Persius/hicric huggingface dataset:
Coilin
Coilin is a protein that in humans is encoded by the COIL gene. Coilin got its name from the coiled shape of the CB in which it is found. It was first identified using human autoimmune serum.

# Function
Coilin protein is one of the main molecular components of Cajal bodies (CBs). Cajal bodies are nuclear suborganelles of varying number and composition that are involved in the post-transcriptional modification of small nuclear and small nucleolar RNAs. In addition to its structural role, coilin acts as glue to connect the CB to the nucleolus. The N-terminus of the coilin protein directs its self-oligomerization while the C-terminus influences the number of nuclear bodies assembled per cell. Differential methylation and phosphorylation of coilin likely influences its localization among nuclear bodies and the composition and assembly of Cajal bodies. This gene has pseudogenes on chromosome 4 and chromosome 14.
To study CBs, coilin can be combined with GFP (Green Fluorescent Protein) to form Coilin-GFP hybrid protein.  The hybrid protein can then be used to locate CBs underneath a microscope, usually near the nucleolus of the cell.  Other proteins that make up the CB include snRNPs and nucleolar snoRNPs.
Coilin has been shown to interact with ataxin 1, nucleolar phosphoprotein p130, SMN, and SNRPB.
Coptis
Coptis (Gold Thread or Goldenthread) is a genus of between 1015 species of flowering plants in the family Ranunculaceae, native to Asia and North America.
- Coptis aspleniifolia
- Coptis chinensis
- Coptis deltoidea
- Coptis groenlandica
- Coptis japonica
- Coptis laciniata
- Coptis occidentalis
- Coptis omeiensis
- Coptis quinquefolia
- Coptis quinquesecta
- Coptis teeta
- Coptis trifolia

# Uses
Coptis teeta is used as a medicinal herb in the Himalayan regions of India, used as a bitter tonic for dyspepsia.  It is also known to help insomnia in Chinese Medicine
Made into a paste, salve, powder, or infusion, it is said to improve digestion, restore appetite, and relieve inflammation of the stomach. It is also employed to assist the treatment of alcoholism.
Dermis
The dermis is a layer of skin beneath the epidermis that consists of connective tissue, and cushions the body from stress and strain.The dermis is the lower layer  of skin; contains main blood vessels. The dermis is tightly connected to the epidermis by a basement membrane, and harbors many nerve endings that provide the sense of touch and heat. It contains the hair follicles, sweat glands, sebaceous glands, apocrine glands, and blood vessels. The blood vessels in the dermis provide nourishment and waste removal to its own cells, as well as the Stratum basale of the epidermis.

# Structure
The dermis is structurally divided into two areas: a superficial area adjacent to the epidermis, called the papillary region, and a deep thicker area known as the reticular region.

## Papillary region
The papillary region is composed of loose areolar connective tissue. It is named for its fingerlike projections called papillae, which extend toward the epidermis. The papillae provide the dermis with a "bumpy" surface that interdigitates with the epidermis, strengthening the connection between the two layers of skin.
In the palms, fingers, soles, and toes, the influence of the papillae projecting into the epidermis forms contours in the skin's surface. These are called friction ridges, because they help the hand or foot to grasp by increasing friction. Friction ridges occur in patterns (see fingerprint) that are genetically determined and are therefore unique to the individual, making it possible to use fingerprints or footprints as a means of identification.

## Reticular region
The reticular region lies deep to the papillary region and is usually much thicker. It is composed of dense irregular connective tissue, and receives its name from the dense concentration of collagenous, elastic, and reticular fibers that weave throughout it. These protein fibers give the dermis its properties of strength, extensibility, and elasticity.
Located within the reticular region are also the hair roots, sebaceous glands, sweat glands, receptors, nails, and blood vessels.
Tattoo ink is injected into the dermis.  Stretch marks are also located in the dermis.

# Additional images
- Cross-section of all skin layers.
Corojo
Corojo is a type of tobacco, primarily used in the making of cigars, originally grown in the Vuelta Abajo region of Cuba.

