OpenLLM-France/wikimedia huggingface dataset:
# Structural Biochemistry/Nucleic Acid/RNA/RNA modification

RNA modification must be performed in order to form the various proteins needed for eukaryotes to function. RNA modification generates mature RNA. Through RNA modification, a eukaryotic cell can use fewer variations in base pairs of the genetic code (DNA and RNA) while creating proteins with diverse functions. One of the most common methods employed by eukaryotes is to use spliceosomes to cleave out introns (intervening sequences/ non coding proteins) of the pre-RNA, leaving only exons (expressed sequences/coding proteins). Cutting out the intron segments allows for the possibility of exon to rearrangement. Spicing all exons together is called mature mRNA.
What's the advantage of spitting genes? Exons are segments that coding proteins and give proteins specific functions. This leads to the concept of exon shuffling. Exons shuffling is the rearrangement of the exons in the mRNA. These mRNA will come up with different types of proteins with different functions, binding sites, and catalytic sites. This path could lead to the evolution of new proteins.
Even though the use of exons and introns are quite common in eukaryotes, such practice is rarely performed by prokaryotes. In addition, evolution has shown that DNA sequences of genes encoding proteins were conserved. They showed that introns were once appeared in the prokaryotes' ancestral genes, and were vanished over time. The reason for this might be because such processes are not time efficient. Time efficiency is very important for prokaryotes because they multiply at a very fast rate.
# Structural Biochemistry/Nucleic Acid/RNA/RNA modification/RNA Splicing

RNA splicing takes place after RNA is transcribed from DNA, but before RNA is translated into mRNA. Splicing takes out the interfering sequences (introns) from the expressed gene sequence (exons). Small nuclear RNAs (snRNAs) contain less than 300 nucleotides and are located within the nucleus. They are mainly used for splicing mRNA precursors and are labeled as U1, U2, U3, U4, U5, and U6.
Small Nuclear RiboNucleoprotein Particles (snRNPs) are the secondary molecules made of small nuclear RNAs (snRNAs) and specific proteins. snRNP molecules make up the larger splicosome molecules. U1 snRNP recognizes the binding site on the 5’ end and the six-nucleotide sequence of the U1 snRNA binds to the splice site on the pre-mRNA. From this, the spliceosome will assemble along the pre-mRNA molecule. The U2 snRNP will bind to the branch site on the intron with its complementary sequence between the U2 snRNA sequence and the pre-mRNA. The U4, U5, and U6 snRNPS then bind with the U1 and U2 complexes and form the necessary spliceosome. The splicing process itself begins with the U5 interaction with the exon sequence on the 5’ splice site. The U6 goes through intramoleculear reorganization after breaking from U4, which allows U2 to base pair and interact with the 5’ end of the intron, taking U1 out of the spliceosome. The U2-U6 complex forms a helix that forms the center of the spliceosome itself. U4 prevents U6 from splicing until the splice sites are correctly aligned. Once alignment has occurred, the transesterification reaction cuts the 5’ exon at the phosphodiester bond and produces a lariat intermediate. Splicing continues with rearrangements with the spliceosome that will then produce the next transesterification reaction on the pre-mRNA. In the rearrangement, the U5 aligns with the 5’ exon so that it is easier to attack the 3’ splice site to produce another spliced product. To finish the splicing process, the U2, U5, and U6 release itself from the lariat intron.
# Structural Biochemistry/Nucleic Acid/RNA/RNA purification

RNA plays a variety of roles in gene expression, from messenger, catalysis to regulations. For instance, in E.coli, 80% of RNA is ribosomal RNA, 15% is transfer RNA, and only 5% is Messenger RNA. Messenger RNA is the template for protein synthesis. Since the amount of mRNA is relatively small, affinity chromotography must be performed to purify it.
This technique exploits the structure of mRNA,which is polyadenylated at the 3' end to form a Poly A tail. The Poly(A)n can pair with the complementary base Poly(T)n through the formation of Hydrogen bonds. The Poly(A) region is used to selectively isolate mRNA from the rest of the RNA via affinity chromatography. Only mRNA with Poly A can be bound by Poly T in the column. RNA that lack Poly A tails elute out of the column at high salt concentrations. The mRNA is separated for other RNAs. Then the Poly(A) mRNA can be washed out from column by adding a low salt eluting buffer.
Affinity chromotography is very useful for the purification of RNA and the synthesis of cDNA.
# Structural Biochemistry/Nucleic Acid/RNA/RNA modification/Exons
## General information

