OpenLLM-France/wikimedia huggingface dataset:
# Flora of New York/Potamogetonales

| ← Acorales & Alismatales | Flora of New York — Potamogetonales | Flora of New York — Potamogetonales | Flora of New York — Potamogetonales | Flora of New York — Potamogetonales | → Acorales & Alismatales |
| ← Acorales & Alismatales | Table of contents | Genus index | Protected species index | Invasive species index | → Acorales & Alismatales |
The order Potamogetonales is now embedded within the Alismatales as defined in the Angiosperm Phylogeny Website.
* ↑ P. F. Stevens, (2001 onwards). "Alismatales," Angiosperm Phylogeny Website. Version 13, September 28, 2013 (and more or less continuously updated since). http://www.mobot.org/MOBOT/research/APweb/orders/Alismatalesweb.htm#Alismatales.
# General Genetics/Genetics, Ecology, and Modern Synthesis Theory

The History of Evolutionary Theory, and the Implications of Genetics
Had Charles Darwin, the man who coined the mechanism of evolution as "natural selection" been introduced to Gregor Mendel, the geneticist who first described gene inheritance, biologists today would be decades ahead of where we are in terms of research. For it is genetics, the phenomenon of traits being inherited by offspring from their parents, that provides the vessel for all evolutionary change. Charles Darwin and the biologists of his day imagined that there was a mechanism for inheritance. They thought there was a means through which the characteristics of parents can be passed on to their offspring, but they couldn't fully describe it. Darwin, in his famous On the Origin of Species, implicated genetics as the vehicle for natural selection, and thus evolution, without even knowing the word.
   ...owing to this struggle, variations, however slight and from whatever cause proceeding, if they be in any degree profitable to the individuals of a species in their infinitely complex relations to other organic beings and to their physical conditions of life, will tend to the preservation of such individuals and will generally be inherited by the offspring. The offspring also will thus have a better chance of surviving, for of the many individuals of any species which are periodically born, but a small number can survive I have called this principle by which each slight variation, if useful, is preserved, by the term Natural Selection in order to mark its relation to natures's power of selection...
In the decades after Darwin's death, his theory of evolution began to fall by the wayside in scientific literature. By the 1920's and 30's, many scientists thought that it was at best an interesting hypothesis, but without merit, as the mechanism for natural selection had yet to be identified and no observation had been made of a single speciation event. Darwin spoke of natural selection as the driving force behind the emergence of new species. In-fact, this was the very thesis of his book. But no one had yet been able to describe the phenomenon. The study of genetics continued to develop separately from evolutionary theory, only occasionally being referenced by biologists interested in heredity. It wasn't until the 1940's, with the publication of British Biologist Julian Huxley's Evolution: The Modern Synthesis, that a solid connection was made between genetics and evolutionary theory. Huxley and many other biologists were the proponents of a rebirth of Darwin's ideas; an intellectual movement known as "neodarwinism." It is through their synthesis of genetics and evolutionary theory that a clearer picture of the evolution we know today emerged.
From Mutations to Modern Synthesis Theory -- How We See Genetics and Evolution Today
The ideas surrounding Populuation Genetics presented in Chapter 6 were the bridge needed between genetics and natural selection that led to what we know as evolution today.
# General Genetics/Molecular Genetics

The importance of Genetics
Alexis's hemophilia illustrates the important role that genetics plays in a person's life. A difference in one gene, of the 20,000 to 25,000 genes that each human possesses, changed Alexis's life, affected his family, and perhaps even altered the course of history. We all possess genes that influence our lives. They affect our height, weight, hair color, and skin pigmentation. They influence our susceptibility to many diseases and disorders and even contribute to our intelligence and personality. Genes are fundamental to who and what we are.
The Role of Genetics in Biology Genetics provides one of biology's unifying principles: all organisms use the same genetic system. Genetics also undergirds the study of many other biological disciplines. Evolution s genetic change taking place through times; so the study of evolution requires an understanding of basic genetics.
Genetic Diversity and Evolution Life of Earth exists in tremendous array of forms and features that occupy almost every conceivable environment. Life is also characterized by adaptation: many organisms are exquisitely suited to the environment in which they are found. The history of life is a chronicle of new forms of life emerging, old forms disappearing, and exiting forms changing. Despite their tremendous diversity, living organisms have an important feature in common: all use the same genetic system. A complete set of genetic instructions for any organism is its genome, and all genomes are encoded in nucleic acids-either DNA or RNA.
Divisions of Genetics Traditionally, the study of genetics has been divided into three major subdisciplines: transmission genetics, molecular genetics, and population genetics. Transmission genetics encompasses the basic principles of genetics and how traits are passed from one generation to the next. Molecular genetics concerns the chemical nature of the gene itself: how genetic information is encoded, replicated, and expressed. It includes the cellular processes of replication, transcription, and translation-by which genetic information is transferred from one molecule to another- and gene regulation -the processes that control the expression of genetic information. Population genetics explores the genetic composition of groups of individual members of the same species and how that composition changes over time and geographic space.
# General Genetics/Introduction

