Persius/hicric huggingface dataset:
Casein kinase 1
The Casein kinase 1 family (EC 2.7.11.1) of protein kinases are serine/threonine-selective enzymes that function as regulators of signal transduction pathways in most eukaryotic cell types.

# Discovery
By the early 1950s it was known from metabolic labeling studies using radioactive phosphate that the phosphate of phosphoproteins inside cells can sometimes undergo rapid exchange of new phosphate for old. In order to perform experiments that would allow isolation and characterization of the enzymes involved in attaching and removing phosphate from proteins, there was a need for convenient substrates for protein kinases and protein phosphatases. Casein has been used as a substrate since the earliest days of research on protein phosphorylation . By the late 1960s, cyclic AMP-dependent protein kinase had been purified and most attention was centered on kinases and phosphatases that could regulate the activity of important enzymes. Casein kinase activity associated with the endoplasmic reticulum of mammary glands was first characterized in 1974 and its activity was shown to not depend on cyclic AMP .

# Roles
Casein kinase activity was found to be present in most cell types and to be associated with multiple enzymes. The type 1 casein kinase family of related gene products are now given designations such as "casein kinase 1 alpha" and "casein kinase 1 epsilon". Casein kinase 1 alpha has been suggested to play a role in phosphorylation of Disheveled in the Wnt signaling pathway .
In humans there are three casein kinase 1 gamma enzymes. Working with the Xenopus system, Davidson et al screened for proteins that can regulate the Wnt signaling pathway by interacting with  the Wnt receptor LRP. They reported that Xenopus casein kinase 1 gamma (CK1gamma) is associated with the cell membrane and binds to LRP. CK1gamma was found to be needed for Wnt signaling through LRP. is both necessary and sufficient to transduce LRP6 signalling in vertebrates and Drosophila cells. Wnt binding to LRP causes a rapid increase in phosphorylation of the cytoplasmic domain of LRP by CK1gamma. Davidson et al proposed that phosphorylation of LRP6 by CK1gamma promotes binding of Axin to LRP and activation of the Wnt signaling pathway.
Casein kinase 1 epsilon is also important in the Wnt signaling pathway  and the  Hedgehog signaling pathway .
Casein kinase 1 epsilon also acts in a molecular pathway that regulates the circadian rhythm .
Catenin alpha-1
E-catenin, also known as Catenin alpha-1 is a protein that in humans is encoded by the CTNNA1 gene. E-catenin is highly expressed in cardiac muscle and localizes to adherens junctions at intercalated disc structures where it functions to mediate the anchorage of actin filaments to the sarcolemma. E-catenin also plays a role in tumor metastasis and skin cell function.

# Structure
Human E-catenin protein is 100.0 kDa and 906 amino acids. Catenins (,,and  (also known as plakoglobin)) were originally identified in complex with E-cadherin, an epithelial cell adhesion protein. E-catenin is highly expressed in cardiac muscle and is homologous to the protein vinculin; however, aside from vinculin, E-catenin has no homology to established actin-binding proteins. The N-terminus of E-catenin binds -catenin or -catenin/plakoglobin, and the C-terminus binds actin directly or indirectly via vinculin or -actinin.

# Function
Though E-catenin exhibits substantial expression in cardiac muscle, E-catenin is most well known for role in metastasizing tumor cells. E-catenin also plays a role in epithelial tissue, both at adherens junctions and in signaling pathways.
In cardiomyocytes, E-catenin is present in cell to cell regions known as adherens junctions which lie within intercalated discs; these junctions anchor the actin cytoskeleton to the sarcolemma and provide strong cell adhesion.
Functional E-catenin is required for normal embryonic development, as a mutation eliminating the C-terminal 1/3 of the protein resulting in a complete loss-of-function phenotype showed disruption of the trophoblast epithelium and arrested development at the blastocyst stage.
E-catenin specifically, not - or -catenin, binds F-actin and organizes and tethers the filaments at regions of cell-cell contact. Studies show that full-length E-catenin binds and bundles F-actin in a superior fashion relative to individual N-terminal or C-terminal domains.
E-catenin, along with -catenin and plakoglobin form distinct complexes with N-cadherin that are involved in forming cell-cell contacts and differentiation of cardiomyocytes. Catenin-N-cadherin complexes are apparently necessary for and precede the first cell to cell contact, precursory to gap junction formation. The anchorage of cadherin-catenin complexes to actin filaments by E-catenin is regulated by tyrosine phosphorylation.
Functional insights into E-catenin function have come from studies employing transgenesis. Mice harboring a cardiac-specific deletion of E-catenin exhibited abnormalities in cardiac dimensions and function, representative of dilated cardiomyopathy. This was further characterized by disorganization of intercalated disc structures and mitochondria, as well as compensatory increases in -catenin and decreases in localization of cadherin and vinculin at intercalated discs. Knockout mice also exhibited high susceptibility to death following stress.