Exons are protein-coding segments and one of the two major divisions of DNA that is transcribed into RNA. All genes start with exons which are often interrupted by introns (non-protein coding segments). Exons received their name because they exit the nucleus and allow the DNA sequences to be expressed (prefix ex-comes from "expressed")$^1$. Exons are the actual part that contains codes for particular protein parts. The number of exons in DNA can vary from one species to another. Before the functional mRNA is formed, a splicing complex called spliceosome cleaves exons to bring them together, then removes all introns and connects exons to each other. Exons join together and travel out of the nucleus where they eventually code for proteins.

## History

Exons were first discovered in 1977 by American molecular biologists and Nobel Prize winners (1993) Richard Roberts and Phillip Sharp. They used electron microscopy to study mRNA and DNA hybrids. In the absence of introns, the entire region that is hybridized to the mRNA would be displaced. In their experiment, they observed regions that were not displaced, creating a loop that is indicative of an intron. Initially it was assumed that the sequence of both DNA and mRNA were identical or continuous. The result of their experiments revealed that DNA had stretches of bases not present in mRNA. Based on that they explained the nature of exons.

## Roles of exons

With the help of introns, exons can undergo recombination or exon shuffling. Crossovers occur in random, but homologous, positions at a frequency that depends on DNA length. Exon shuffling is a natural process that allows the formation of new functional proteins by creating new arrangements and thus new interactions with minimal risk to the sequence encoding of the functional parts. In the absence of introns, crossovers are likely to disrupt the exon sequence and often create a loss of function. Moreover, exon shuffling can produce new and useful proteins which lead to evolution. It encode different domains of the protein products with the processes of transcription, RNA processing, and translation.

## References

$^1$ Jerry Bergman, The Functions of Introns: From Junk DNA to Designed DNA
# Structural Biochemistry/Nucleic Acid/RNA/RNA modification/RNA Degradation

RNA degradation is a very ancient and important process. It is a physiological process of the cell cycle to maintain a balanced RNA concentration. To do this, cells secret an abundance of RNases, or ribonucleases, enzymes that help to break apart RNA. RNases play a significant role in cellular immune system by defending against RNA viruses, eradicating of old and non-viable RNAs, and manipulating of the nucleotides for RNA sequencing and gene expression. Viable RNAs avoid degradation by RNases by protecting themselves with “armors” such as the G-cap and the poly-A-tail. Also there are RNase inhibitors that bind to RNases, prohibiting them from cleaving RNA strands.
# Structural Biochemistry/Enteral

Definition The route of administration drug by which a drug taken into the body via the Gastrointestinal Tract and then it absorbs to the blood. It can be classified into three categories.
Categories
* Oral - Consumption of drug by mouth
* Rectal - Insertion of drug into the rectum
* Sublingual - Placement of drug under the tongue
Reference ROUTES OF DRUG ADMINISTRATION - P. Verma , IJPSR/Vol. I/ Issue I/July-September,2010/Pg.54-59
# Structural Biochemistry/Enzyme-Linked ImmunoSpot Assay (ELISpot)
## Overview

A modified version of the ELISA immunoassay, the ELISpot or enzyme-linked immunosorbent spot, allows for the detection of cells that secrete cytokines or antibodies. Unlike ELISA, ELISpot is able to detect a single cell that secretes a protein of interest making it one of the most sensitive cellular assays.
A quick and simplified procedure is listed below: 1) Cytokine-specific antibodies are placed onto an ELISpot plate 2) Cells of interest are then added 3) Cells become activated and begin to produce cytokine which binds to the antibodies 4) The cells are then removed whilst detection antibodies that can bind with the enzyme are added 5) Finally a substrate forms a colored spot the secreting cell 6) The cells are then counted through a microscope

