OpenLLM-France/wikimedia huggingface dataset:
# IB Biology/Molecular biology
## Light and Photosynthesis

How does chlorophyll respond to the different wavelengths of light?
(Chlorophyll is found in the chloroplasts of plants. Plants are green because of the chlorophyll pigment. ) Chlorophyll absorbs certain wavelengths of light within the visible light spectrum. Green is obviously not absorbed, but reflected.
As shown in detail in the absorption spectra, chlorophyll absorbs light in the red (long wavelength) and the blue (short wavelength) regions of the visible light spectrum.
Which Wavelengths have the most and least energy?
Looking at a visible light and electromagnetic radiation graphic, it can be noticed that the colour red has the least energy in visible light. This is because red has the longest wavelength of visible light and the longest frequency of any visible light colour. Red light has a wavelength of 610 - 740nm. Meaning that red has the least amount of energy level, whereas violet has the highest amount of visible light. Blue light has a wavelength that is shorter in the visible spectrum as compared to red light and has a higher energy. The visible light color with the moost energy is blue.
How Does Whitelight differ?
White light having a better balance of chlorophyll a, chlorophyll b, and the carotenoids and having all the photons of the visible light spectrum gave a better growth environment.
Outline the light-dependent reactions of photosynthesis.
* (chlorophyll/antenna) in photosystem II absorbs light;
* absorbing light/photoactivation produces an excited/high energy/free electron;
* electron passed along a series of carriers;
* reduction of NADP / generates NADPH H ;
* absorption of light in photosystem II provides electron for photosystem I;
* photolysis of water produces 2 H /O ;
* called non-cyclic photophosphorylation;
* in cyclic photophosphorylation electron returns to chlorophyll;
* generates ATP by H pumped across thylakoid membrane / by chemiosmosis / through ATP synthetase/synthase;
Outline the light-independent reactions of photosynthesis.
* reactions take place in the stroma
* carbon dioxide reacts with RuBP
* catalysed by RuBP carboxylase
* GP formed
* GP converted to triose phosphate
* reduction reaction involving use of NADPH + H+
* energy from ATP also needed from this conversion
* triose phosphate converted to glucose(phosphate)/starch
* RuBP regenerated from triose phosphate
* Calvin cycle
Draw and label the structure of a chloroplast as seen in electron micrograph The structure consists of: double/inner and outer membrane/envelope – shown as two concentric continuous lines close together; granum/grana – shown as a stack of several disc-shaped subunits; (intergranal) lamella – shown continuous with thylakoid membrane; thylakoid – one of the flattened sacs; stroma; (70S) ribosomes/(circular) DNA / lipid globules / starch granules / thylakoid space
* REDIRECT
Draw and label the absorption and action spectra
* REDIRECT
Draw and label a simple representation of a photosystem, including chlorophyll molecules, the reaction center chlorophyll,and accessory pigments
# IB Biology/Introduction

IB Biology refers to the International Baccalaureate (IB) group 4 experimental science Biology.
The following is (or will hopefully eventually be) an explanation of the entire IB Biology Syllabus: For first examinations in 2003. Please nte that this is now replaced by the 2009 examinations and the content of the pages are out of date. The syllabus has had significant revisions.
The Syllabus provided by the International Baccalaureate Organization (IBO) consists of the titles displayed in bold. The explanations written in plain text below these titles have been added as supplementation and/or when further clarification is required. Basically, it takes away the need to research the "answers" to the syllabus and gives everyone a study-guide which can be accessed from anywhere, whenever needed. The following only covers the core material, all that is required for standard level Biology, and a few of the available HL/SL options.
Some Advice: Some may suggest that a large part of Biology is memorization which is a common mistake when studying Biology. The real difference is that between the Biological sciences (based on concepts) and those of the physical sciences (based on laws and theories). Thiis affects the style of learning required to master the biological sciences. Go through each part individually, don't try to digest everything at once. If you manage to go through each part individually over a long period of time, you will ace the exam. Good luck!
# IB Biology/Option C - Cells and Energy

