OpenLLM-France/wikimedia huggingface dataset:
# Sikhism/Sri Guru Granth Sahib Ji

The Guru Granth Sahib Ji (ਗੁਰੂ ਗ੍ਰੰਥ ਸਾਹਿਬ}, gurū granth sāhib ji, or Adi Sri Guru Granth Sahib, is the holy scripture and the final Guru of the Sikhs. The book is sometimes referred to using the shortened title of Adi Granth which means First Volume.
The Guru Granth Sahib opens with the Mool Mantar (Main Chant or Root Verse):
Aykankaar (ੴ) Symbol of The Whole Universe and his only one creator. It is called By the name of Aykankaar
Sat Naam (ਸਤਿ ਨਾਮੁ ) Truth is his name
Kartaa Purakh (ਕਰਤਾ ਪੁਰਖੁ ) He is the creator of whole and continuously present in his creation
Nirbhao (ਨਿਰਭਉ ) He is without fear
Nirvair (ਨਿਰਵੈਰੁ ) He is without hate
Akaal Moorat (ਅਕਾਲ ਮੂਰਤਿ) He is timeless and without form
Ajoonee Saibhang (ਅਜੂਨੀ ਸੈਭੰ) He is beyond birth and death, The enlightened one
Gur Parsaad (ਗੁਰ ਪ੍ਰਸਾਦਿ) He can be known by the Guru’s grace
Jap Embrace His meditation
Aad Sach He was present in the beginning
Jugaad Sach He was present before the Yugas (ages) began.
Hai Bhee Sach He Is present now
Naanak Hosee Bhee Sach (Guru) Nanak (Dev Ji) says that he shall certainly be present in the future
Every Sikh is expected to memorize this prayer and recite it upon waking. It is a mantra that Sikhs meditate on and its place at the beginning of the Sri Guru Granth Sahib ensures that all that follows is connected to the Mool Mantar.
# Silesian

This handbook was written especially for those who want to get to know some basics of a very interesting Slavic language. Silesian is spoken in the south-west of Poland in the Silesia region. If you are interested in Polish, you'll probably be in love with Silesian too! After this course you will be proud to say that you can communicate at a basic level in this language.
The course starts from zero and was prepared for non-Polish speakers, but it will also come in handy for Poles interested in getting to know some Silesian, or the natives trying to refresh their knowledge, or learning the Silesian recent codification (this course is written in ślabikŏrzowy szrajbōnek which is the most popular Silesian spelling now, but I also mention about other common orthographies).

## Contents
### Basic learner's material

* Anfang – Introduction – A look at Upper Silesia, its languages, culture, history and people
* Bildōng we ślōnskij gŏdce – Learning Silesian – Learning an endangered language and using this handbook
* Wymŏwa – Pronunciation – Alphabets and pronunciation
* Ślōnsko-Angelski Dykcjōnŏrz – Silesian-English Dictionary – The dictionary containing each word from this course and more divided by subject

### Beginner level

* Lesson 1 - Alphabet and pronunciation
* Lesson 2 – Greetings and other basics
* Lesson 3 – What is that?
# Sikhism/Sri Guru Hargobind Ji

Guru Har Gobind (ਗੁਰੂ ਹਰਿ ਗੋਬਿੰਦ ਸਾਹਿਬ) also Sacha Badshah (ਸੱਚਾ ਪਾਦਸ਼ਾਹ True King) (19 June 1595–2 March 1644) was the sixth of the Ten Gurus of Sikhism and became Guru on 25 May 1606 following in the footsteps of his father Guru Arjan Dev. He was not, perhaps, more than eleven at his father's execution. Before ascension, he nominated Guru Har Rai, his grandson as the next Guru of the Sikhs.

### References

* ↑ Joseph Davey Cunningham (1853). A History Of The Sikhs. John Murray,London. {{cite book}}: Cite has empty unknown parameter: |coauthors= (help)
# Sikhism/Sri Guru Amar Das Ji

Guru Amar Das (Gurmukhi: ਗੁਰੂ ਅਮਰ ਦਾਸ) (5 May 1479 - 1 September 1574) was the third of the Ten Gurus of Sikhism and was given the title of Sikh Guru on 26 March 1552 at the age of 73, following in the footsteps of Sri Guru Angad Dev Sahib Ji, who died on 29 March 1552 at age 48. Das established his headquarters in the town Goindwal Sahib, which was established by Sri Guru Angad Dev Sahib Ji.
# Sikhism/Sri Guru Arjun Dev Ji