# Clinical significance

# Interactions
E-catenin has been shown to interact with:
- APC,
- Beta-catenin,
- CDH1,
- CDH2,
- CDH3
- Plakoglobin,  and
- VE-cadherin.
Cauliflower ear

# Overview
Cauliflower ear or hematoma auris or perichondrial hematoma is a condition most common among wrestlers, rugby players, mixed martial artists, and 1920s boxers. If the external portion of the ear suffers a blow, a blood clot or other fluid may collect under the perichondrium. This separates the cartilage from the overlying perichondrium that is its source of nutrients, causing the cartilage to die. When this happens, the outer ear becomes permanently swollen and deformed, thus resembling a Cauliflower.
Headgear that protects the ears is worn in wrestling, many martial arts and other contact sports to help prevent this condition.

# Treatment
When fluid collection in the outer ear occurs, it is important to contact a doctor immediately and have it treated. The doctor will evacuate the fluid and apply a compressing tie to the outer ear to reconnect the perichondrium and the cartilage. The compressing tie must be left in place for some time, generally 10 days, to prevent the fluid from building up again. The outer ear is prone to infections, so antibiotics are usually prescribed. If the pressure is left alone without medical intervention, the ear can suffer very serious damage.  Pressure can build up and eventually rupture the ear drum.  When this occurs, the ear may further wrinkle, and can become slightly pale; hence the common term 'Cauliflower Ear'. Should the ear drum rupture, the only treatment option is to heal the existing wound with stiches. Even with treatment, significant hearing loss may occur. Today, cosmetic procedures are available which can greatly  improve the appearance of the ear, even though internal damage will persist.

# Diagnosis

## Physical Examination

### Ear Nose and Throat
Cavernous sinus
The cavernous sinus (or lateral sellar compartment) is a large collection of thin-walled veins creating a cavity bordered by the sphenoid bone and the temporal bone of the skull.

# Contents
Each cavernous sinus (one for each hemisphere of the brain) contains the following:
- vertically, from superior to inferior
-culomotor nerve (CN III)
trochlear nerve (CN IV)
-phthalmic nerve, the V1 branch of the trigeminal nerve (CN V)
maxillary nerve, the V2 branch of CN V
- oculomotor nerve (CN III)
- trochlear nerve (CN IV)
- ophthalmic nerve, the V1 branch of the trigeminal nerve (CN V)
- maxillary nerve, the V2 branch of CN V
- horizontally
internal carotid artery (and sympathetic plexus). See also cavernous part of internal carotid artery.
abducens nerve (CN VI)
- internal carotid artery (and sympathetic plexus). See also cavernous part of internal carotid artery.
- abducens nerve (CN VI)
One mnemonic for remembering the contents is "OTOM CAT"

# Venous connections
It receives tributaries from:
- Superior and inferior ophthalmic veins
- Superior parietal sinus
- Superior and middle cerebral veins
The veins of exit are to the superior and inferior petrosal sinuses as well as via the emissary veins through the foramina of the skull.
There are also connections with the pterygoid plexus of veins via inferior ophthalmic vein, deep facial vein and emissary veins.