# Origin
Corojo was originally developed and grown by Diego Rodriguez at his farm or vega, Santa Ines del Corojo and takes its name from the farm. It was used as a wrapper extensively for many years on Cuban cigars, but its susceptibility to various diseases, Blue Mold in particular, caused the Cuban genetic engineers to develop various hybrid forms that would not only be disease-resistant, but would also display excellent wrapper qualities.

# Hybrid or Pure?
Today, both hybrid and pure strains of Corojo are used in the production of cigars.  Most of the pure Corojo leaf is currently grown in Honduras' Jamastran Valley, while the hybrid varieties are more widely grown and used.

# Reference
The basis for summary article is Bernardo, Mark. A Tale of Two Seeds, Smoke Magazine, Spring, 2004 issue (vol. 9, issue 2).
Cortef
Cortef is a steroid tablet containing hydrocortisone, which is a glucocorticoid.  Glucocorticoids are adrenocortical steroids, both naturally occurring and synthetic, which are readily absorbed from the gastrointestinal tract.  Hydrocortisone USP a is white, ordorless, crystalline powder with a melting point of about 215 degrees Celsius.  It is slightly soluble in water and in ether, and is sparingly soluble in acetone and alcohol.  It is also slightly soluble in chloroform.  The chemical name for hydrocortisone is pregn-4-ene-3,20-dione,11,17,21-trihydroxy-(11b)-. Its molecular weight is 362.46g/mol.
Cortef tablets are available for oral administration in three strengths: 5mg, 10mg, or 20mg of hydrocortisone.  The inactive ingredients include calcium stearate, cornstarch, lactose, mineral oil, sorbic acid, and sucrose.  Cortef is combination of naturally occurring glucocorticoids (hydrocortisone and cortisone), which also have salt-retaining properties.  Glucocorticoids are frequently used as replacement therapy in adrenocorical deficiency states.  Their synthetic analogs are primarily used for their potent anti-inflammatory effects in disorders of many organ systems.
Indications and Usage
Cortef is used for the following:
1. Endocrine disorders
- Primary or secondary adrenocortical insufficiency
- congenital adrenal hyperplasia
- nonsuppurative thyroiditis
- hypercalcemia associated with cancer
2. Rheumatic Disorders
- As adjunctive therapy for thort-term administration for:
Psoriatic arthritis
Rheumatoid arthritis
Ankylosing spondylitis
Acute and subacute bursitis
Acute nonspecific tenosynovitis
Acute gouty arthritis
Post-traumatic osteoarthritis
Epicondylitis
- Psoriatic arthritis
- Rheumatoid arthritis
- Ankylosing spondylitis
- Acute and subacute bursitis
- Acute nonspecific tenosynovitis
- Acute gouty arthritis
- Post-traumatic osteoarthritis
- Epicondylitis
3. Collagen Diseases
- During an exacerbation or as maintenance therapy in selected cases of:
Systemic lupus erythematosus
Systemic dermatomyositis
Acute rheumatic carditis
- Systemic lupus erythematosus
- Systemic dermatomyositis
- Acute rheumatic carditis

# Notes and references
-  (pdf)
Cowpox

# Overview
Cowpox (also known as Catpox) is a disease of the skin that is caused by a virus (Cowpox virus) that is related to the Vaccinia virus. The ailment manifests itself in the form of red blisters and is transmitted by touch from infected animals to humans. The virus that causes cowpox was used to perform the first successful vaccination against another disease, smallpox, which is caused by the related Variola virus. Therefore the word "vaccination" has the Latin root vacca meaning cow.
The first vaccination was performed in 1774 by a farmer, Benjamin Jesty, in Dorset, England. He inoculated his wife and two young sons and thus spared them probable death by smallpox which was raging in the area in which they lived. His patients who had contracted and recovered from cowpox (mainly dairymaids), a disease similar to but much milder than smallpox, seemed to be immune not only to further cases of cowpox, but also to smallpox. By scratching the fluid from cowpox lesions into the skin of healthy individuals, he was able to immunize those people against smallpox.
However, credit was stolen by the politically astute Dr. Jenner who performed his first inoculation, having heard of Jesty's work, 22 years later. Even today he is falsely credited with the first vaccination.
The term vaccination was first used by Edward Jenner (an English physician) in 1796.
The virus is found in Europe and mainly in the UK.  Human cases today are very rare and most often contracted from domestic cats.  The virus is not commonly found in cows; the reservoir hosts for the virus are woodland rodents particularly voles.  It is from these rodents that domestic cats contract the virus.  Symptoms in cats include lesions on the face, neck, forelimbs, and paws, and less commonly upper respiratory tract infection.  Symptoms of infection with cowpox virus in humans are localized, pustular lesions generally found on the hands and limited to the site of introduction.  The incubation period is 9-10 days.  The virus is prevalent in late summer and autumn.

