OpenLLM-France/wikimedia huggingface dataset:
# Structural Biochemistry/Periodic trends

Periodic trends are specific patterns that are present in the periodic table, which illustrate different aspects of a certain element, including its size and its properties with electrons. When comparing the properties of the chemical elements, recurring ('periodic') trends are apparent. This led to the creation of the periodic table as a useful way to display the elements and rationalize their behavior. When laid out in tabular form, many trends in properties can be observed to increase or decrease as one progresses along a row or column.
These period trends can be explained by theories of atomic structure. The elements are laid out in order of increasing atomic number, which represents increasing positive charge in the atomic nucleus. Negative electrons are arranged in orbitals around the nucleus; recurring properties are due to recurring configurations of these electrons.
The main periodic trends include: electronegativity, ionization energy, electron affinity, atomic radius, melting point, and metallic character. The periodic trends that arise from the arrangement of the periodic table provide chemists with an invaluable tool to quickly predict an element's properties. These trends exist because of the similar atomic structure of the elements within their respective group families or period and the periodic nature of the elements.
Reference
http://chemwiki.ucdavis.edu/Inorganic_Chemistry/Descriptive_Chemistry/Periodic_Table_of_the_Elements/Periodic_Trends
# Structural Biochemistry/Protein function/VHL
## Beta-Cantenin gets jaded and von Hippel-Lindau is to blame

This research papers delves into the idea of the von Hippel-Lindau protein that is negatively regulated by beta-Catenin and Jade-1 via various mechanisms. One must first understand the proteins to connect the significance of their partnership.

### Proteins Discussed

Von Hippel-Lindau is a tumor suppressor protein encoded by the VHL gene. The inactivity of the protein is associated with Von Hippel-Lindau disease. The VHL protein works through E3 ubiquitin ligase activity which targets specific proteins for degradation. However, the inactivity of the protein may cause an excess growth of cells, or a tumor.
Beta-Catenin, or β-catenin, is part of a series of proteins that constitute adherens junctions and maintain epithelial cell layers in organs. The protein is used to regulate the production of VHL through negative feedback. This research paper focuses on Wnt- β-catenin which undergoes signal transduction. Wnts in particular “comprise a conserved family of secreted” (Berndt).
Jade-1 binds to β-catenin to “negatively regulates β-catenin levels in the absence of the Wnts stimulation” (Berndt). The expression of Jade-1 is what primarily determines the reduction of β-catenin. In some cases, the over expression of Jade-1 can reduce the presence of β-catenin by 50-60%. Jade-1 may be used in conjunction with VHL to regulate the production of β-catenin.
Summary of process:
Increase VHL => Increase Jade-1 => Decrease β-catenin
Decrease VHL => Decrease Jade-1 => Increase β-catenin

### Mechanism Discussed

HIF-1

### Reference

http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCV-4VKK6TW-1&_user=4429&_coverDate=03/31/2009&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000059602&_version=1&_urlVersion=0&_userid=4429&md5=38c4e891e16b7812a84b8685464d6ac6&searchtype=a
# Structural Biochemistry/Protein function/Protein function/Binding Sites/Cooperativity
## Sequential Model

The Sequential Model of the hemoglobin explains the cooperativity involved in the binding of oxygen. This model follows the concept that after binding occurs at one site in the active site, the binding affinity in the other sites around the protein will increase as well. Hence, the plot of substrate concentration versus reaction rate is of a sigmoidal shape. Because of this cooperativity, it does not follow Michaelis-Menten Kinetics. The difference between this model and concerted model is that the T states do not have to convert to R states. In this model, the ligand will change the conformation of the subunit that it is bound to and induce changes in the neighboring subunits. The Sequential model does not require the states to be in an "either T or R" ultimatum. Simply, each binding site influences nearby binding sites until all of the binding sites are in the same state. Neither the sequential model or the concerted model fully explains the nature of hemoglobin. Properties from both models appear in a real system.
# Structural Biochemistry/Proteins/ADP-Ribosylation

ADP-ribosylation is a posttranslational modification of proteins that involves the addition of one or more ADP and ribose moieties.
These reactions are involved in cell signaling and the control of many cell processes, including DNA repair and apoptosis.