For standard level, the same as topics 6.5 (Proteins), 6.6 (Enzymes), 7.1 (Cell Respiration) and 7.2 (Photosynthesis) in your syllabus.
# MINC/Resources
## minclookup

Here is an example of a double ended lookup table that you can use with files output from programs like mincblob to make pretty images.
Note that in order to use this you will have to ensure that your input file to minclookup has a symmetric range (ie: ranges from -x to x).
# Scripts

These scripts can all be downloaded from packages

## volrot

volrot is will rotate a MINC volume about the centre of the volume. This script would typically be used to sort out orientation issues with a MINC volume. A typical usage to rotate a volume 90 degrees about the x axis would be as such:

## nlpfit

nlpfit performs a hierarchical nonlinear fit of one volume to another. This is done via fitting one image to the other using progressively finer nonlinear grid functions. minctracc from the mni_autoreg package is used to perform the fits. The default fitting profile consists of a 16mm, 8mm and 4mm fit. As part of the fitting the volumes are also blurred with progressively smaller FWHM kernels, this is done in order to reduce the chances of a fit a particular level falling into local minima.
The default fit profile can be changed by creating a fit config file and using the -config_file option. An example (the default fit config) is below:
# MINC/Future/Actions201102/minctoollist
## list of minc tools

Please add to the list.
We need to identify the author, the contributors, is the software orphaned (without an owner), the person responsible for the code now, the license agreement, etc...

### image processing

N3 (Sled)
classify_clean (Zijdenbos, Cocosco)
PVE (Jussi Tohka)

### structure segmentation tools

ANIMAL structure segmentation (Collins)
Hippocampus + MTL structures fusion labelling (Collins)
thalamus + basal ganglia (Mallar)

### surface segmentation

CLASP (Evans)

### Analysis tools

fMRI stat (K Worsley). The maintenance and development of fMRIstat as such is, sadly, not supported anymore as far as I know (PB). All modules of fMRIstat have been included in NIAK though (see the pipeline section).
ITK Snap (Vlad's mods for minc; if minc properly supported in ITK, then this mod not needed)
ElastiX (Dante)
viewnup (Andrew)

### Imaging pipelines

NIHPD pipeline for pediatric data (Vlad)
CIVET pipeline for surface analysis (CLaude, Alan)
NIAK (Pierre B et al) pipeline for fMRI preprocessing and GLM analysis (based on an update of fMRIstat tools).
Other recipe pipelines for other tasks...
# Where to shift development of MINC

This book/page is an attempt to record the history of the big MINC2.0 CVS change of 2011 with perhaps a well written rationale for the choice that is to be made. For now it is nothing more than a bunch of headings that need content added in them but I hope that others will fill in more things so that we can all make a reasonably informed choice.
Add your vote by adding your name and perhaps a reason why. If you have other choices, feel free to add them.

### Leave it at the BIC

The BIC uses a CVS system that requires the user to have a BIC login (and be part of the coders group) in order to commit to CVS. This is done exclusively via SSH logins. There is no strictly used bug tracking system although mantis.bic.mni.mcgill.ca was proposed and used a little. Most of the tracking is still done via the minc-users and minc-development mailing lists.
Pros
* nothing changes
* CVS
Cons
* nothing changes
* CVS

### NITRC - http://www.nitrc.org/

NITRC is a NIH funded initiative that was designed to host projects such as MINC, you can make a choice of CVS or SVN and nothing else that I can see. The bug tracking and others things are done via eForge.
Pros
* Made for the Neuroimaging community
* Uses eForge? for issue tracking/lists/etc
* GIT/SVN/CVS
Cons
* not as pretty of a code interface as github/others
Votes
* Andrew Janke

### Don't care as long as it's public and DVCS

Options are:
* Github (Git), Sourceforge (Git), Launchpad (Bazaar), Google Code (Mercurial?), NITRC (Git)
Votes
* Jason Lerch

### NITRC + DVCS wherever

NITRC : for users (mailing list, forum, MINC wiki books as a plugin ?)
Anything public and DVCS : for developpers (nice bug tracking & project management a +, not too good on NITRC).
Votes
* Pierre Bellec