Guru Arjan Dev Ji or Guru Arjun Dev Ji (ਗੁਰੂ ਅਰਜੁਨ ਦੇਵ) (born in Amritsar, Punjab, India on 15 April 1563 – 30 May 1606 Lahore, Punjab, Pakistan) was the fifth of the Ten Gurus of Sikhism and became a Guru on 1 September 1581 following in the footsteps of Guru Ram Das. He was born at Goindval, and was the youngest of the sons of Guru Ram Das and Bibi Bhani, the daughter of Guru Amar Das. Before his death, he nominated his son Har Gobind as the next Guru of the Sikhs.

### References

* ↑ Mcleod, Hew (1997). Sikhism. London: Penguin Books. p. 28. ISBN 0-14-025260-6.
# Sikhism/Sri Guru Nanak Dev Ji

Guru Nanak Dev Ji (Guru Nānak) (15 April 1469 -22 September 1539) is the first of the ten Sikh Gurus. Sikhs believe that all subsequent Gurus possessed Guru Nanak's divinity and religious authority. Guru Nanak may be referred to by other titles such as Baba Nanak or Nanak Shah. Sikhs acknowledge Guru Nanak to be the founder of their religion and the composer of hymns found in their sacred scripture Guru Granth Sahib. The Sikh literature janam-sākhī (life stories) is the main source for the details of Guru Nanak's life.
Guru Nanak was born in 1469 in the village of Rāi Bhoi dī Talvandī (now called Nankana Sahib) in the Punjab to a family that belonged to the Hindu Khatrī caste. His father, Mehta Kalyan Das Bedi, was a patwari (accountant) for the village of Talwandi; employed by a local Muslim landlord, *Rai Bular Bhatti. Guru Nanak's mother was called Tripta Devi and his elder sister, Bebe Nanaki. Guru Nanak's family belonged to the Bedi clan. The word Bedi means "those who study the Vedas". A series of events during Guru Nanak's childhood led many to recognise his affinity with religious matters. At a very young age he is said to have surprised his teachers with his questions about God. He also refused the 'Janaeu' (sacred thread) that is traditionally given to a Hindu child who is ready to be initiated into the religious community. Guru Nanak was nine years old when this ceremony took place and when the Hindu priest asked Guru Nanak for the reasons of his refusal, Guru Nanak replied:
   Though men commit countless thefts, countless adulteries, utter countless falsehoods and countless words of abuse; though they commit countless robberies and villainies night and day against their fellow creatures; yet the cotton thread is spun, and the Brahman cometh to twist it. For the ceremony they kill a goat and cook and eat it, and everybody then says 'Put on the Janaeu'. When it becomes old, it is thrown away, and another is put on. Nanak, the string breaketh not if it is strong. (Asa di Var, Mohalla 1)
The priest in utter despair asked, What kind of sacred thread O Nanak, would you wear?
The Guru replied:
   Out of the cotton of compassion spin the thread of contentment. Tie knots of continence. Give it a twist of truth. That would make a Janaeu for the soul, if thou have it, O Brahman, put it on me. Such a thread once worn will never break nor get soiled, burnt or lost. The man who wears such a thread is blessed.
After the disappearance of Guru Nanak both Hindus and Muslims laid their claim to the Holy Body of Sri Guru Nanak Sahib but when they lifted the sheet covering the Sacred Body there was no trace of the Holy Body. Only fragrant flowers could be found which they distributed amongst themselves.
# Rebol Programming/Design Guide/Take advantage of return values

Many functions return useful values.
For instance, the INSERT function returns the series just past the insertion.
IF, EITHER, and most of the looping functions return the value of the block they evaluated.

### Don't use RETURN in every function you write

The last value evaluated is returned automatically in user-defined functions. While you can use the RETURN function to exit a function early and return a value, you do not need to use it in every function you write. One reason not to do so is that it is another function call, with the overhead that entails. Another is that using RETURN only for early exit scenarios (as you would use EXIT) makes those special cases more obvious.
# Rebol Programming/Examples

You may try out the following examples, launching do followed by one of the link below:
| http://www.rebol.com/view/demos/clock.r http://www.rebol.com/view/demos/retro-clock.r http://www.rebol.com/view/demos/easy-vid.r http://www.rebol.com/view/demos/effect-lab.r http://www.rebol.com/view/demos/emailer.r http://www.rebol.com/view/demos/feedback.r http://www.rebol.com/view/demos/gel.r http://www.rebol.com/view/demos/rebodex.r http://www.rebol.com/view/demos/vball-vid.r http://www.rebol.com/view/demos/paint.r http://www.rebol.com/view/demos/splash.r http://www.rebol.com/view/demos/bubbles.r | http://www.rebol.com/view/demos/warp-image.r http://www.rebol.com/view/demos/particles.r http://www.rebol.com/view/demos/tiger.r http://www.rebol.com/view/demos/tiger-boom.r http://www.rebol.com/view/demos/imagination.r http://www.rebol.com/view/demos/pointillize.r http://www.rebol.com/view/demos/rzoom.r http://www.rebol.com/view/demos/spiral.r http://www.rebol.com/view/demos/reb-circle.r http://www.rebol.com/view/demos/gismo.r http://www.rebol.com/rebgui-demo.r http://www.rebol.com/scripts/pongo.r |
or copy and paste in the console the code of the following examples:
# Rebol Programming/Foreword

This book covers the basics of Rebol programming, what REBOL actually does and why it's designed the way it is. It's not a reference manual and therefore doesn't contain a complete overview of all functions, but aims to teach the mechanics and principles of the language to give you a deeper understanding of it.
# Rebol Programming/Design Guide/Think Simple

Yes, think simple, but not simply.
Most beginner scripts are too complicated.
It is more difficult to write something simple and elegant.
Small, simple scripts are easier to read and maintain.
"A designer knows he has achieved perfection not when there is nothing left to add, but when there is nothing left to take away." -Antoine de Saint-Exupery
For example to return the days in a month you could write something like:
It works .... but is a bit long for what it provides.
This should be easier to follow and maintain:
Or we don't need to define a variable for the month block:
Now you might decide to make this a function so that it can be re-used or you might have that sneaking suspicion that because you needed this function someone else has already written it.
If you decide to make it a function, you now have the ability to add the leap-year decision.
# Rebol Programming/Design Guide/Use the shell

The command shell is a good way to test an idea or find a quick answer about a function.
In the shell, you can quickly display information about a particular function and its arguments.
In addition the SOURCE function can show you how other functions are written.
# Rebol Programming/Developer

Discuss available resources here ...

### Rebol.com

http://www.rebol.com -- Home of Rebol Technologies.

### Rebol.net

http://www.rebol.net -- Links to many other developer resources.

### Rebol.org

http://www.rebol.org -- Script library and searchable archive of the mailing list.

### RIX

http://babelserver.org/rix - Search engine indexing only sites related to Rebol.
# Rebol Programming/Installing Rebol
## Installing Rebol

Rebol/Core does not come with an installer. It's a simple executable file which starts the console when you execute it. When it's started, you can start writing and running Rebol scripts.

### Windows

Rebol/View for Windows comes with an installer which allows you to optionally install Rebol/View. If you choose to install Rebol/View, it adds registry entries that allows you to run Rebol scripts directly by doubleclicking them in File Explorer or another file manager.
If you choose not to install Rebol/View, you can run scripts through the Viewtop or the console, you can even add the registry entries manually, if you prefer.

### Linux

Rebol/View for Linux does not have an official installer like on Windows. There are installers made by fans that you can use at this site, remember to reboot your PC in order to initialize new fonts.
Official Rebol comes in a compressed archive, which can be opened using "tar" at a command line or using a graphical program like Xarchiver or File-Roller. Once extracted, Rebol/View can be run from the console just like Rebol/Core.
Rebol for Linux has some library dependencies, which can be determined by doing an "ldd rebol" in the console. For Rebol/Core, these are typically the C library, the math library, and the linker. On 64-bit systems a 32-bit library installation may be needed.
Rebol/View has more dependencies, since it is dependent on Xorg to display graphics. The list of dependencies for Rebol/View is long, and some distributions separate Xorg into many pieces, such as Arch Linux and Gentoo; make sure that all needed libraries are installed before running Rebol/View.

### OS X

Rebol for OS X requires OS X Jaguar to run.
# Rebol Programming/Design Guide/Use words not strings

A common mistake of beginners is to use text strings to dynamically compose code and data.
This is unnecessary, inefficient, and does not maintain the context of words appropriately.
All dynamic code and data can be composed directly with words, blocks, and data values.
This is also the best way to experience the power of REBOL dialecting.
For example:
# Rebol Programming/Design guide
## Design guide

The basis for this section is the Rebol Design Guide published by REBOL Technology.
The topics:
* Forget the past
* Think simple
* Scripts start with a header
* Data drives it
* Names are critical
* Use words not strings
* Code in style
* Embed your documentation
* Define the problem
* Use the shell
* Dialects are key
* Take advantage of return values
# Structural Biochemistry/The "fuzzy" interactome

The "fuzzy" interactome refers to the concept that the current protein-protein interactome is inaccurate. The research suggests that scientists are satisfied with the protein-protein interactome acquired through insufficient data and inconclusive lab results. Additionally, the study suggests that the current model for defining protein-protein interactions is overly simplified as it neglects several physiological variables.
The main foundation of the "fuzzy" interactome theory is the inability to perfectly replicate all physiological protein-protein interactions in the a lab setting. For example, many experiments do not consider the importance of unstable intermediates, which cannot be isolated. Additionally, results wrongly suggest that protein-protein interactions are extremely simple and can be mapped and identified through simple experimentation. As a result, the current protein-protein interactome tends to reflect the results of technology driven experiments as opposed to hypothesis driven experiments.
This conclusion emphasizes the difference between physiological conditions and what can be replicated in the laboratory.

## References

* G. Rickey Welch, The `fuzzy' interactome, Trends in Biochemical Sciences, Volume 34, Issue 1, January 2009, Pages 1-2, ISSN 0968-0004, DOI: 10.1016/j.tibs.2008.10.007. (http://www.sciencedirect.com/science/article/B6TCV-4V03JYW-1/2/286f850f0f310d9acb0f379eede62c0f)
# Structural Biochemistry/The Hypochromic Effect

The course of denaturation of DNA can be followed spectrophotometrically because the relative absorbance of UV by DNA solutions at 260 nm increases as much as 40% as the bases unstack. This absorbance increase is called hyperchromic shift

## Definition

Hypochromicity describes a material’s decreasing ability to absorb light. Hyperchromicity is the material’s increasing ability to absorb light.
The Hypochromic Effect describes the decrease in the absorbance of ultraviolet light in a double stranded DNA compared to its single stranded counterpart. Compared to a single stranded DNA, a double stranded DNA consists of stacked bases that contribute to the stability and the hypochromicity of the DNA.
When a double stranded DNA is denatured, the stacked bases break apart and thus becomes less stable. It also absorbs more ultraviolet light since the bases no longer forms hydrogens bonds and therefore are free to absorb light. Ways to denature DNA include high temperature, addition of denaturant, and increasing the pH level.

## Importance of Hypochromic Effect

The measurement of absorption of light is important in monitoring the melting and annealing of DNA. At the melting temperature (Tm), the DNA is half denatured and half double stranded. By lowering the temperature below the Tm, the denatured DNA strands would anneal back into a double stranded DNA. When temperature is above the Tm, the DNA is denatured.
Because melting occurs almost instantly at a certain temperature, monitoring the absorbance of the DNA at various temperature would indicate the melting temperature. By being able to find the temperature at which DNA melted and annealed, scientists are able to separate DNA strands and anneal them with other DNA strands. This is important in creating hybrid DNAs, which consists of two DNA strands from different sources. Since DNA strands can only anneal if they are similar, the creation of hybrid DNAs can indicate similarities between genomes of different organisms.

## References

* Berg, Jeremy & Tymoczko, John. (2006). Biochemistry 6th edition. W.H. Freeman and Company.
# Structural Biochemistry/Bioinformatics/Structural Alignments/Programs Used For Structural Alignment/MAMMOTH
## MAMMOTH Introduction

MAMMOTH stands for MAtching Molecular Models Obtained from THeory. This program was originally developed for comparing models produced from structure prediction since it is tolerant of large unalignable regions. However, it has proven to work well with experimental models, especially when looking for remote homology. Benchmarks on targets of blind structure prediction and automated GO annotation have shown it to tightly rank correlated with human curated annotation. A largely complete database of MAMMOTH based structure annotation for the predicted structures of unknown proteins covering 150 genomes facilitates genomic scale normalization.

## MAMMOTH Method

MAMMOTH based structure alignment methods decompose the protein structure into short peptides (heptapeptides for example) which are compared with the same length peptides of another protein. Similarity scores between the two polypeptides is then calculated using a unit-vector RMS (URMS) method. These cores are stored in a similarity matrix, and with a hybrid (local-global) dynamic programming, the optimal residue alignment is calculated. Protein similarity scores calculated with MAMMOTH are derived from the likelihood of obtaining a given structural alignment by chance.

## MAMMOTH-mult

MAMMOTH-mult is an extension of the MAMMOTH algorithm used to align related families of protein structures. This algorithm is very quick and produces consistent high quality structural alignments. Multiple structural alignments calculated with MAMMOTH-mult produce structurally implied sequence alignments that can be further used for multiple-template homology modeling, HMM-based (Hidden Markov model) protein structure prediction, and profile-type PSI-BLAST searches.
# Structural Biochemistry/Bioinformatics/Structural Alignments/Programs Used For Structural Alignment/RAPIDO
## RAPIDO

RAPIDO stands for Rapid Alignment of Proteins in terms of DOmains. RAPIDO is a web sever for 3D alignment of crystal structures of different protein molecules in the presence of conformational changes. Similar to CE's first step, RAPIDO identifies fragments that are structurally similar in two different proteins using an approach that uses difference distance matrices. The MFPs (Matching Fragments Pairs) are represented as nodes in a graph which are chained together to form an alignment by means of an algorithm for identification of the longest path on a DAG (Directed Acyclic Graph). The last step of refinement is performed to improve quality of the performed alignment. After aligning the two structures, the server applies a genetic algorithm for identification of conformationally invariant regions. These regions correspond to groups of atoms with constant inter atomic distances (within a defined tolerance). By doing this, RAPIDO takes into account variation in the reliability of atomic coordinates by employing weighting-functions based on the refined B-values. The regions that are identified as conformationally invariant by RAPIDO represent reliable sets of atoms for the superposition of the two structures that can be used for detailed analysis of changes in the conformation. RAPIDO can identify structurally equivalent regions even when these consist of fragments that are distant in terms of sequence and separated by other movable domains.
# Structural Biochemistry/Bioinformatics/Structural Alignments/RNA Structural Alignment
## RNA Structural Alignment

Structural alignment techniques have traditionally only been applied to proteins, as they are the primary biological macromolecules that form characteristic three dimensional structures. However, large RNA molecules also form characteristic tertiary structures, which mostly consist of hydrogen bonds formed between base pairs as well as by base stacking. Functionally similar noncoding RNA molecules can be particularly difficult to extract from genomics data because structure is more strongly conserved than sequence in RNA as well as proteins, while the more limited alphabet of RNA decreases the information content of any given nucleotide at any given position. A recent method for pairwise structural alignment of RNA sequences with low sequence identity has been published and implemented in the program FOLDALIGN. This method is not truly analogous to protein structural alignment techniques because it computationally predicts the structure of the RNA input sequences rather than requiring experimentally determined structures as input. Although computational prediction of the protein folding process has not been particularly successful to date, RNA structures without pseudoknots can often be sensibly predicted using free energy-based scoring methods that account for base pairing and stacking.
# Structural Biochemistry/Bioinformatics/Structural Alignments/Programs Used For Structural Alignment/DALI
## DALI

DALI stands for Distance Alignment Matrix Method. DALI is a common and popular method that breaks down the protein that is inputted into hexapeptide fragments and then calculates a distance matrix through the understanding of the contact pattern between successive fragments. Secondary structure features with residues that are contiguous in sequence are shown on the matrix's main diagonal. The other diagonals represent residues that are not next to each other in sequence. When the diagonals are parallel to the main diagonal, the features they represent are also parallel. When the diagonals are perpendicular, however, their features are anti parallel. If two proteins' distance matrices are the same or share similar features in almost the same positions, they can be said to have similar folds and length loops connecting the secondary structure elements. When two matrices are built, DALI's actual alignment process involves conducting a series of overlapping sub matrices that are 6x6. These 6x6 matrices are then reassembled to a final alignment through a standard score-maximization algorithm. The DALI method has been used to construct the FSSP database (Fold classification based on structure-structure alignments of proteins, or families of structurally similar proteins). This database holds all known protein structures and aligns them with each other to determine structural neighbors and fold classification. This database information can easily be found on the internet for ease of access. A DALI online database can found here. A downloadable program and web search are other available DALI resources.