic "Quick People Can't Have Sushi." Next, the "add 'd's" are "venir," "valer," "salir," "tener," and "poner." For these, the 2nd to last letter of the infinitive is replaced with a 'd'. These can be remembered by the mnemonic "Vroom Vroom, Said The Porsche." Finally, the verbs "decir" and "hacer" change their infinitives to "dir" and "har" respectively before adding the ending. These must simply be memorised.
The alternate way to describe the future is to use the present tense of "ir," followed by the infinitive of the action verb.
Voy a saber: I am going to know
Vas a mentir: You are going to lie
Va a cazar: He/she is going to hunt
Vamos a contar: We are going to count
Van a poner: They are going to put
# Spanish/Grammar Index

* Parts of Speech
* Personal pronouns
* Gender of nouns
* Formation of the feminine in nouns
* Formation of the feminine in adjectives
* Matching adjectives
* Word Order
* Diminutives
* Tener que ...
* Tener ganas de ...

## External links

* Gramática y Ortografía de la Universidad de Indiana Grammar and Spelling from the University of Indiana
* Learn Spanish Online Free Spanish lessons
* Notas sobre la gramática del diccionario de la Universidad de Chicago University of Chicago Spanish dictionary grammar notes.
* Tutorial de la gramática Grammar tutorial from StudySpanish.com
# Spanish/Gerund

This conjugation is the equivalent of -ing in English (ex. I am talking. Estoy hablando.)
* It is used to indicate an action that is continuous.
* for -er and -ir verbs the suffix is -iendo
* for -ar verbs the suffix is -ando
Escribir--->Escribiendo writing Correr----->Corriendo running Crear------>Creando creating
# Spanish/Gustar

Gustar only uses the third person singular and plural forms, along with a direct object pronoun: me, te, le, nos, os, les. For example:
Me gusta el perro. I like the dog. Me gustan los perros. I like the dogs. Te gusta el perro. You like the dog. Te gustan los perros. You like the dogs. Le gusta el perro. She like the dog. Le gustan los perros. She like the dogs.
Nos gusta el perro. We like the dog. Nos gustan los perros. We like the dogs. Vos gusta el perro. You like the dog. Vos gustan los perros. You like the dogs. Les gusta el perro. They like the dog. Les gustan los perros. They like the dogs.
There are several verbs like this, such as encantar, fascinar, importar, chocar, and flipar, and are referred to as gustar-type verbs
Back to Spanish.
# Structural Biochemistry/Enzyme Catalytic Mechanism/Glutathione Reductase
## General Information

Oxidation-reduction enzyme
Uses coenzymes NADP+/NADPH and FAD/FADH2
In humans, this is a dimer of 478-amino acid subunits linked by disulfide bond
Two-stage reaction
1st stage: E + NADPH + H+ EH2 + NADP+
Oxidized E binds NADPH, immediately reduces FAD, producing NADP+.
E contains redox-active disulfide bond (Cys58-Cys63), which has accepted an electron pair in EH2 to form a dithiol (one S- is in a charge transfer complex with FADH-)
2nd stage: EH2 + GSSG E + 2GSH
GSSG binds to EH2
Cys58 nucleophile attacks one S of GSSG yielding mixed disulfide, promoted by His467' acting as general base
One GSH is kicked-off by protonation by His467' (general acid)
Cys63 nucleophile attacks Cys58 to form redox-active disulfide, kicking off second GSH

## Reference

http://books.google.com/books?id=fSORbNITJ0QC&pg=PA6&lpg=PA6&dq=acid+base+enzyme+catalysis&source=bl&ots=SA3h6Afvdc&sig=0VpMXdejjvFQ7HdfgjSTt3602lQ&hl=en&ei=j48YS8qECouotgPajcyHBw&sa=X&oi=book_result&ct=result&resnum=8&ved=0CCsQ6AEwBw#v=onepage&q=acid%20base%20enzyme%20catalysis&f=false
# Structural Biochemistry/Enzyme Catalytic Mechanism/EcoRI
## Overview

Escherichia coli (EcoRI) is an endonuclease enzyme that is located in the restriction modification system. EcoRI is also isolated from the E. coli strain. EcoRI DNA is responsible for the specificity of E. coli strains harboring the fi+ drug resistance transfer factor RTFI. This is due to the introducing of two single strands staggered within the recognition sequence. Since EcoRI enzymes are considered to be the simplest sequence-specific DNA enzymes, they are well suited for the study of DNA sequence recognition by proteins. It is also possible to potentially compare two proteins interactions with the same DNA sequence using this enzyme.
http://www.scq.ubc.ca/wp-content/endonuclease2.gif
It is extracted from strains of E. coli and is part of the restriction modification system. In molecular biology, it is used as a restriction enzyme and it creates sticky ends with 5' end overhangs. The nucleic acid sequence where the enzyme cuts is GAATTC and the complementary sequence is CTTAAG. EcoRI is used in a wide variety of molecular genetics techniques including cloning, DNA screening and deleting sections of DNA in vitro. Restriction enzymes like EcoRI that generate sticky ends of DNA are often used to cut DNA prior to ligation, as the sticky ends make the ligation reaction more efficient. EcoRI can exhibit non site-specific cutting, known as star activity, depending on the conditions present in the reaction. Conditions that cause activity when using EcoRI include low salt concentration, high glycerol concentration, excessive amounts of enzyme present in the reaction, high pH and contamination with certain organic solvents. A procedure for large scale isolation of Escherichia coli RI endonuclease in high yield has been developed. The purified enzyme is homogeneous as illustrated by polyacrylamide gel electrophoresis and analytical sedimentation.

## References

1. Modrich, Paul, and Donna Zabel. EcoRI Endonuclease: Physical and Catalytic Properties of the Homogenous Enzyme. USA: The Journale of Biological Chemistry, 2 Mar. 1976. PDF.