Welcome to Genetics - the study of heredity. More precisely, it is the study of how living organisms inherit characteristics or traits from their ancestors.
It has only been in the past one hundred years that we have begun to understand how information in the form of physical characteristics is transferred from parent to child.
In genetics, a feature of an organism is called a trait. Some traits are features of an organism's physical appearance, for example, a person's eye-color, height or weight. There are many other types of traits and these range from aspects of behavior to resistance to disease. Traits are often inherited, for example tall and thin people tend to have tall and thin children.
Other traits come from the interaction between inherited features and the environment. For example a child might inherit the tendency to be tall, but if there is very little food where they live and they are poorly nourished, they will still be short. The way genetics and environment interact to produce a trait can be complicated: for example, the chances of somebody dying of cancer or heart disease seems to depend on both their family history and their lifestyle. Genetics will help to examine the dynamic between the often asked "Nature vs. Nurture" question.
Genetic information is carried by a long molecule called deoxyribonucleic acid, DNA for short. DNA consists of two long chains of nucleotides twisted into a double helix and joined by hydrogen bonds between the complementary bases adenine and thymine or cytosine and guanine that encodes the genetic information which is copied and inherited across generations.
Traits are carried in DNA as instructions for constructing and operating an organism. These instructions are contained in segments of DNA called genes. DNA is made of a sequence of simple units, with the order of these units spelling out instructions in the genetic code. This is similar to the orders of letters spelling out words. The organism "reads" the sequence of these units and decodes the instruction.
Not all the genes for a particular instruction are exactly the same. Different forms of one type of gene are called different alleles of that gene. As an example, one allele of a gene for hair color could carry the instruction to produce a lot of the pigment in black hair, while a different allele could give a garbled version of this instruction, so that no pigment is produced and the hair is white.
Mutations are either random or induced events that alter the sequence of a gene and can produce new or different traits. There are some exceptions to this, which will be discussed later. A new trait could be turning an allele for black hair into an allele for white hair.The appearance of new traits is important in evolution.
# General Genetics/Molecular Evolution
## Recombination
### Site-Specific Recombination

When recombination is site-specific, it can only occur at specific regions of homology.

### Illegitimate Recombination

Originally called "bastard recombination," illegitimate recombinations can occur even when there is little to no homology. Transposons are capable of illegitimate recombination.

### Homologous or Generalized Recombination
#### Holliday model of recombination

After homologous chromosomes align, a single strand of each DNA breaks and invades the other DNA. Enzymes such as ligase seal the crossed strands, and the two double-helices swap
The Holliday intermediate will be resolved in one of two ways: creation of a patched duplex or creation of a spliced duplex.

#### Meselson and Radding model of recombination

After homologous chromosomes align, a single strand of DNA is nicked and replicated. The replicated DNA displaces the original strand, which now dangles from the double-helix and is known as a whisker. The whisker invades the homologous double-helix and displaces that DNA, which is excised. The whisker is ligated to the new double-helix. Branch migration ensues and, from there, this model is identical to the Holliday model.
This model is supported by the discovery of Rec A and Rec BCD. Rec BCD is an E. coli protein with DNA helicase activity capable of making single-stranded nicks. This would allow it to form the "whiskers" characteristic of the Meselson-Radding model. Rec A is capable of coating exposed ssDNA and integrating it into dsDNA, which would occur during whisker invasion of the homolog in the Meselson-Radding model. E. coli is not recombination when the genes that encode Rec A and Rec BCD are knocked out.

#### Other proteins with potential roles in recombination

PRDM9 is a zinc finger protein. methylates lysine 4 of histone 3. In the process, it recruits enzymes that creates double-stranded DNA breaks. Since PRDM9 is polymorphic, it can promote DNA cleavage at different sites. A zinc finger is a common protein structural motif characterized by stabilization of its folds by zinc ions. Most DNA-binding proteins have the zinc finger motif.
Ruv (repair UV radiation) AB promotes branch migration. Ruv C binds to the Holliday junction and cleaves the crossover strands.
# General Genetics/Polyadenylation
## The Mechanism of Polyadenylation

There are a number of factors that must bind to the pre-mRNA for 3' cleavage and polyadenylation. Poly A polymerase (PAP) catalyzes poly A synthesis. Uniquely amongst polymerases, it does not require a template for polymerization. Cleavage and Polyadenylation Specificity Factor (CPSF) binds to the CPSF binding site (characteristic sequence: AAUAAA). PAP attaches to CPSF. Cleavage Stimulation Factor (CstF) binds the CstF binding site (characteristic sequence: GUNU, where N can stand for any nitrogenous base). The pre-mRNA folds so that CPSF and CstF can interact. Cleavage Factor I and II (CFI/II) bind to the mRNA between the CPSF and CstF binding sites. Cleavage occurs at this site. Poly A binding proteins bind to polyadenylated regions after PAP synthesizes them.