# Historical use
Cowpox was the original vaccine of sorts for smallpox. After infection with the disease, the body (usually) gains the ability of recognizing the similar smallpox virus from its antigens and so is able to fight the smallpox disease much more efficiently.  The vaccinia virus now used for smallpox vaccination is sufficiently different from the cowpox virus found in the wild as to be considered a separate virus. Cowpox got its name from cow maids touching the udders of infected cows.
Crista

# Overview
Cristae (singular crista) are the internal compartments formed by the inner membrane of a mitochondrion. They are studded with proteins, including ATP synthase and a variety of cytochromes. The maximum surface for chemical reactions to occur is within the mitochondria. This allows cellular respiration (aerobic respiration since the mitochondria requires oxygen) to occur.

# Electron transport chain of the cristae
NADH is split into NAD+, H+ ions, and electrons by an enzyme. FADH2 is also split into H+ ions, electrons, and FAD. As those electrons travel further through the electron transport chain in the inner membrane, energy is gradually released and used to pump the hydrogen ions from the splitting of NADH and FADH2 into the space between the inner membrane and the outer membrane (called the intermembrane space), creating an electrochemical gradient. As a result, chemiosmosis occurs, producing ATP from ADP and a phosphate group when ATP synthase harnesses the potential energy from the concentration gradient formed by the amount of H+ ions. H+ ions passively pass into the mitochondrian matrix by the ATP synthase, and later on help to reform H2O.
The electron transport chain requires a constant supply of electrons in order to properly function and generate ATP. However, the electrons that have entered the electron transport chain would eventually pile up like cars traveling down a one-way dead-end street. Those electrons are finally accepted by oxygen (O2), which combine with some of the hydrogen ions from the mitochondrian matrix through ATP synthase and the electrons that had traveled through the electron transport chain. As a result they form two molecules of water (H2O). By accepting the electrons, oxygen allows the electron transport chain to continue functioning.
The electrons from each NADH molecule can form a total of 2.5 ATPs from ADPs and phosphate groups through the electron transport chain, while each FADH2 molecule can produce a total of 1.5 ATPs. As a result, the 10 NADH molecules (from glycolysis and the Krebs cycle) and the 2 FADH2 molecules can form a total of 34 ATPs from this electron transport chain during aerobic respiration. This means that combined with the Krebs Cycle and glycolysis, the efficiency for the electron transport chain is about 65%, as compared to only 3.5% efficiency for glycolysis alone.

# Usefulness
The cristae greatly increase the surface area on which the above mentioned reactions take place. If they were absent, the inner membrane would be reduced to a single spherical shape, and with less reaction surface available, the reaction efficiency would be likewise reduced. Therefore, cristae are a necessity for the mitochondria to function efficiently.
ca:Cresta mitocondrial
de:Crista
Crutch
Crutches are medical tools used in the event that one's leg or legs may be injured or unable to support weight. The term, crutch, can also refer to anything used by a person as a psychological or emotional prop, or to something used as an excuse not to engage in normal life activities.

# Medical crutches

## Types
There are several different types of medical crutches:

## Information on use
Several different gait patterns are possible, and the user chooses which one to use depending on the reason the crutches are needed. For example, a person with a leg injury generally performs a "swing-to" gait: he lifts the injured leg, places both crutches in front of himself, and then swings his uninjured leg to meet the crutches. Other gaits are used when both legs are equally affected by some disability, or when the injured leg is partially weight-bearing.
Crutch is also used as a verb to refer to the use of crutches to travel somewhere.  For example: "I am going to crutch to the store," or "I will be crutching over to your place."
The word "crutch" can refer to an object that is a weakness, that the bearer requires in order to function (metaphorically)
Example: Can sexuality be used as a social crutch?