## ADP-Ribosylation Enzymes

This protein posttranslational modification is produced by ADP-ribosyltransferase enzymes, which transfer the ADP-ribose group from nicotinamide adenine dinucleotide (NAD+) onto acceptors such as arginine, glutamic acid or aspartic acid residues in their substrate protein. In humans, one type of ADP-ribosyltransferases are the NAD: arginine ADP-ribosyltransferases, which modify amino acid residues in proteins such as histones by adding a single ADP-ribose group.
These reactions are reversible; for example, when arginine is modified, the ADP-ribosylarginine produced can be removed by ADP-ribosylarginine hydrolases.
As well as the transfer of single ADP-ribose moieties, multiple groups can also be transferred to proteins to form long branched chains, in a reaction called poly(ADP-ribosyl)ation. This protein modification is carried out by the poly ADP-ribose polymerases (PARPs), which are found in most eukaryotes, but not prokaryotes or yeast. The poly(ADP-ribose) structure is involved in the regulation of several cellular events and is most important in the cell nucleus, in processes such as DNA repair and telomere maintenance.

## Bacterial Toxins

ADP-ribosylation is also responsible for the actions of some bacterial toxins, such as cholera toxin, diphtheria toxin, and pertussis toxin. These toxin proteins are ADP-ribosyltransferases that modify target proteins in human cells. For example, cholera toxin ADP-ribosylates G proteins, which causes massive fluid secretion from the lining of the small intestine and results in life-threatening diarrhea.

## References

Belenky P, Bogan KL, Brenner C (2007). "NAD+ metabolism in health and disease". Trends Biochem. Sci.
Ziegler M (2000). "New functions of a long-known molecule. Emerging roles of NAD in cellular signaling". Eur. J. Biochem.
Corda D, Di Girolamo M (2003). "Functional aspects of protein mono-ADP-ribosylation". EMBO J.
Diefenbach J, Bürkle A (2005). "Introduction to poly(ADP-ribose) metabolism". Cell. Mol. Life Sci.
# Structural Biochemistry/Proteins/Adenylation

Adenylation, also known as adenylylation or AMPylation, is the process of attaching an AMP molecule to a protein side chain by covalent bonding. It has two main functions: 1) to regulate enzyme activity via post-translational modification and 2) to produce unstable intermediates of a protein, peptide or amino acids to allow reactions that are not thermodynamically favored to occur.

## Adenylation Applications

Adenylations has a particular application when it involves the adenylation of RNA. There is a known procedure that allows for RNA 5' adenylation using T4 DNA ligases. Basically this is an approach to adenylate RNA so that it becomes a 5',5'-adenyl pyrophosphoryl cap structure. This new adenylated RNA structure is desirable in the sense that it can investigate certain natural biochemical pathways that require such intermediates. The 5' adenylated RNA is also useful for a certain amount of in vitro selection procedures to identify nucleic acid enzymes that specificially use the 5' adenlyated RNA as a reactive RNA substrate. This is particularly favorable given that the adenylated RNA is considered a transition state molecule which has evolved to become the most favorable of states when it comes to enzyme substrate complexes. in other words, the adenylation of the 5' RNA allows for a better enzyme substrate complex due to its nature of being a transitional state substrate for biochemical pathways that wish to be observed. In addition to being a RNA substrate for selective catalysis reactions, there are also applications to RNA '5 capping and 5' labeling. It was shown in the "Efficient RNA5' adenylation by T4 DNa ligase to facilitate practical applications" paper that the protein enzyme T4 RNA ligase was used along with some DNA oligonucleotides to create a net transfer of the AMP group onto a monophosphorolyated terminus of the desired RNA substrate.