### GIThub

Pros
* DVCS
* Awesome UI
* Bug Tracking included
* Large Open Source community
Cons
Votes

### launchpad

Pros
* DVCS (Bazaar)
* makes package building for Ubuntu easier.
Cons
Votes

### google code

Pros
* DVCS
Cons
Votes
# MINC/History
## A step back in Time

MINC was originally written by Peter Neelin back in the dark ages (1992). Here is his original "Justification" for MINC:
And here is his original sales pitch for MINC:
Peter Neelin then maintained and coded for the minc library for the next 10 years or more at which point the reins were handed over to the current group of MINC authors.
# MINC/Installation
## Installing and configuring MINC
### Current Version

Currently, MINC tools are distributed as part of minc-toolkit, details on installation are located at bic-mni.github.io, all the source code is now hosted on GitHUB

### Historical information (out-of date)

The minc tools and related software can be installed under Unix, Linux, Windows and Mac OS X. Below is the list of detailed installation types depending on the operating system used. You can download all available software at the "MNI software repository"
* Source means having the source code in a tar.gz compression format, to be compiled and installed manually. See SourceInstall for more information. You will have to configure your system and to install additional supplementary PERL modules.
* Binary means there are installable binaries for this system. It can take the form of a package (e.g. a .deb format for Ubuntu) or a tar.gz with executables. See BinaryInstalls for more information.
* Note that "MINC-Bundle" means there is a bundle with all the MINC tools & associated software available, as opposed to installing each package separately.
The following table summarizes the recommended installation method for each platform.
Distribution List :
| Distribution | Source | Package | MINC-Bundle | Notes |
| Cygwin | X | | | tar dumps of Cygwin builds |
| deb | | X | | old Debian packages |
| debian-lenny (64 bits) | | X | X | Debian packages |
| osx-10.3 | X | | | osx package builds |
| osx-10.4-intel | X | | | osx package builds |
| osx-10.4 | X | | | osx package builds |
| osx-10.5-x86_64-alex | | | | osx package builds |
| osx-10.5 | X | | | osx package builds |
| tgz | X | | | source packages |
| ubuntu-gutsy (7.10) | | X | | Ubuntu packages |
| ubuntu-hardy (8.04) | | X | X | Ubuntu packages |
| ubuntu-intrepid (8.10) | | X | X | Ubuntu packages |
| ubuntu-jaunty (9.04) | | X | X | Ubuntu packages |
| ubuntu-karmic (9.10) | | X | X | Ubuntu packages |
| ubuntu-lucid (10.04, 64 bits) | | X | X | Ubuntu packages |
| ubuntu-maverick (10.10, 64 bits) | | X | X |
| virtual-machines | X | | | pre-built virtual machines with MINC tools |
| win32 | | X | | Windows builds of MINC |
# MINC/MincWorld

Currently MINC (as in file format) and MINC tools are being actively developed by following labs, mostly based in Canada:
* Montreal Neurological Institute: McConnell Brain Imaging Centre (BIC)
** MRS: Magnetic Resonance Studies Lab
** Neuro Imaging and Surgical Technologies lab (NIST)
** NOEL: Neuroimaging of Epilepsy Laboratory
* The McGill Centre for Integrative Neuroscience (MCIN)
* SIMEXP lab, Research centre of the Montreal Geriatric Institute
* NeuroRX research
* Douglas Mental Hospital
** Computational Brain Anatomy Laboratory (CoBrA)
** McGill Centre for Studies in Aging
* Mouse Imaging Centre, Hospital for Sick Children, Toronto Canada
* Centre for Advanced Imaging, Brisbane, Australia
* Biospective Inc.
# Interpretations of Quantum Mechanics and Quantum Field Theory/Introduction

Misconceptions about the meaning of quantum mechanics have persisted from its beginning up until the present among laypeople and physicists alike. Most physics textbooks on quantum mechanics and quantum field theory focus primarily on the mathematical formalism and only spend a couple of pages, if any, on the interpretation of quantum mechanics. Even the limited discussion of the interpretation of quantum mechanics is often presented in a confused muddled way. By constrast, most popularizing books for laypeople tend to oversensationalize and hype the "mysticalness" of quantum mechanics in imprecise language, leading to more confusion and misconceptions. In practice, most working physicists adopt a purely formal utilatarian use of quantum mechanics. They work with it mathematically to obtain mathematical results which they compare to experiments without thinking much about the meaning of what they are doing.
This book intends to correct the confusion and misconceptions about quantum mechanics by presenting a detailed analysis of the pros and cons of various popular interpretations and thought experiments and leave it to the reader to decide which interpretation is the most appealing.
Prior to 1925/1926, there was much confusion about the meaning and implications of quantum mechanics, leading to many radical claims. Even when the mathematical details of quantum mechanics had been worked out, there was still much confusion. It took a couple of years and many philosophical debates before an "orthodoxy" called the Copenhagen interpretation developed. Over the decades since then, gradually, more and more concepts have been clarified and newer interpretations have cropped up.
This book intends to study "problems" like measurement, quantum entanglement, causality, determinism/probabilistic, etc.
# Intro To C++/Functions

In C++ and many other languages, you will want to create and use various functions. Think of functions as a box. You will (most of the time) put something in, and then something else will come out. If you remember functions from math, it is practically the same thing. Let's take a look at this example:
So first, notice that i placed the new block of code Sum before the main function. That is because during compilation time, the compiler has to know where the functions are before they are called. So if i placed it after the main function, it wouldn't compile, and it would throw an error.
Now look at the very first line, int Sum(int a, int b). Int means that the return value will be an integer value, Sum is the name of the function (for when we call it), and (int a, int b) simply means that there will be two integers that need to be used as arguments when you call the function.
Let's look at the main function. First, we define to integer variables, left which equals 4, and right which equals 8. Then we create a new variable called SumOfLeftAndRight, and set it equal Sum(left, right)? Simply put, it calls the function, sets a equal to left, and b equal to right. Now inside the new function, it creates a new integer SumOfAandB and sets it equal to a + b, which is the same thing as left + right, then it returns the value of SumOfAandB. So whatever the new function returns, it sets that equal to SumOfLeftAndRight in our main function. That is how the return value works. It returns whatever value you set it to return. Just be sure that type of value you return matches the type you defined the function as. That is why we defined Sum as an integer function. Then it counts SumOfLeftAndRight, which is equal to 12.
You can do different types of things, it doesn't just have to add things up, it can be used to compare certain things, maybe type certain things out. Whatever you can do in the main function, you can do in your own functions. But be aware, if we create a variable inside of the main function, we are not able to access that variable in any other functions, since that variable is local to the main function. That is also vice-versa with your own functions and main.
# Interpretations of Quantum Mechanics and Quantum Field Theory
## Contents

* Introduction
* Mathematical Formalism
** Hilbert Space
** Cstar Algebra and Quantum Logic
* Thought Experiments
** Bohr-Einstein Debates
** Schrdinger's Cat
** The EPR experiment aka quantum entanglement
** Wheeler's Delayed Choice Experiment
* The problem of measurement in quantum mechanics
* Copenhagen Interpretation
* Bohm's pilot wave interpretation
* Many-worlds Interpretation
* Coherent Histories
* Decoherence
* Quantum Field Theory
** Local Quantum Physics
** Causality
# Intro To C++
## Intro To C++

Welcome to the Intro To C++ wikibook.
C++ is the extension of C programming language and developed by Dr. Bjarne Stroustrup between 1983-1985 at AT&T Bell labs in New Jersey. C++ is widely used in software infrastructure including desktop applications, servers like e-commerce, web search or SQL servers, and performance-critical applications like telephone switches or space probes).
This book just tries to cover the basics of C++ in easy way. Nothing more, nothing less.
* C++
* First Program
* Variables
* Playing with operator
* Making statement
* Reading & Writing Files
* Pointing to Data
* C++,Peeking Advanced topics

## Further Reading

For more information, see the following books:
* C++ Primer by Stanley B. Lippman, Josée Lajoie, Barbara E. Moo(2012)
* Accelerated C++: Practical Programming by Example by Andrew Koenig and Barbara E. Moo(2000)

## Footnotes and References

* ↑ Stroustrup, B. (6 May 2014). "Lecture:The essence of C++. University of Edinburgh". Retrieved 12 June 2015.
* ↑ Stroustrup, Bjarne (17 February 2014). "C++ Applications". stroustrup.com. Retrieved 5 May 2014.
# Interpretations of Quantum Mechanics and Quantum Field Theory/Many-worlds Interpretation

The many-worlds interpretation of quantum mechanics or MWI, also known as the relative state formulation, theory of the universal wavefunction, many-universes interpretation, Oxford interpretation or just many worlds, is an interpretation of quantum mechanics that claims to resolve all the "paradoxes" of quantum theory by allowing every possible outcome to every event to define or exist in its own "history" or "world", via the mechanism of quantum decoherence, instead of wavefunction collapse. Many worlds reconciles how we can perceive non-deterministic events (such as the random decay of a radioactive atom) with the deterministic equations of quantum physics; history, which prior to many worlds had been viewed as a single "world-line", is rather a many-branched tree where every possible branch of history is realised. MWI was first theorized in a dissertation by Hugh Everett which was initially rejected by Neils Bohr but gradually gained acceptance with the encouragement of Everett's thesis advisor John Wheeler.
# Copyright and Patents in the Internet Age
## History of Copyright and Patents
### Early History

Printing press initiated copyright regulations ... Monarchy maintained them Later parliament maintained them and police tried to enforce them (which wasn't feasible).

### U.S. Constitutional Basis for Copyright and Patent Law

Article I, Section 8 of the Constitution grants the Congress the power, among other things,
http://www.law.cornell.edu/constitution/constitution.articlei.html#science%20and%20useful%20arts

## Patent Law

Most content in this section comes from the FTC/DOJ 2003 report on Patents and Competition

### What is a patent?

A patent is essentially a monopoly on creation of a product or method for creating a product (or providing a service) granted by the government for a limited periodof time (usually 20 years from date of file or 17 years from date of grant, which ever comes first).
There are three types of patents
* utility patent (new invention or process)
* design patent (new original or ornamental design for a manufactured object)
** Examples of design patent application drawings: http://www.uspto.gov/web/offices/pac/design/drawing.html
* plant patent (patent on a new variety of plant)
For further information see the Wikibooks on US Patent Law or Canadian Patent Law.

### How can a patent promote the progress of science and useful arts

A patent guarantees exclusive rights to the inventor for a given period of time and this by consequence enhances the ability for commercialization and may be an incentive to foster innovation.
* inventor has 20 years to recoup research and development costs
* inventor may have easier time getting financing
* with venture capital it should allow small firms to compete with big ones, but small firms may have trouble litigating.

### How might patents serve to slow the progress of useful arts?

It may discourage innovation because once the exclusivity of a patent exists no one else is allowed to build on that specific idea without paying royalties to the patent holder (or breaking the law).
* the advent of 'patent thickets' can create an environment where it is difficult to remain competitive without infringement.
* a monopolist may create higher prices and lower availability of the product
* a monopolist can inhibit add-on innovation

## How can competition without patents promote the progress of science and useful arts

With no restrictions on further development of a product, innovators are free to begin to improve the product as soon as it is made public.

### Innovation -- what are the competitive advantages to funding R&D independent of patents

An R&D infrastructure would become experienced in the area of interest and would be more capable of follow-on innovation.
# Latin/Supine

The supine is a verbal noun. In ordinary verbs it is formed by adding -tum to the present stem, with the modification of e to i in the second conjugation (mone- > moni-)
When a supine is translated to English, the suffix -tum turns into -tion. Here are some examples.
There are lots of words in Latin that end in -um; the supine is just one of them.