# Materials
- Wooden
- Steel/ other metals
- Aluminium
- Carbon fiber
- Titanium
Cyclin
Cyclins are a family of proteins involved in the progression of cells through the cell cycle. They are the "regulatory subunits of the heterodimeric protein kinases that control cell cycle events."

# Function
A cyclin forms a complex with its partner cyclin-dependent kinase (Cdk), which activates the latter's protein kinase function.
Cyclins are so named because their concentration varies in a cyclical fashion during the cell cycle; they are produced or degraded as needed in order to drive the cell through the different stages of the cell cycle.
When its concentrations in the cell are low, the cyclin detaches from the Cdk, inhibiting the enzyme's activity, probably by causing a protein chain to block the enzymatic site.

# Types
There are several different cyclins which are active in different parts of the cell cycle and which cause the Cdk to phosphorylate different substrates. However, there are several "orphan" cyclins for which no Cdk partner has been identified. For example, cyclin F is an orphan cyclin that is essential for G2/M transition.
Other specific types include:
- Cyclin D
- Cyclin E
- Cyclin A
- Cyclin B

# Domain structure
Cyclins contain two domains of similar all-alpha fold, N- and C-terminal.

# Human proteins with cyclin domains
CABLES2;   CCNA1;     CCNA2;     CCNB1;     CCNB2;     CCNB3;     CCNC;      CCND1;
CCND2;     CCND3;     CCNE1;     CCNE2;     CCNF;      CCNG1;     CCNG2;     CCNH;
CCNI;      CCNJ;      CCNJL;     CCNK;      CCNL1;     CCNT1;     CCNT2;     CCNY;
CCNYL1;    CNTD2;     UDG2;

# History
Leland H. Hartwell, R. Timothy Hunt, and Paul M. Nurse won the 2001 Nobel Prize in Physiology or Medicine for their discovery of cyclin and cyclin-dependent kinase, central molecules in the regulation of the cell cycle.
Cytome

# Overview
Cytomes are the cellular systems, subsystems, and functional components of the 
body. The cytome is the collection of the complex and dynamic cellular processes (structure and function) underlying physiological processes. It describes the structural and functional heterogeneity of the cellular diversity of an organism. The study of cytomes is called Cytomics.
The Human Cytome Project is about the study of the biological system structure and function of an organism at the cytome level. It relates to Cytomics, which is the study of cell systems (cytomes) at a single cell level. At the Focus on Microscopy (FOM) meeting in Philadelphia, on Wednesday afternoon, 7 April 2004, the idea of a Human Cytome Project was for the first time discussed at a scientific meeting.
Cytrel
Cytrel is a cellulose-based tobacco substitute used in some low-tar cigarette brands, famously comprising 25% of the Silk Cut brand.
Development began on a replacement for tobacco in cigarettes in the 1950s, to reduce 'undesirable tobacco smoke components' present in cigarettes. Cyrel was developed by Celanese Fiber Marketing Company.
The fiber went through a difficult development, with scientists struggling to achieve acceptable smoking, taste and manufacturing properties. However, the product was of a lower density than tobacco and useful as a bulking agent so development continued. After five revisions the Celanese Fiber Marketing Company released Type 308 to the market.
It was one of the NSM (New Smoking Materials) that came into popularity in the 1970s.
DEPTOR
DEP domain-containing mTOR-interacting protein (DEPTOR) also known as DEP domain-containing protein 6 (DEPDC6) is a protein that in humans is encoded by the DEPTOR gene.

# Structure
The gene DEPTOR can be found only in vertebrates. In human, DEPTOR gene locates at chromosome 8, 8q24.12 with protein size 409 a.a. Human DEPTOR contains two N-terminal DEP domains and a C-terminal PDZ domain.

# Function
DEPTOR is involved in mTOR signaling pathway as an endogenous regulator. A direct interaction between DEPTOR and mTOR has been shown. Overexpression of DEPTOR downregulates the activity of mTORC1 and mTORC2 in vitro. mTORC1 and mTORC2 can both inhibit DEPTOR through phosphorylation.

# Metabolism
DEPTOR cell-autonomously regulates adipogenesis. In the muscle, Baf60c promotes a switch from oxidative to glycolytic myofiber type through DEPTOR-mediated Akt/PKB activation. Within the brain, DEPTOR is highly expressed in the hippocampus, the medio-basal hypothalamus and the circumventricular organs. Overexpression of DEPTOR in the medio-basal hypothalamus protects mice against high-fat diet-induced obesity by modulating Akt/PKB signaling.

# Clinical cancer
Although in most cancer, mTOR pathway is constitutively activated and the expression of DEPTOR is low, one study has found that DEPTOR is overexpressed in multiple myeloma cells and is necessary for their survival.
DESOXY
4-desoxymescaline, 4-methyl-3,5-dimethoxyphenethylamine, is a phenethylamine and mescaline analogue with psychedelic properties. It is usually known as DESOXY. It was discovered by Alexander Shulgin and published in PiHKAL.

# Legality
(US) In 1970 the Controlled Substances Act placed mescaline into Schedule I. It is similarly controlled in other nations. 4-desoxymescaline could be considered an analogue of mescaline, under the Federal Analogue Act, making it illegal to manufacture, buy, possess, or distribute without a DEA license.

## Dosage
A typical dosage is within the range of 40-120 mg and lasts 6-8 hours.

## Effects
The effects of DESOXY vary significantly from mescaline, despite their chemical similarity. Users report an elevated mood and some hallucinations, although nothing as intense as visuals reported on mescaline. There has been some suggestion that the dosage level of 40-120 mg might be too small to achieve mescaline-like effects, but since this compound has undergone only limited human experiments it may be unsafe to increase the dosage.

# Reference
-  Template:CitePiHKAL
DFNB31
Whirlin is a protein that in humans is encoded by the DFNB31 gene.
In rat brain, WHRN interacts with a calmodulin-dependent serine kinase, CASK, and may be involved in the formation of scaffolding protein complexes that facilitate synaptic transmission in the central nervous system (CNS). Mutations in this gene, also known as WHRN, cause autosomal recessive deafness.

# Model organisms
Model organisms have been used in the study of WHRN function. A conditional knockout mouse line, called Whrntm1a(EUCOMM)Wtsi was generated as part of the International Knockout Mouse Consortium program  a high-throughput mutagenesis project to generate and distribute animal models of disease to interested scientists.
Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Twenty tests were carried out on mutant mice and two significant abnormalities were observed. Whrntm1a(EUCOMM)Wtsi homozygote mice show a moderate to severe hearing loss at 14 weeks. Female homozygous mutant animals also displayed an increased thermal nociceptive threshold in a hot plate test.
DGLUCY
DGLUCY (D-glutamate cyclase) is a protein that in humans is encoded by the DGLUCY gene.

# Orthologs
The human gene, DGLUCY, is highly conserved in mammals and birds. Orthologs gathered from BLAST and BLAT searches reveal that the human DGLUCY mRNA sequence is conserved with a sequence identity of 98% in chimpanzees, 88% in mice, and 81% in platypus and chicken. The following table contains a list orthologs that were gathered from BLAST searches.  Sequence alignments were performed using blastn to derive sequence identity, score, and E-values between the human c14orf159 variant 1 mRNA and its orthologs.
The protein that the human gene DGLUCY encodes has been found to be highly conserved among mammals, birds, amphibians, fish, tunicates, cnidarians, and echinoderms.  However, no protein orthologs have been found in nematodes, arthropods, fungi, protists, plants, bacteria, or archea.  Fungi and bacteria contain the DUF1445 conserved domain which is found in human c14orf159 and its orthologs.  BLAST and BLAT searches have been utilized to find orthologs to the c14orf159 protein.  The following table lists protein orthologs for the human protein with sequence identity, sequence similarity, scores, and E-values derived from blastp sequence comparisons.

# Post-translational modification
The protein product of the DGLUCY gene is predicted and was found to be translocated to mitochondrion.
Post-translational modifications are predicted for the protein DGLUCY.  All predicted sites in human DGLUCY were compared to orthologs using multiple sequence alignments to determine likelihood of modification.

# Regulation
Estrogen receptor alpha, in the presence of estradiol, binds to the DGLUCY gene and likely regulates its expression.