# Clinical significance
It is the only anatomic location in the body in which an artery travels completely through a venous structure. If the internal carotid artery ruptures within the cavernous sinus, an arteriovenous fistula is created (more specifically, a carotid-cavernous fistula).
The pituitary gland lies directly below the cavernous sinus. An abnormally growing pituitary adenoma, surrounded on all other sides by the bony walls of the sella turcica, will expand in the direction of least resistance and eventually compress the cavernous sinus. Cavernous sinus syndrome may result from mass effect of these tumors and cause ophthalmoplegia (from compression of the oculomotor nerve, trochlear nerve, and abducens nerve), ophthalmic sensory loss (from compression of the ophthalmic nerve), and maxillary sensory loss (from compression of the maxillary nerve).

# Additional images
- Veins of orbit.
- Pathways in the Ciliary Ganglion.
Celera Genomics

# Overview
Celera Genomics (Template:Nyse) is a business unit of the Applera Corporation that focuses on genetic sequencing and related technologies.  Headquartered in Rockville, Maryland, it was established in May 1998 by the Perkin-Elmer Corporation (and was later purchased by Applera), with Dr. J. Craig Venter from The Institute for Genomic Research (TIGR) as its first president. While at TIGR, Venter and Hamilton Smith led the first successful effort to sequence an entire organism's genome, that of the Haemophilus influenzae bacterium. Celera was formed for the purpose of generating and commercializing genomic information to accelerate the understanding of biological processes.  Its stock is a tracking stock of Applera, along with the tracking stock of Applera's larger Applied Biosystems Group business unit.
Celera Genomics researchers were among the first to show the feasibility of the whole genome shotgun strategy for sequencing large eukaryotic genomes.  The strategy was already in widespread use for smaller prokaryotic genomes, which include bacteria and archaea.  This strategy contrasted with the publicly funded Human Genome Project, which used a slower but safer clone by clone sequencing strategy. Celera sequenced the human genome at a fraction of the cost of the public project (approximately $3 billion of taxpayer dollars versus about $300 million of private funding). However, it must be noted that a significant portion of the human genome had already been sequenced when Celera entered the field and thus Celera did not incur any costs with obtaining the existing data, which was freely available to the public from GenBank. Celera's use of the shotgun strategy spurred the public HGP to change its own strategy, leading to a rapid acceleration of the public effort.
Critics of initial efforts by Celera Genomics to hold back data from sections of genome they sequenced for commercial exploitation felt that it would retard progress in science as a whole.  These critics pointed to the open access policy for gene sequences from the publicly funded Human Genome Project.  Later, the company changed their policy and made their sequences available for non-commercial use, but set a maximum threshold for amount of sequence data a researcher could download at any given time.
The rise and fall of Celera as an ambitious competitor of the Human Genome Project is the main subject of the book The Genome War by James Shreeve, who takes a strong pro-Venter point of view.  (He followed Venter around for two years in the process of writing the book.)  A view from the public effort's side is that of Nobel laureate Sir John Sulston in his book The Common Thread: A Story of Science, Politics, Ethics and the Human Genome.

# Genomes sequenced by Celera Genomics
Eukaryotes:
- Drosophila melanogaster (fruit fly)
- Human genome
- Mouse genome
- Elephant genome
- Three-toed Sloth genome
Cellular memory

# Overview
Cellular memory is the unproven hypothesis that such things as memories, habits, interests, and tastes may somehow be stored in all the cells of human bodies, i.e. not only in the brain. The suggestion arose following a number of organ transplants in which the recipient was reported to have developed the memories and interests of the donor.
An article, "Changes in Heart Transplant Recipients That Parallel the Personalities of Their Donors", published in the Spring 2002 issue of the Journal of Near-Death Studies without peer review, sources or evidence, reported anecdotes in which recipients "inherited" a love for classical music, a change of sexual orientation, changes in diet and vocabulary, and in one case an identification of the donor's murderer.
The academic organ transplant community rejects this notion as pseudoscientific and absurd, as it has never been demonstrated in a scientific manner. There is also the fear that such notions may hinder organ donation.
Centrophenoxine

# Overview
Centrophenoxine (also called Meclofenoxate, and formerly sold under the brand name Lucidril) is a drug used to treat the symptoms of senile dementia and Alzheimer's Disease. It is a compound of two biochemicals: dimethylaminoethanol (DMAE) and parachlorophenoxyacetate (pCPA).  DMAE is a natural substance, found especially in fish, and also produced in the human brain.  pCPA is a synthetic compound that resembles to a variety of plant hormones called auxins.
Like DMAE, it is a precursor to the neurotransmitter acetylcholine and may increase levels of this chemical in the CNS. It is reported to improve memory and general cognition.
It is also used off-label as a nootropic, often combined with a racetam drug such as piracetam.