## Functions of Polyadenylation

Addition of the poly-A tail facilitates translation and transportation of mRNA out of the nucleus.
# General Genetics/Mutations and Evolution

Its often not grandiose, overlapping theories such as the Neutral Theory of Evolution, or Modern Synthesis, that biologists work with in their research on a day-to-day basis. Instead, it is the beautiful basics of genetics that are the cornerstone of experiments. The basics are then used to reflect on bigger ideas, such as population ecology and evolution. It is the beautiful basics of genetics with which we concern ourselves in this section.
Every organism has a set of genes and half of the genes of that organism come from each parent. The combinations of the genes causes the variation of individuals within the species. The genes of a butterfly, an ape or a fowl carry the code that determines the appearance and the character of the butterfly, the ape and the fowl. The genetic code allows an overwhelming variety within the species of the kind. A mutation is basically a gene that has an abnormality in relation to its normal configuration. The abnormality can then be passed to successive offspring, thereby producing a marked difference. There are many different types of mutations. The smallest possible genetic mutation is a 'point-mutation'. This occurs in the DNA when the base-pairs combine with the 'wrong' partner. Multiple point-mutations are common and are found to increase substantially by the effect of mutagens. Mutations are, of course, heritable and these can extend to whole or part chromosomal mutations. Because many genes are affected by a chromosomal mutation, these often have drastic ramifications on the offspring.
# General Genetics/Genomes

In biology the genome of an organism is the whole hereditary information of an organism that is encoded in the DNA (or, for some viruses, RNA). This includes both the genes and the non-coding sequences. The term was coined in 1920 by Hans Winkler, Professor of Botany at the University of Hamburg, Germany, as a portmanteau of the words gene and chromosome.
More precisely, the genome of an organism is a complete DNA sequence of one set of chromosomes; for example, one of the two sets that a diploid individual carries in every somatic cell. The term genome can be applied specifically to mean the complete set of nuclear DNA (i.e., the nuclear genome) but can also be applied to organelles that contain their own DNA, as with the mitochondrial genome or the chloroplast genome. When people say that the genome of a sexually reproducing species has been "sequenced," typically they are referring to a determination of the sequences of one set of autosomes and one of each type of sex chromosome, which together represent both of the possible sexes. Even in species that exist in only one sex, what is described as "a genome sequence" may be a composite from the chromosomes of various individuals. In general use, the phrase genetic makeup is sometimes used conversationally to mean the genome of a particular individual or organism. The study of the global properties of genomes of related organisms is usually referred to as genomics, which distinguishes it from genetics which generally studies the properties of single genes or groups of genes.
# General Genetics/Mendelian Inheritance

Gregor Johann Mendel was a monk in the Augustinian Monastery in the Brunn, Czech Republic. In 1854 he began the experiments which started modern genetics. His work with garden peas, Pisum sativum, was vital to our understanding of inheritance. He is known as the Father Of Genetics.

### Mendel's Experiment

Mendel's first step was breeding pure breeding strains of peas. The traits he studied included:
* Pea colour
* Height of pea plants
* and whether the Peas were wrinkled or smooth.
Mendel crossed the pure breeding Parental Generation (designated P). He found that the first generation (F1) was exclusively phenotypically one of the parental types. Mendel then crossed his F1 generation with itself. He found that the F2 generation showed a surprising trait, three quarters were like the F1 generation, while the remaining quarter were like the other Parents.
From this Mendel realised that there were two versions of each loci, one of which expressed dominance over the other. He called this Biparticulate Inheritance. If a gene was following this 3:1 pattern it was said to be segregating Normally.
By looking at multiple genes, Mendel showed that they were not linked to each other and that each loci he studied had no influence over the others. He called this Independent assortment.
By studying cases where the Mendelian laws we can also learn a lot. For instance, if a gene isn't segregating normally it may be sex linked. If two genes aren't Assorting Independently they're probably on the same chromosome
Mendel's laws are the first step to understanding Genetics, they lay down the basic concept of inheritance.
# Git/Advanced

This tutorial covers some of the more advanced, multi-user features of git. For the single-user features, please go to the Single developer basics.

