OpenLLM-France/wikimedia huggingface dataset:
# Structural Biochemistry/Enzymes Used for Cloning

Enzymes that modify nucleic acids are used to synthesize, degrade, join, and/or remove portions of nucleic acids. Cloning enzymes are enzymes that are important in nucleic acid cloning procedures. The activities of the cloning enzymes consist of ligases, kinases, phosphatases, and RecA Protein.
DNA ligase, for example is used in joining DNA molecules together. Within the cell, the double ends of the strands are attached covalently. While RNA primers replace DNA during DNA replication, DNA ligase seals in the gaps.
1. Ligases are used to join nucleic acid segments, especially when one is cloning a DNA fragment into the vector DNA.
2. Phosphatases remove the 5′-phosphate from nucleic acid strands. This prevents vector downgrading, which would reduce the number of background colonies as well as producing substrate to which a kinase can attach a new radio-labeled phosphate.
3. Kinases add new phosphate groups to nucleic acids. This is usually done in order to label the nucleic acid fragments or the synthetically made oligonucleotide.
4. RecA Protein and AgarACE® Enzyme are used primarily to protect in certain cloning procedures or facilitate the nucleic acid purification. The E. coli RecA Protein is able to facilitate the pairing of homologous DNA sequences. AgarACE® Enzyme is a patented agarose-lysing enzyme produced for the harvest of DNA from agarose gels.
# Structural Biochemistry/Enzyme Regulation/Myristoylation
## General Info

One of the common covalent modifications of protein activity found in animals, palnts, and some viruses. It's donor molecule are Myristoyl CoA which is commonly used to modify protein called Src, main function of signal transduction. The myristoyl group is covalently attached to the N-terminal amino acid of a polypeptide. It is then catalyzed by the N-myristoyltransferase enzyme. It also plays an important role in membrane targeting in response to environmental stress on plants.

## Reference

http://www.ncbi.nlm.nih.gov/pubmed/9067626
# Structural Biochemistry/Enzyme Regulation/Transcription activation
## Overview

Transcription activation is the regulation by which a change in the rate of DNA transcription may alter the expressed gene in question. Regulatory proteins are utilized to activate an expression of a certain gene or to repress it (regulate). The activators catalyze interaction of RNA polymerase in the synthesis or expression of the gene in hand. This is accomplished by increasing the binding affinity of the RNA polymerase to the promoter site, the region of DNA that is vital in the transcription process. Transcription factors are activated, and transcription occurs at the promoter site. Histone interactions occur during acylation as DNA is transcribed into RNA.

## Mechanism

First, the binding of a ligand to a certain receptor occurs, initiating a reaction signal. This activates a transcription factor, which is a protein that binds specific DNA sequences and controls the rate of the transcription process. The transcription factor additionally binds to other reagents necessary in transcription. These proteins (transcription factors) are then able to be regulated by reversible regulation processes such as phosphorylation or proteolysis.
The transcription of DNA to RNA and its subsequent translation to proteins can be regulated by acylation and methylation. DNA is negatively charged and is wrapped around positively charged histone proteins. In order for transcription to occur the DNA must be unbound to the histones. This is accomplished by acylating the positively charged residues found in the histones such as lysine. This neutralizes the positive charge allowing for a looser binding with DNA. This allows RNA polymerase to enter and transcribe the desired gene. In order to reverse this effect and tighten the binding, methylation occurs. Methylation of the residues restores the positive charges to restore the electrostatic interactions between the histones and DNA and tighten the binding. It is in this method that gene expression is regulated.

## References

1. Berg, Jeremy M. (2007). Biochemistry, 6th Ed., Sara Tenney. ISBN0-7167-8724-5. pp. 902-903. 2. Campbell, Neil A. Biology. 7th ed. San Francisco, 2005.
# Structural Biochemistry/Enzymes Used in Molecular Biology