## References

"The ELISpot Method Explained." ELISpot Info. MabTech, n.d. Web. 6 Dec. 2012. <http://www.elispotinfo.com/?page=elispot-method-explained>.
# Physics Textbook/Conservation of Momentum

Conservation of momentum states that in a given system,the total momentum is constant provided no external forces except collision act on it
# Physics Textbook/Energy Conservation Process: Light Energy

Light energy is the energy that allows us to see objects.
# Physics Textbook/Physics is a Way of Thinking

Physics is a way of thinking, a way of doing things, and a way of learning about the world around us.
Much information about the natural world is gathered through our five senses. Thus, the subject matter of scientific inquiry is sensory information, which is obtained through the use of our senses. Observations and experiences evolve into concepts. For example, the push or pull we experience in our muscles is conceptualized as force.
In physics, concepts take on meaning only as we operate with them, that is, we do something with them or about them, or use them in a special way. In this module, you will do laboratory investigations (anytime you can, if you can). You will also make estimates of human speeds or calculate the acceleration of a skater. You will also be required to design solutions to everyday problems and perform a series of tests on the solution you have provided, like in the following activity.

## Problem Solving and the Scientific Method

The following activity is an example of a problem that physicists, scientists, or engineers may be working on. Remember the moon buggy and the Mars explorer? These vehicles were actually designed and built for navigating and investigating extra-terrestrial locations. Concepts on forces and motion were considered in the design.
Activity 1.1 Balloon-powered Car
Materials
    2 large balloons
    drinking straw
    various materials to construct a race
Your Task
    To design, construct, and test a race car that:
* is powered by no more than two large balloons.
* is made from any materials available.
* must have at least three wheels. The wheels cannot be taken from a toy car, but from something that was not originally meant to be used as wheels.
* must remain in contact with the ground at all times.
* must be capable of traveling at least 5 meters.
Scientists do not just come up with one design—rather, they plan and work with several possible solutions to the problem. From a list of possible solutions, they select a few and start constructing the design which is most likely to work. Once a working model is available, they perform various tests to answer problems related to the design and construction aspects. Figure 1.14 outlines the steps that a problem solver like you can follow in coming up with a balloon-powered race car.
# Physics Textbook/Curved Mirrors
## Reflection at curved surfaces

For studying such reflection, all we do is draaw normals at each point on the curved surface and apply i=r on each of them. The curved surfaces we'll study would be sphere cutouts. No parabolic/hyperbolic mirror.

### Shed misconceptions

* Not every ray parallel to the principal axis is sent to focus after reflection. Geometrical optics formulae are valid only for paraxial rays (rays incident close to the pole; close is not a scientific term; exactly what range is close to the pole is dependent upon size of mirror, distance involved, etc).
* Not all rays are paraxial. The beam of ray (i) will be sent to focus, but (ii) will be sent to a point little away from the focus. We'll keep this in mind and developthese ideas little by little as we learn more of optics.
* Even objects which are of comparable size to the mirror can't be dealt with the formulae we derive.
* Formulae in geometrical optics are valid only for paraxial rays. Only the basic laws are universal.
What we have described above is exactly the reason why we use parabolic mirrors to focus parallel rays. Well, parabolic curves have the property of focusing each and every parallel ray of light to the axis on one point. Actually, a curve having this property is defined a parabolic curve [Ref. coordinate]

### Checkpoint

* Focusing. A beam of paraxial rays parallel to the principal axis converge to a point on the axis after reflection from a concave mirror [real image] [draw diagram].
* When such rays reflection from a convex mirror, they diverge away. However, the one who sees these rays feels they're diverging from a point behind mirror [visual image] [draw diagram].
These points are focuses, and their distance from pole is focal length.. Now, it so happens that the focal length for convex/concave mirror comes out to be R/2.