# Side Effects & Contraindications
Possible side effects may include nausea or mild dizziness. People with severely high blood pressure or convulsive disorders such as epilepsy should avoid Centrophenoxine.  Large doses may cause tight jaw clenching.
Cervical plexus

# Overview
The cervical plexus is a plexus of the ventral rami of the first four cervical spinal nerves which are located from C1 to C4 cervical segment in the neck.  They are located laterally to the transverse processes between prevertebral muscles from the medial side and vertebral (m.scalenus, m.levator scapulae, m.splenius cervicis) from lateral side.  Here there is anastomosis with accessory nerve, hypoglossal nerve and sympathetic trunk.
It is located in the neck, deep to sternocleidomastoid. Nerves formed from the cervical plexus innervate the back of the head, as well as some neck muscles.  The branches of the cervical plexus emerge from the posterior triangle at the nerve point, a point which lies midway on the posterior border of the Sternocleidomastoid.

# Branches
has two types of branches: cutaneous and muscular.
- Cutaneous (4 branches):
Lesser occipital nerve - innervates lateral part of occipital region (C2,C3)
Greater auricular nerve - innervates skin near concha auricle and external acoustic meatus (C2&C3)
Transverse cervical nerve - innervates anterior region of neck (C2&C3)
Supraclavicular nerves - innervate region of suprascapularis, shoulder, and upper thoracic region (C3,C4)
- Lesser occipital nerve - innervates lateral part of occipital region (C2,C3)
- Greater auricular nerve - innervates skin near concha auricle and external acoustic meatus (C2&C3)
- Transverse cervical nerve - innervates anterior region of neck (C2&C3)
- Supraclavicular nerves - innervate region of suprascapularis, shoulder, and upper thoracic region (C3,C4)
- Muscular
ansa cervicalis (loop formed from C1-C3), etc. (geniohyoid (C1 only), thyrohyoid (C1 only), sternothyroid, sternohyoid, omohyoid)
- ansa cervicalis (loop formed from C1-C3), etc. (geniohyoid (C1 only), thyrohyoid (C1 only), sternothyroid, sternohyoid, omohyoid)

# Diagram

# Additional images
- Plan of the cervical plexus.
- The nerves of the scalp, face, and side of neck.
- The right sympathetic chain and its connections with the thoracic, abdominal, and pelvic plexuses.
- Side of neck, showing chief surface markings.
Charles Nicolle

# Overview
Charles Jules Henry Nicolle (September 21, 1866 Rouen - February 28, 1936) was a French bacteriologist who earned the 1928 Nobel Prize in Medicine for his identification of lice as the transmitter of epidemic typhus.

# Biography
He learned about biology early from his father Eugene Nicolle, a doctor at a Rouen hospital.  He received his M.D. in 1893 from the Pasteur Institute.  At this point he returned to Rouen, as a member of the Medical Faculty until 1896 and then as Director of the Bacteriological Laboratory.
In 1903 Nicolle became Director of the Pasteur Institute, where he did his Nobel Prize-winning work on typhus.  He was still director of the Institute when he died in 1936.
He also wrote fiction and philosophy through his life, including the books Le Patissier de Bellone, Les deux Larrons, and Les Contes de Marmouse.
He married Alice Avice in 1895, and had two children, Marcelle (b. 1896) and Pierre (b. 1898).

# Accomplishments
Nicolle's major accomplishments in bacteriology were:
- The discovery of the transmission method of typhus fever
- The introduction of a vaccination for Malta fever
- The discovery of the transmission method of tick fever
- His studies of cancer, scarlet fever, rinderpest, measles, influenza, tuberculosis and trachoma.
During his life Nicolle wrote a number of non-fiction and bacteriology books, including Le Destin des Maladies infectieuses; La Nature, conception et morale biologiques; Responsabilites de la Medecine, and La Destinee humaine.