1. Type II restriction endonucleases: Enzymes cleave DNA at specific sequences to form DNA fragments. It cuts double stranded DNA at a specific base sequences. In prokaryote, enzyme is used to cleave foreign DNA molecules.
2. DNA ligase DNA ligase is an enzyme that joins two DNA molecules or fragments together They are used in cloning where the recombination DNA molecules occur. The DNA ligase can also be used in DNA replication.
3. DNA polymerase I DNA polymerase I (E.Coli) is an enzyme that fills gaps in duplexes by stepwise addition of nucleotides to 3'-ends for DNA sequence. DNA polymerase I is an important enzyme to be used in DNA sequencing, DNA replication, and PCR. It is used to insert the right nucleotides into a primer to start base-pairings.
4. Reverse Transcriptase Reverse Transcriptase is an enzyme to make a DNA copy of an RNA molecule. It is used in retrovirus reaction where genetic information flows from RNA to DNA. Retrovirus Reaction: single stranded RNA --(reverse transcriptase to synthesize RNA to DNA)--> double stranded DNA-RNA hybrid --(reverse transcriptase is used again to degrade RNA)--> single stranded DNA transcript --(reverse transcriptase to synthesize the second strand of DNA)--> double stranded DNA
5. Polynucleotide Kinase Polynucleotide kinase is added to a phosphate to the 5’-OH end to label or permit DNA/RNA in a ligation.
6. Exonuclease III Exonuclease III is an enzyme that removes nucleotide residues from 3’-end of DNA strand.
7. Alkaline Phosphate: Alkaline Phosphate is used to remove phosphates terminal.
# The History of Trench Wars/Writer's Note
## March 15, 2002

   The history of Trench Wars stretches over almost five years, from Trench Wars’ humble beginning as a hated “newbie” zone, to its current position as the most popular zone in all of Subspace. To present a fully accurate and complete history of all of Trench Wars is inevitably impossible. No, if few records survive from the early periods, or even a couple of years ago. The histories and stories live in the players, which unfortunately are never perfect as they are distorted by time, perspective and personal exaggeration.
   Even with all of these difficulties, I will attempt to present a history as complete and accurate as possible. Unfortunately as I do not have the time to do a fully complete survey, I will rely on my own personal knowledge with some help from outside. If you do spot an error or omission, please feel free to let me know, as I apologize in advance for any errors I might have made. In fact in light of the fact that the history mostly lives inside all of us instead of having real solid written evidence, I will attempt to portray this history in the style of the great Greek historians Herodotus and Thucydides.
   No history of Trench Wars is complete if we do now know about the history of the game and see how we got here, and how it was Trench Wars that ultimately became a leader in Subspace. This will be a bit long, and I’m sorry if you don’t like reading, but I feel that it’s necessary to have a lot of material in order to cover the complex history of the zone. Yet even though it is so long, I will not be able to mention every single player who ever played in the zone. I will concentrate on what I think were the greatest trends and events in the zone and focus on that, with mentioning names to humanize the context.
   I would also apologize for the lack of history for the last year, but this is mostly due to my leave of the zone and so my lack of knowledge of events. Hopefully most of you know enough about this time that it doesn’t matter.
   Finally I will have to state that this history is presented in my own view of things. This means a view centered mostly in Elim, in the Warbird leagues and in the workings of the middle levels of Staff of which I was part of for over a year. This by no means represents the view of an unbiased observer, but I have taken great pains to present both sides of the store. Yet for all of that, I will refer to myself in the third person, as this isn’t really my story, but the story of the zone.
   As readers of the Trench Wars UBB undoubtedly know, I do like writing a lot, but I am by no means an English major. I also do enjoy history, and so my aim in writing this is to share all that I have learned in my years in this zone, and that hopefully after reading this, you the players of Trench Wars will learn a bit more about how the zone got to where it is today.
       -Epinephrine
       Originally Written: February 23, 2002
Pre-History →
# The History of the Native Peoples of the Americas