## Checking out remote repositories

One way to check out a remote git repository is
Now you have a local copy of that repository. You can use all the commands that were introduced in the Single developer basics. Once you are done, you might want to check in your changes to the central repository again.
First you want to do a git pull in case the repository has changed in the meantime and you might have to merge your branch with the repository. After merging, you can use git push to send your changes to the repository:
or
then

### Checking out local repositories

git clone also works for local repositories:

### Checking out remote branches

You might also want to check out remote branches, work on them and check in your local branches. First you might want to know which branches are available:
Get a remote branch (pull into a local branch):
Update a remote branch (push a local branch into a remote branch):
This assumes that you have a remote repository called "origin". You can check this with git remote.
If you want to create a local branch from a remote branch, use:
Deleting remote branches works like this
The following command synchronizes branches $ git fetch origin

### Tags

Git allows you to specify some tags in order to focus on some things in the history.
In order to add an annotated tag:
or also:
To add a lightweight tag:
To force overwriting existing tag:
To display previous tags:
Tags can be pushed to remote with
To position the repo on a tag:

### Tags vs Branches

Both tags and branches point to a commit, they are thus aliases for a specific hash and will save you time by not requiring to type in a hash.
The difference between tags and branches are that a branch always points to the top of a development line and will change when a new commit is pushed whereas a tag will not change. Thus tags are more useful to "tag" a specific version and the tag will then always stay on that version and usually not be changed.
In practice, tags are used to designate the software versioning, and are named with numbers (ex: v1.0.2).

## Create and Apply a Patch

In order to create a plain text patch (series) for the changes between origin and master, use
In order to apply a submitted plain text patch (series), use

## References

* ↑ http://git-scm.com/book/en/Git-Basics-Tagging
# Git/Getting help
## IRC

* #git on irc.freenode.net (webchat)

## Forums & mailing lists

* Mailing list: gitvger.kernel.org

## Web pages

* FAQs
** FAQ from kernel.org
** A FAQ with fast answers
* Tutorials
** Official Git documentation
** ProGit
** A very nice and concise tutorial that also explains advanced features like branches, rebasing etc.
** Git Community Book
* For users of other VCS
** Crash course for SVN users
* Misc
** Seminars and presentations about Git
** Lots of Git-related links
** The Git Parable
# Git/Gitosis

Gitosis is a tool to secure centralized Git repositories, permitting multiple maintainers to manage the same project at once, by restricting the access to only over a secure network protocol.

## Installing Gitosis
### Checkout the Gitosis Repository

To install Gitosis, you first must have the Git client installed. Once installed, checkout a copy of Gitosis from its repository:
Install:

### Create a User to Manage the Repositories

Create a user to manage the repositories:
If you don't already have a public RSA key, create one on your local computer:

### Copying Your Public Key to the Gitosis Server

Copy this key to the Gitosis server. Assuming you are in your home directory:

## Setting up Gitosis
### Initializing Gitosis

Initialize Gitosis:
Upon success, you will see:
Ensure the Git post-update hook has the correct permissions:

## Configuring Gitosis
### Clone the Gitosis Repository

Gitosis creates its own Git repository. To configure Gitosis, you will clone this repository, set your configuration options, then push your configuration back to the Gitosis server.
Cloning the Gitosis repository:

### Creating a Repository

Edit gitosis.conf
An example of a default gitosis.conf:

### Defining Groups, Members, Permissions, and Repositories

You can define groups of members and what permissions they will have to repositories like so:
In this example, anyone in the group blue_team, in this case john, martin, and stephen, will be able to write to the Git repositories tea_timer and coffee_maker
Save, commit, and push this file.

### Creating a Repository

Next, create one of the repositories. You'll want to change to the directory where you you want to store your local copy of the Git repository first.
Create the repository:

### Adding Users to a Repository

Users are identified by their public RSA keys. Gitosis keeps these keys inside the directory keydir within the gitosis-admin repository. Users are linked to their Git username by the name of the key file. For example, adding an RSA key to keydir/john.pub will link the user john to the machine defined by the RSA within john.pub. Keys must end in .pub!
Add a user:
John can now clone the git repositories he has access to as defined by gitosis.conf. In this case, he can both read and write to the repository as he has writable permissions.

## External Links

* Scie.nti.st
# Getting around Los Angeles by Rail/Stops and Facilities/Metrolink Transfer Stations and Concurrencies

Metrolink passengers connect from one line to another line at transfer stations. The three major Metrolink transfer stations are Los Angeles Union Station, San Bernardino, and Riverside-Downtown.
Sometimes, two or more Metrolink lines share the same track. This occurs four times in the system (see below).

## Transfer Stations

* Los Angeles Union Station
* San Bernardino
* Riverside-Downtown
Metrolink Transfer Stations :
| Los Angeles Union Station | San Bernardino | Riverside-Downtown |
| San Bernardino Line | San Bernardino Line | |
| Riverside Line | | Riverside Line |
| 91 Line | | 91 Line |
| Inland Empire-Orange County Line | Inland Empire-Orange County Line | |
| Antelope Valley Line | | |
| Ventura County Line/Burbank-Bob Hope Airport Line | | |
| Metro Red, Purple, and Gold Lines | | |
| Amtrak | | |