## Enzyme Regulation

Glutamine synthetase regulation by adenylation

## Formation of Unstable Intermediates

Carboxyl groups of small molecules or amino acids may be adenylated to form unstable intermediates as shown in the diagram to the left.
For many decades, the example of glutamine synthetase has been used to explain the principles of adenylation, but recent discoveries in adenylation of Rho and Rab GTPases have shown potential in revealing the other aspects of adenylation.

## References

* Itzen A, Blankenfeldt W, Goody RS. Adenylylation: renaissance of a forgotten post-translational modification. Trends Biochem Sci. 2011 Apr;36(4):221-8. Epub 2011 Jan 20.
Efficient RNA 5′-adenylation by T4 DNA ligase to facilitate practical applications, Yangming Wang, Scott K. Silverman
# Structural Biochemistry/Proteins/Agglunation reactions

Agglutination occurs when an antibody interacts with antigen, resulting in cross-linking of the antigen particles by the antibody. This eventually leads to clumping. "Agglutination" comes from the Latin root agglutinare. "Agglutinare" means, "to glue". Cross-linking, or cross-matching is done to determine matches. Agglutination may occur when an unideterminate, multivalent antigen interacts with a single antibody. It may also occur if a multi determinate, univalent antigen interacts with at least two distinct antibodies.
Cross Agglutination: when an antibody that is raised against a similar antigen agglutinates that antigen.
Group Agglutination: when a collection of similar organisms is agglutinated by an agglutinin that is specific for that collection.
Applications for the agglutination test
BLOOD TYPING
There are different blood groups like A,B, AB and O. The different blood types are differentiated according to the types of proteins on the surfaces of the red blood cells. Human red blood cells may either posses both of epitopes A and B on their surfaces. Individuals possessing only epitope A have anti-B antibody in their serum, while individuals possessing only epitope B on their red blood cells have circulating anti-A antibody. Some individuals have neither epitope and both antibodies present, while others have both epitopes and neither antibody. Blood type determination can be performed by mixing a sample of the individual’s blood with w solutions: one containing anti-A antibody and the other containing anti-B antibody. Agglutination occurs if the antibodies match the epitopes of the blood cells. By observing the agglutination patterns, the blood type of the individual can be determined.
DETERMINING MATING TYPES IN ORGANISMS Agglutination can be used to determine mating types in organisms such as Chlamydomonas. Extracts from cloned Chlamydomonas cells of either of the minus or plus type are added to cells of the opposite mating type as well as of the same mating type. What is observed is that, in the cells of similar type, no agglutination occurs. However, in the type with opposite mating type, agglutination does occur. Thus, this proves that the cells of different mating types are chemically different.
# Textbook of Psychopharmacology
## Table of Contents

* Opioids
** Prescription forgery
# Textbook of Psychopharmacology/Opioids

Opioids are a class of drugs derived from opium, or synthetically engineered to be similar in molecular structure and effect on the body. They are usually prescribed by a doctor for the treatment of moderate to severe pain. Due to their addictive nature and impairment of cognitive function, they have fallen from favor in the medical community. These drugs are currently popular on the black market and are often obtained by illegal means such as prescription forgery.

## Formulations

A short sampling of popular opioid drugs include the following: Codeine - Sold under many names and included in many formulations used for the treatment of minor to moderate pain, cough and cold, etc. Vicodin or Lortab - "Hydrocodone" used to treat moderate to severe pain. Vicodin and Lortab formulations combine hydrocodone with acetaminophen or ibuprofen Percocet or Oxycontin - "Oxycodone" used to treat moderate to severe pain. The percocet formulation combines oxycodone with acetaminophen. The Oxycontin formulation is a time-release oxycodone tablet. Dilaudid - "Hydromorphone" used for moderate to severe pain Morphine - Usually injected for treatment of severe pain

## History

In the 1800s and before, opioids were unregulated by law. Opioid extracts were often a major component of "snake oil" remedies sold by peddlers. These peddlers touted their formula as a cure-all which would alleviate anything from a headache to arthritis to depression. In reality these formulas served only to get the user "high" and create a false feeling of well-being without actually curing the illness. Many users became addicted to these formulations.
# Wings 3D/User Manual/User Interface/The Icon Bar

2.4 The Toolbar
There are three sets of Icons above the workspace as illustrated here.
The two on the left determine what Display Mode your model is in. They are, from left to right, Wire-shaded on/off, and Perspective on/off. These are used to toggle on and off these features as you work. Perspective off, also called Orthogonal view, is useful for lining an object up to a reference image plane.
The next four icons display what Edit/Selection Mode you are in. They are Vertex, Edge, Face and Body. The red highlighting gives you a quick visual key as to just what elements are affected in each mode and the white outline box indicate which mode you are currently in. In the above illustration we are in Face selection mode. Your Edit Mode will be important when it comes to using any of the modeling tools, since most tools are presented in context sensitive menus within the Workspace. The context of those menus is determined by the current Edit Mode.
The last two are Ground Plane and Reference Axes. These icons are used to quickly toggle on or off these features as needed.
# Wings 3D/User Manual/Wings3D Links

8.1 Wings3D Links Wings3D Home Page – Here you will find the latest source code and Windows binaries, several tutorials and some useful links. Link: http://www.wings3d.com
SourceForge Wings Project Page – Here you can find both the current and historical source code and release notes, file a bug reports, or log feature requests. Link: http://sourceforge.net/projects/wings
Erlang – the Wings programming language. The best reference is the PDF document Concurrent Programming in Erlang which is the first six chapters of a book by the same name. Most of the people now writing plug-ins for Wings got started by reading this document. You will also find a Glossary, an Index and a Getting Started guide at the same site. Link: http://www.erlang.org/
Wings Warm & Fuzzy 3D – Wings discussions. This is the unofficial Official Wings Board. This is where most of the on-line Wings discussion takes place, especially oriented to helping new users and for hashing out development issues. Link: http://www.wings3d.com/forum/ and Wings3D - Official Development Forum Link:http://nendowingsmirai.yuku.com/directory#.VN3CHSzUVFY
CGChat Wings Board – A Wings discussion board more centered around the art of modeling with Wings. They tend to run Seminars on a given modeling topic. Link: http://www.cgchat.com/board/forumdisplay.php?s=&forumid=69
Bernie's Downloads – Many free models in .wings format plus other 3D resources. Link: http://www.bernieloehn.de/downloads.html
3dbaseart – a Wings tutorial on building a drag car. Link: http://www.3dbasedart.com/
Wings3D Tutorial: Soccer Ball – a tutorial by Anthony D'Agostino on making a soccer ball with wings. Anthony is a master at modeling geometric shapes, and this tutorial is Wings3D specific. Link: http://home.comcast.net/~chronosphere/tut-wings-soccer1.htm
And there are two links that may help you understand the winged edge data structure of Wings that I would like to point you to. The first one is The Winged Edge Data Structure by Dr. Ching- Kuang Shene. This is the reference used by Bjorn Gustravson to develop Wings. Link: http://www.cs.mtu.edu/~shene/COURSES/cs3621/NOTES/model/winged-e.html
And you can find winged edge topology illustrated from a geographic point of view here: Link: http://www.bequia.swinternet.co.uk/edgeex.html
# Wings 3D/User Manual/User Interface/The Information Line
### The Information Line

The Information Line runs along the bottom of the main Wings window. This is probably the most important thing to keep your eye on, especially if you are new to Wings. The Information Line's main purpose is to display every possible button option available for any operation, tool, or menu item. Many of the tools and menu options have more than one function, and some of the more advanced options are only displayed in the Information Line. To display any menu item's possible options or described function, simply hover over the item with the mouse cursor.
The Information Line uses the letters L, M and R for the Left, Middle and Right mouse buttons. When several options are available for a tool, menu item, or during an operation, those options are displayed in the Information Line preceded by L, M, or R. Sometimes the user will be prompted to depress a Modifier Key in conjunction with the designated mouse button. Modifier Keys are often Control <Ctrl>, <Alt>, or <Shift>, or sometimes a combination of two or more are used with the mouse buttons. There are other instances when Numeric or other keys are used to present option. In cases where Number Keys are used to change the result of a command, Do Not Use The Number Pad Keys. For Number Key Modifiers in the Information Line, use the Number Keys across the top of your keyboard instead.
IMPORTANT: The Information Line Displays Important Information About Tools, Menu Items and Other Options Available During An Operation. Remember To Always Keep An Eye On The Information Line.
# Wings 3D/User Manual/User Interface/The Information String

DRAFT 1.6 15
� Section 2: The Wings3D User Interface WINGS3D USER MANUAL 2.8 The Information String If you have an element of geometry selected Wings will display some basic information on that element (or elements) in a string at the top left-hand side of the workspace.
2.9 Wings Units A Wings Unit (wu) is arbitrary in size and can be thought of in terms of any real world units desired. The Wings grid is composed of squares each 1x1 wu in size. The standard Wings cube is cube is 2 x 2 x 2 Wings Units in size. If building a model from scratch you can arbitarily decide that a wu will represent inches, feet, meters or miles; whichever is most appropriate for the task at hand.
Quick Tip: Working With Wings Units
When working with many Wings commands dragging with the Shift key depressed will cause movement to be constrained to whole units, while the Ctrl key will cause movement to be constrained to tenths of units. Holding down Shift + Ctrl keys constrains operations to hundredths of a wings unit. While it seems the same as the readout – as this is only 2 decimal places – it is possible to do unconstrained drags and get elements that are 3 decimal places when measured, even though the read out only shows two. Had me tearing my hair out on more than one occasion. Where it matters I use Shift + Ctrl.
The color of this text is set in the Edit | Preferences menu via the Text Color parameter. If you find this text string annoying you can hide it by simply changing the text color to match the background color of the workspace. I do not recommend this course of action since you can glean some useful information here. If you select an element, a vertex for example, Wings will inform you of the Vertex ID and it's position in X, Y, and Z. Furthermore, if you select another vertex, so that two are selected at the same time, it will tell you how far apart they are. If you select a single edge it will tell you how long that edge is. This can be very useful, especially in modeling buildings and the like.
It is not uncommon for Wings units and other 3D packages units to be vastly different in size. Therefore you will need to experiment with the import/export sizing options to get suitably sized objects on import/export. Scaling by 1000, for example, brings in a Poser model at a decent working scale.
Quick Tip Provided by Puzzled Paul
# Wings 3D/User Manual/User Interface/The Menu Bar
## The Menu Bar

Below the Title Bar and inside the Geometry window is the Menu Bar. Here you will find options more common to Wings in general such as settings and tools that are not specific to any one Selection Mode.
* Edit, File, View, Select, Tools, Windows, Help.
Each Menu item will be discussed fully in Section 5, The Wings3D Command Reference Guide.
# Wings 3D/User Manual/User Interface/The Title Bar
### The Title Bar

* The Title Bar along the top of the application window identifies the program's name (Wings 3D). At the far right of the Title Bar are the standard GUI widgets for Minimize, Restore, and Close. If a previously saved file is open in Wings 3D, the Title Bar will display its file name. When a file is Auto-Saved the title bar displays that the file has been auto-saved.
* The Auto-Save feature can be turned on and set to the number of minutes the user desires between auto-saves and can be found in Edit|Preferences|Misc. The default setting is 10 minutes between auto-saves. Auto-save will only save that has been previously saved. Auto-save creates a separate file from the one the user saved and overwriting the auto-save file for each iteration. If Wings is closed during an auto-save session without the user saving changes manually, the next time Wings is asked to opens that file may prompt the query:
# Wings 3D/User Manual/User Interface/The Status Bar
### The Status Bar

The Status Bar is just below the Toolbar in the Geometry Window.