* The History of the Native Peoples of the Americas
* This project discovers the history of the indigenous peoples of North, Central, and South America and the Caribbean Islands. All aspects of each people is discussed such as politics, art, technology, social structure, etc. The information in this text is organized by individual cultures by region.
* Introduction - The First People in the New World
* Discusses how the New World came to be populated and describes the earliest pre-historic cultures of Native Americans.
* Chapter 1 - Mesoamerican Cultures
* Mesoamerica stretches from central Mexico to Central America. Mesoamerican cultures were largely sedentary and agricultural. They had centralized political systems, a sophisticated understanding of astronomy and mathematics, had methods of writing, and a shared core religious belief system.
* Chapter 2 - Andean Cultures
* The Inca built a vast empire high in the Andes
* Chapter 3 - Amazonian Cultures
* The natives of the jungles of the Amazon
* Chapter 4 - Caribbean Cultures
* The first natives in contact with Europeans
* Chapter 5 - Southwest Cultures
* The mighty Apache and Navajo tribes
* Chapter 6 - Californian Cultures
* Tribes along the western coast of North America
* Chapter 7 - Northwest Cultures
* Natives of the Northwestern portions of America
* Chapter 8 - Great Basin Cultures
* Insert summary here
* Chapter 9 - Plateau Cultures
* Insert summary here
* Chapter 10 - Plains Cultures
* Insert summary here
* Chapter 11 - Southeast Cultures
* Insert summary here
* Chapter 12 - Northeast Cultures
* Insert summary here
* Chapter 13 - Subarctic & Arctic Cultures
* Insert summary here
* References
* Bibliographies, Appendices, and Glossaries can be found after each chapter.
# The History of Trench Wars/The Dark Days
## (November 1998 – May 1999)

With no more central billing server, and without the more secure version of the server client that VIE used, SS was in shambles. iNet quickly asserted itself as the central billing server for most of the old VIE zones that were now housed in different servers around the world. The VIE zones were now called SVS or Standard VIE Settings. The population dropped, and the greatest of the new zones had stabilized around 80 players during peak times. At this time, there was no guarantee that any zone, even Trench Wars would not languish in obscurity. The population reached an all time low at around 450 people on peak times during early 1999. Without the VIE server, cheating was now rampant everywhere and some of the most popular zones turned inwards and towards the old Pro League policy of putting a private list of players allowed to enter. Eventually that very same policy allowed for these zones to forever languish in population size. The stage was now set: Subspace would die and fade forever into obscurity, unless someone stepped up and something miraculous happened.
That something turned out in the form of Baudchaser, a player from Euro League who started the SSCx project. With the additional creation of the SS Council, every zone in Subspace was asked to join under the banner of SSC under the central billing server of iNet. SSCE (Pro League server), SSCU (iNet), and SSCX (a US West Coast server) were created. A server upgrade was given to the SSCx participants and some of the major cheats were blocked. But still there were gaps. Then the second miraculous event happened. At mid-1999, a single programmer decided to step up, and single-handedly create something, which in effect saved Subspace. And this is where our story really begins.
← Early History · The Archaic Age →
# The History of the Mental Health Consumer Movement

This is a book on the history of the mental health consumer movement.

## A History of Recovery

In researching the history of the mental health consumer-recovery movement, we come upon many obstacles. These obstacles range from a lack of clarity over terminology, miscommunication or misunderstanding of what recovery is.
When asking about the history being told to consider books by Dr. E. Fuller Torrey or the Williard suitcase exhibit which are quite interesting to any person who would be interested in learning about mental illness and the history of mental illness; but not necessarily about recovery. Other consumer efforts such as Patricia Deegan’s activism to reclaim the history of lives lost due to the uncaring mental health system of the past hundred years are by all means worthy to mention.
This is known as “recovery of our heritage as consumers.” Tragic as it is, and we do not want to disregard the waste of human life, this is not the history of recovery but the history we need to recover.
The history of recovery must be about recovery. In the Williard suitcase exhibit part of the work of Darby Penney and Peter Statsny “The Lives They Left Behind” also tells of more tragic stories of human lives disregarded and gives us a better understanding of psychosocial aspects of mental illness. But again the creation of the exhibit as well as the reclaiming of history are current events and therefore do not constitute the history of recovery but more so are the making of history that will endure.
Many users (clients) of mental health services refer to themselves as “consumers.” This term “consumer” is often resented by those being labeled as such. They feel that being a consumer erroneously signifies that service users have the power to choose services most suitable to their needs. Others feel it is an affirmation of “empowerment” as a part of the supply and demand cycle.
Those who object contend that consumers have neither choices, leverage, nor power to select services. Instead, some consumers refer to themselves as “survivors” or “ex-patients” to denote that they have survived what they experienced as oppression by the mental health system. This distinction can best be understood in its historical context.
Some may break down the Mental Health Consumer Movement into to two other movements such as the psychiatric survivor movement and the consumer movement; one side of the recovery spectrum as being more propsychiatry while the prior being more closer identified with the antipsychiatry movement.