# Discovery of the Vector
Nicolle's discovery came about first from his observation that, while epidemic typhus patients were able to infect other patients inside and outside the hospital, and their very clothes seemed to spread the disease, they were no longer infectious when they had had a hot bath and a change of clothes. Once he realized this, he reasoned that it was most likely that lice were the vector for epidemic typhus.
In June 1909 Nicolle tested his theory by infecting a chimpanzee with typhus, retrieving the lice from it, and placing it on a healthy chimpanzee.  Within 10 days the second chimpanzee had typhus as well. After repeating his experiment he was sure of it: lice were the carriers.
Further research showed that the major transmission method was not louse bites but excrement: lice infected with typhus turn red and die after a couple of weeks, but in the meantime they excrete a large amount of microbes. When a small quantity of this is rubbed on the skin or eye, an infection occurs.

# Attempt at a Vaccine
Nicolle surmised that he could make a simple vaccine by crushing up the lice and mixing it with blood serum from recovered patients.  He first tried this vaccine on himself, and when he stayed healthy he tried it on a few children (because of their better immune systems), who developed typhus but recovered.
He did not succeed in his effort to develop a practical vaccine. The next step would be taken by Rudolf Weigl in 1930.
Charles Mantoux
Charles Mantoux (1877 - 1947) was a French physician, the developer of the eponymous serological test for tuberculosis.
He graduated from the University of Paris where he studied under Broca. For health reasons he relocated to Cannes but continued to work in Paris during the long vacation periods granted to patients in sanatoriums.
In 1908 he presented his first study of intradermal injections to the French Academy of Sciences and published this work in 1910, and in the following years the intradermal test replaced the subcutaneous test (Pirquet test).
This, and other contributions to Public health and radiology, was done away from major universities and institutions.
Cheminformatics
Cheminformatics (also known as chemoinformatics and chemical informatics)  is the use of computer and informational techniques, applied to a range of problems in the field of chemistry. These in silico techniques are used in pharmaceutical companies in the process of drug discovery. These methods can also be used in chemical and allied industries in various other forms.

# History
The term Chemoinformatics was defined by F.K. Brown  in 1998:
Chemoinformatics is the mixing of those information resources to transform data into information and information into knowledge for the intended purpose of making better decisions faster in the area of drug lead identification and optimization.
Since then, both spellings have been used, and some have evolved to be established as Cheminformatics , while European Academia settled in 2006 for Chemoinformatics. 

# Basics
Cheminformatics combines the scientific working fields of chemistry and computer science for example in the area of chemical graph theory and mining the chemical space. It is to be expected that the chemical space contains at least 10^{60} molecules.
Cheminformatics can also be applied to data analysis for various industries like paper and pulp,dyes and such allied industries.

# Applications

## Storage and retrieval
The primary application of cheminformatics is in the storage of information relating to compounds. The efficient search of such stored information includes topics that are dealt in computer science as data mining and machine learning. Related research topics include:
- Unstructured data
- Structured Data Mining and mining of Structured data
Database mining
Graph mining
Molecule mining
Sequence mining
Tree mining
- Database mining
- Graph mining
- Molecule mining
- Sequence mining
- Tree mining

### File formats
The in silico representation of chemical structures uses specialized formats such as the XML-based Chemical Markup Language, or SMILES.  These representations are often used for storage in large chemical databases. While some formats are suited for visual representations in 2 or 3 dimensions, others are more suited for studying physical interactions, modeling and docking studies.

## Virtual screening
In contrast to high-throughput screening, virtual screening involves the creation of large in silico virtual libraries of compounds, which are then submitted to a docking program in order to identify the most active members. In some cases, combinatorial chemistry is used in the development of the library to increase the efficiency in mining the chemical space. More commonly, a diverse library of small molecules or natural products is screened.

## Quantitative structure-activity relationship (QSAR)
This is the calculation of quantitative structure-activity relationship and quantitative structure property relationship values, used to predict the activity of compounds from their structures. In this context there is also a strong relationship to Chemometrics. Chemical expert systems are also relevant, since they represent parts of chemical knowledge as an in silico representation.