### Sign convention

* Direction of incident rays --> +ve x direction
* Principal axis --> x axis (-ve & +ve)
* Pole is the origin
* Height above principal axis, positive below principal axis, negative.
# Physics Textbook/Lenz's Law

Lenz's law is use to find the direction of flow of current due to induced e.m.f
It states that"the direction of the current always opposes the cause which produces it."
Lenz's law is also used to explain the law of conservation of energy.
# Physics Textbook/Physics is the Pioneer Science

Physics is the pioneer science. Its development into a full-blown science is largely attributed to the successful works of Galileo (1584-1642) and Newton (1642-1727). Moreover, the concepts of the younger sciences, like chemistry, are reducible to that of physics.
Like all other sciences, though, physics employs the scientific method. It deals with the basic nature of all matter and various ways that matter interacts with other matter.
Chemistry deals with the interaction between atoms and properties of substances that result from such interaction. Geology and astronomy are specialized sciences in which the basic principles of physics and chemistry are used to understand Earth and other heavenly bodies.
Biology is concerned with the nature of living things. You have learned that the cell is the basic unit of life. Inside the cell, particularly in the nucleus, are the molecules of deoxyribonucleic acid or DNA—the storehouse of information about different life forms in this planet Earth.
The boundary between sciences has been broken down. Most of the promising fields of research today lie at the borders of physics and other sciences. Some examples are biophysics, physical chemistry and chemical physics. The interface of physics, biology and chemistry is most important in the molecular and atomic levels.

## Physics and Mathematics

Physics has progressed using the tools of mathematics. On the other hand, mathematics has developed from its association with physics. Differential calculus and integral calculus were developed by Newton to cope with the problem of motion and rates. Vector analysis arose as a tool of mechanics.
# Physics Textbook/Impulse and Momentum

Momentum is product of mass and velocity of the object
Where p is momentum(kg•ms-1, m is mass, of the object(kg) v is velocity(in ms-1)
# Physics Textbook/Kinetic Energy

Kinetic Energy is the energy of moving things. Some examples are a moving car, bicycles, and thrown balls.
# Pokémon Crystal/Development/Sandbox Draft

This page was used for staging changes.
# Pokémon Crystal/Beginnings in New Bark Town
## Exploring New Bark Town (Optional)

New Bark town is a sleepy rural town with little to see.
South of the player home is the house where the family of Professor Elm lives.
To the southwest is a generic house.
The real attraction of the town is the Elm Pokémon Lab in the northwest corner of the town. Currently a man with long red hair is sulking in a nook next to the building. Try talking to him if desired, he'll just shove you a substantial distance away when he notices you.

## Visiting the Elm Pokémon Lab

When you are ready, enter the lab. Your character will automatically walk to the professor and talk to him. Professor Elm will ask the player to raise a Pokémon to help with his research. Elm then gets an email from Mr. Pokémon, and asks you to further help by meeting with him.
Inside you can pick from three different Pokémon: Chikorita (grass type), Cyndaquil (fire type), or Totodile (water type). Every time you select a Pokéball, you'll see a name, picture, and type given. Confirm the one you want to pick once you are sure.
After picking, you'll have the option to nickname the Pokémon. Nicknaming the Pokémon is a good idea if you want to make it a main party member. The gender of the Pokémon is shown on the upper left of the naming screen.
The player character will then automatically walk to Professor Elm, who explains that Mr. Pokémon lives past Cherrygrove City, a nearby settlement.
No matter which you pick, your Pokémon will be holding a berry, a nice held item. Before you leave the lab, Elm's assistant will stop you to give you a potion for your journey.
Before you leave New Bark Town, there are some optional dialogues you can partake in. Check the lower left bookshelves of the Elm Pokémon Lab for travel tips. Talk to townsfolk if desired, then head on.
When you are ready, go west and enter Route 29.

### Items

* Potion: Get this from the assistant in Prof. Elm's lab.

### Pokemon

* Chikorita: Pick from the three Starter Pokémon in Prof. Elm's lab. [MDN] (M=Morn;D=Day;N=Nite)
* Cyndaquil: Pick from the three Starter Pokémon in Prof. Elm's lab. [MDN]
* Totodile: Pick from the three Starter Pokémon in Prof. Elm's lab. [MDN]

## Questions

* Is having a rural lab conductive to some kinds of scientific research? Why?
* Email was a new and exciting technology for the general public at the time of release. If this game was released today, what technology would be showcased instead to excite the audience?
# Pokémon Crystal/About
## About this Wikibook

This Wikibook was created in 2006 by an IP user. Shortly thereafter it was deleted.
It was restored in 2021 and developed further from that point.
# Pokémon Crystal/Introduction
## About the game

Pokémon Crystal is an enhanced remake of Pokémon Gold and Pokémon Silver for the Nintendo GameBoy Color. This game features greater player customization, more animations, and additional content.
It later received a re-release for the Nintendo 3DS virtual console, with slight modifications to disable certain virtual console functions and to enable trading between 3DS systems and to the then current line up of Pokémon games.

## Differences

If you started playing Pokémon before playing this game, understand that there are a few major differences between this generation and others.
* Fairy typing for Pokémon did not exist this generation. Many Pokémon that become Fairy type in generation six onwards are simply Normal type in this game.
* This generation introduced Dark and Steel type Pokémon, adding important counters to many types, especially Psychic type.
# Pokémon Crystal/New Game

The game will ask if you are a boy or a girl, which determines the gender of the player character. This is mainly cosmetic. The player is then asked to set the time of the in game clock. You should probably set this to match your real world time.
Afterwards, Professor Oak introduces himself to the player and briefly explains the setting of the game. The player is then able to introduce themselves in turn by giving a name, either by entering a custom name or by choosing one of 4 presets. Custom names can be up to seven characters (Letters) long. Names can include both upper and lower case letters, as well as a few symbols, though not Arabic numerals.
The player is now able to begin the game in earnest, starting in the room of the player character. At this point the player character can now be moved, and the in game menu can now be accessed. This is a good time to save the game progress.
The room offers a good place to experiment with the game controls. Here are some things one can do to acclimate themselves to the game control scheme here:
* Inspect the radio to listen to a broadcast.
* Inspect the PC to manage item storage and room decorations.
* Inspect the television or bookcase for flavor text.
* Inspect the town map to see the regional map. The name is slightly misleading: This map is a map of the towns in the region, not a detailed map of any specific towns.
In the upper right hand corner of the room is are some stairs. Walk down the stairs to descend to the first floor where the mother of the player character is waiting at the table. Speak to her to learn about Professor Elm, as well as to receive the Pokégear. The Pokégear is essentially a PDA with phone functions, and could be compared to a smartphone from the 2010's or 2020's in terms of in game purpose. Initially the Pokégear functions solely as a mobile phone, though later on additional functions can be earned.
Talk to the other person in the room for some flavor text, and then head out through the red tiles in the southeast corner of the room, leading to New Bark Town.

## Questions

* In the late 1990's and early 2000's, consumer mobile phones were a new and emerging technology. Does the Pokégear represent a cultural zeitgeist about mobile phones of the time? How does it compare with later developments in mobile phones and smart devices?
* The room of the player features a radio, a television, a desktop computer, and other amenities. This is a fairly accurate depiction of a middle to upper class bedroom of the era. How does it compare to a modern bedroom today? What appliances are still present, and what have been merged into other devices or been eliminated?
# Pokémon Crystal/Exploring Route 29
## Introduction

This is the first of the many routes you will discover in the game. It is relatively safe and straightforward, and makes a good training area for beginners. On the other end of it lies your goal, Cherrygrove City.

## Training on the Way

Currently you do not have access to Pokéballs, so right now focus on training up your Pokémon and getting through to the next area. Beat about three Pokémon to raise the level of your starter to level 6. Defeat some more to reach level 7 with relative ease.
If you need to heal, you can head back to New Bark Town to use the healing machine in the Elm Pokémon Lab, use a healing item, or push on to Cherrygrove City to heal there.

## Walkthrough

Snake through the ledges to reach Cherrygrove City. In the upper right of the map, a free potion item can be found.
Midway through the route is a northern gatehouse with leads to Route 46. This is a mountainous road with sheer cliffs and can not be traversed from this direction, so simply keep on route 29. Instead continue and forage from a berry tree which can be found in the upper left for a berry. Continue west from here to reach Cherrygrove City.

## Route Info
### Items

* Potion: In the top righthand corner of Route 29.
* Berry: Berries are found in berry trees throughout the Game.
* Pink Bow: Get from a person, only after winning one badge and only on Tuesday. Powers up Normal-type Pokémon.

### Wild Pokémon

* Hoothoot - Nite
* Ratatta - Nite