## Chapters

* The Rise of the Consumer Movement
# Strategy for Information Markets/Information Cascades
## Conditional Probability

If $Pr(A|B)=$ "Probability of A given B" or "Probability of A conditioned on B"
then,
$Pr(A|B)={\frac {Pr(A\ AND\ B)}{Pr(B)}}$

### Bayes' Rule

$Pr(B|A)={\frac {Pr(A|B)Pr(B)}{Pr(A|B)Pr(B)+Pr(A|NotB)Pr(NotB)}}$

## Condorcet Jury Theorem
### Binomial Distribution

If the probability of one success is ${\text{ }}p$, then
$Pr(k{\text{ successes in}}\ n\ {\text{trials}})={\binom {n}{k}}p^{k}(1-p)^{(n-k)}$
while
* $p^{k}\$ stands for the probability of a particular ${\text{ }}k$ trial being a success
* $(1-p)^{(n-k)}$ stands for the probability of a particular ${\text{ }}(n-k)$ trial being a failure
and in math,
* ${\binom {n}{k}}={\frac {n!}{k!(n-k)!}}$

### Group Decision/Voting

In order to determine if a group decision/voting is correct, the number of successes ${\text{ }}C$ needs to be more than half of ${\text{ }}n$. The following formula derived from the Binomial Distribution Function tells the chance of the right group decision.
In the case here, by eliminating the situation that the vote is a tie, let's assume that the number of votes ${\text{ }}n$ is odd so that ${\text{ }}C$ could be more than half of ${\text{ }}n$.
Therefore,
$Pr(C)=\sum _{k={\frac {n+1}{2}}}^{n}{\binom {n}{k}}p^{k}(1-p)^{(n-k)}$

### Influence-Dependent Model of Group Decision/Voting

In daily lives, people usually make votes with other influences, instead of absolutely independent decision making. Let's derive another model to determine the probability of correct group decision on other influences.
Let
* $p=$ the probability of being correct
* $C=$ the group makes the correct decision (more than half of the votes are correct)
* $P_{I}=$ the probability of the influence being correct
* $\alpha =$ the probability of the voter following the influence to make decision
* $Pr({\text{Voter votes correctly}})=(1-\alpha )p+\alpha P_{I}$
* $P_{T}=Pr({\text{Voter Correct}}|{\text{Influence Correct}})=(1-\alpha )p+\alpha =$ the probability of the voter being correct if the influence is correct
* $P_{F}=Pr({\text{Voter Correct}}|{\text{Influence Wrong}})=(1-\alpha )p=$ the probability of the voter being correct if the influence is wrong
Therefore,
$Pr({\text{Group Correct}})=Pr({\text{Influence Correct}})Pr({\text{Group Correct}}|{\text{Influence Correct}})$
    $+Pr({\text{Influence Wrong}})Pr({\text{Group Correct}}|{\text{Influence Wrong}})$
$Pr(C)=P_{I}\sum _{k={\frac {n+1}{2}}}^{n}{\binom {n}{k}}P_{T}^{k}(1-P_{T})^{(n-k)}+(1-P_{I})\sum _{k={\frac {n+1}{2}}}^{n}{\binom {n}{k}}P_{F}^{k}(1-P_{F})^{(n-k)}$

## Central Limit Theorem

Let $x_{1},x_{2},...,x_{n}$ be a series of independently and identically distributed random variables. The mean of these variables is $\mu _{x}$ and the variance is $\sigma _{x}^{2}$.
Let $y={\frac {1}{n}}(x_{1}+x_{2}+...+x_{n})$.
When $n$ gets larger, $y$ gets closer to be a random variable that is normally distributed and has mean $\mu _{y}=\mu _{x}$ and variance $\sigma _{y}^{2}={\frac {\sigma _{x}^{2}}{n}}$
# SPM/The DCM Equation. 1. Motivation
## Networks in the Brain

Statistical Parametric Mapping (SPM) enables researchers to label which brain regions are significantly activated by an experimental task, relative to some baseline. The coloured blobs produced by SPM tell us which brain regions are involved in a particular task, but they say nothing about the network of brain regions used by the subject. In the simplest terms, we want to draw arrows between the coloured blobs, showing how information flows through the brain.
Dynamic Causal Modelling (DCM) enables us to ask questions about brain connectivity. Is brain region A responsible for the change in activation of brain region B? Where does sensory stimulus enter a network of brain regions? Which connections are modulated by factors such as attention?

## A DCM Experiment

The basic plan for a DCM experiment is as follows:
* Select the set of brain regions involved in a particular task. This will likely be guided by the results of a standard SPM analysis.
* Decide on a set of hypotheses for how these regions may be connected. Each hypothesis may have a different set of connections between regions, different places where external input enters the network, or different connections modulated by the experimental tasks or internal factors such as attention.
* Embody each hypothesis in a Dynamic Causal Model (DCM).
* Test each DCM for how well it describes the observed fMRI data (when combined with a model of blood-oxygen flow).
* Compare the models to select the best, or compare the strengths of individual connections between models.
Before we get on to the practical guide of how to implement a DCM experiment, we will start with the theory. At the heart of DCM is a state equation, and the first part of the tutorial describes what it is and how it works.
# SPM/Spatial smoothing

Spatial smoothing is usually performed as a part of the preprocessing of individual brain scans.
In SPM the spatial smoothing is performed with a spatially stationary Gaussian filter where the user must specify the kernel width in mm "full width half max". Kernel widths of up to 16mm are being used in the literature.
The purpose of spatial smoothing is to cope with functional anatomical variability that is not compensated by spatial normalization ("warping") and to improve the signal to noise ratio. In other words: smoothing increases statistical power. The less one smoothes, the less likely it is to obtain significant results. Understanding the exact impact of spatial smoothing on statistical power is not trivial: smoothing not only increases the signal to noise ratio of each voxel, it also reduces the number of resolution elements ("resels") that are assumed to be independent and used for correction of multiple testing. With respect to the signal to noise ratio, it is being argued that an ideal filter kernel matches the size of the signal to detect [1]. After all, the level of smoothing that is optimal for real, measured data can only be determined empirically [2] and it may make sense to reanalyze the same data with several levels of smoothing [3].
The drawback from smoothing is a loss of spatial precision. Especially when using larger smoothing kernels (and when separately estimating the local variance for each smoothed voxel, which has been the standard in SPM, including SPM2, [4]), one should keep in mind that the loss of spatial precision is more dramatic in the resulting t-map than in the images itself due to nonlinear effects on the voxel variances [5]. In the worst case, the maximum t-value may be located in an area with no signal at all (e.g. white matter).

## References

[1] Rosenfeld A, Kak AC (1982) Digital Picture Processing. New York: Academic Press
[2] Hopfinger JB, Büchel C, Holmes AP, Friston KJ (2000) Study of analysis parameters that influence the sensitivity of event-related fMRI analyses. Neuroimage 11:326–33
[3] Worsley KJ, Marrett S, Neelin P, Evans AC (1996) Searching scale space for activation in PET images.Hum Brain Mapping 4:74–90.
[4] Friston KJ, Frith CD, Liddle PF, Frackowiak RSJ (1991) Comparing functional (PET) images: the assessment of significant change. J Cereb Blood Flow Metab 11:690–699
[5] Reimold M, Slifstein M, Heinz A, Mueller-Schauenburg W, Bares R (2006). Effect of spatial smoothing on t-maps: arguments for going back from t-maps to masked contrast images. J Cereb Blood Flow Metab 26:751–759
# Compilation of SPM12 on Windows 10

This page describes the compilation of SPM12 MEX files on Windows 10 with MATLAB R2018b (9.5) and MSYS2 MinGW-w64 GCC.
If you use other versions of MATLAB and/or compiler, make sure that they are compatible: Supported compilers

## Installation of MSYS2/MinGW-w64

Download and install MSYS2 from:
in directory C:\msys64. Then, from MSYS2, type:

## Configuration of MATLAB compilation environment

Start MATLAB and type:
Do not worry if there is a warning:

## Compilation

In MSYS2, move to the SPM12 source directory with
then set the PATH appropriately
and then type the following to start the compilation process

## Notes for compilation with MSYS2 for Octave

Install mingw-w64-octave
then start Octave with:
and compile with: