Persius/hicric huggingface dataset:
Nyctalopin
Nyctalopin is a protein located on the surface of photoreceptor-to-ON bipolar cell synapse in the retina. It is composed of 481 amino acids. and is encoded in human by the NYX gene. This gene is found on the chromosome X and has two exons. This protein is a leucine-rich proteoglycan which is expressed in the eye, spleen and brain in mice. Mutations in this gene cause congenital stationary night blindness in humans (CSNB). which is a stable retinal disorder. The consequence of this mutation results in an abnormal night vision. Nyctalopin is critical due to the fact that it generates a depolarizing bipolar cell response due to the mutation on the NYX gene. Most of the time, CSNB are associated to hygh myopia which is the result of a mutation on the same gene. Several mutations can occur on the NYX gene resulting on many form of night blindness in humans. Some studies show that these mutations are more present in Asian population than in Caucasian population. A mouse strain called nob (no b-wave) carries a spontaneous mutation leading to a frameshift in this gene. These mice are used as an animal model for congenital stationary night blindness.

# Discovery
The first evidence of the existence of mutation in NYX gene, encoding the leucine-rich proteoglycan nyctalopin, cause X-linked complete congenital stationary night blindness was provided by Richard G. Weleber at the University of Alberta in 2000.

# Gene location
The NYX gene is located on the short arm (p) of chromosome X, from base pair 41,447,434  to base pair 41,475,710.

# Protein structure
Nyctalopin contains a N-terminal signal peptide and a C-terminal glycosylphosphatidylinositol (GPI) anchor. Predicted signal sequence is likely to be processed by a co-translational mechanism. Nyctalopin does not have two transmembrane domains and the only transmembrane domain is found to be between the amino acid 452 ad 472. In the endoplasmic reticulum, the protein is oriented with the N-terminus in the lumen of the endoplasmic reticulum and the C-terminus is located in the cytoplasm. The central part of the polypeptide encodes 11 consecutive leucines-rich repeats (LRRs). These LRR are flanked by N-terminal and C-terminal rich LRRs Tandem LRRs domains are folded into -sheets and -helices, all joined by loops. According to the cysteine pattern, nyctalopin is part of the class II small leucine-rich proteoglycans. These proteins, are involved in several functions such as cell signalling, growth control, and formation of the extracellular matrix. LRR domains are involved in the proteinprotein interaction in small leucine rich repeat proteoglycan family members. Also, LRR domains have a critical role in nyctalopin function. Congenital stationary night blindness in humans appears when a mutation in the LRR domains of nyctalopin occurs.

# Mutations
The complete form of congenital stationary night blindness is due to the absence of nyctalopin. This absence is due to a mutation involving an 85 base pair deletion. In humans, more than 30 mutations are found in the NYX gene and most of them have an impact either on the tertiary structure of the LRR domains of nyctalopin or to truncate the protein.
OGN (gene)
Osteoglycin (also called mimecan), encoded by the OGN gene, is a human protein.
This gene encodes a protein which induces ectopic bone formation in conjunction with transforming growth factor beta. This protein is a small proteoglycan which contains tandem leucine-rich repeats (LRR). The gene expresses three transcript variants.
The level of expression of this gene has been correlated with enlarged hearts and more specifically left ventricular hypertrophy.
OS9 (gene)
Protein OS-9 is a protein that in humans is encoded by the OS9 gene.

# Function
This gene encodes a protein that is highly expressed in osteosarcomas. This protein binds to the hypoxia-inducible factor 1 (HIF-1), a key regulator of the hypoxic response and angiogenesis, and promotes the degradation of one of its subunits. Alternate transcriptional splice variants, encoding different isoforms, have been characterized.

# Model organisms
Model organisms have been used in the study of OS9 function. A conditional knockout mouse line called Os9tm1a(EUCOMM)Wtsi was generated at the Wellcome Trust Sanger Institute. Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Additional screens performed:  - In-depth immunological phenotyping
Ochronosis

# Overview
Ochronosis is a dermatological disorder that results in the adverse pigmentation of cartilage from a long term buildup of phenylalanine or tyrosine.
In this disorder, a pigment substance resulting from incomplete catabolism of tyrosine and phenylalanine is deposited, over the years, in cartilage, the eye, and to a lesser degree in the skin.

# Symptoms
Pigmented cartilage may appear blue due to scattering phenomenon, and to a lesser degree this may be true for skin with dermal deposition of this pigment. The skin of the axilla is very likely to be pigmented due to deposits of homogentisic acid in sudoriferous glands in these areas. The clinical features of this metabolic disorder are dark urine, pigmentation of the skin and arthritis. Particularly helpful is the almost constant presence of a patch of pigmentation (gray to brown in color) in the sclera, between the margin of the cornea and the outer or inner canthus. Because of the bluish color produced by the deep pigmentation, this condition may be confused with argyria.
Octopamine

# Overview
Octopamine is a biogenic amine which is closely related to noradrenaline, and has a similar action to dopamine.

# Role in invertebrates
Octopamine was first discovered by Italian scientist Vittorio Erspamer in 1948 in the salivary glands of the octopus and has since been found to act as neurotransmitter, neurohormone and neuromodulator in invertebrates. It is widely used in energetically demanding behaviours by all insects, crustaceans (crabs, lobsters, crayfish) and spiders. Such behaviours include flying, egg-laying and jumping.
The best understood role for octopamine is in the locust jump. Here it modulates muscle activity, making the leg muscles contract more effectively. This is at least in part due to an increase in the rate of contraction and of relaxation.
In the honey bee and fruit fly, octopamine has a major role in learning and memory. In the firefly, octopamine release leads to light production in the lantern.
Octopamine also plays a role in mollusks, though the role of octopamine has only been examined in the central nervous system of the model organism, the pond snail.
Heberlein et al  have conducted studies of alcohol tolerance in fruit flies; they found that a mutation that caused octopamine deficiency also caused lower alcohol tolerance.

# Role in vertebrates
In vertebrates, octopamine also replaces norepinephrine in sympathetic neurons with chronic use of monoamine oxidase inhibitors.  It is responsible for the common side effect profile of orthostatic hypotension with these agents.
In mammals, octopamine may mobilise the release of fat from adipocytes (fat cells), and this has led to its promotion on the internet as a slimming aid.  However, the released fat is likely to be promptly taken up into other cells, and there is no evidence that octopamine facilitates weight loss.  Octopamine may also increase blood pressure significantly when combined with other stimulants, as in some weight loss supplements.

# Use in humans
In some countries octopamine is gaining increased commercial interest as an ingredient in benzylpiperazine free 'party pills'  due to the fact that in countries such as New Zealand where it is currently legal, BZP faces a probable ban before the end of 2007. It should be noted however that the structure of octopamine falls within the definition of an "amphetamine analogue" in Class C7 of the New Zealand Misuse of Drugs Act, and so would probably be considered an illegal drug if it were tested in court, although no prosecutions involving this compound have been carried out so far.
Odds ratio
The odds ratio is a measure of effect size particularly important in Bayesian statistics and logistic regression.
It is defined as the ratio of the odds of an event occurring in one group to the odds of it occurring in another group, or to a sample-based estimate of that ratio.  These groups might be men and women, an experimental group and a control group, or any other dichotomous classification.  If the probabilities of the event in each of the groups are p (first group) and q (second group), then the odds ratio is:
An odds ratio of 1 indicates that the condition or event under study is equally likely  in both groups.  An odds ratio greater than 1 indicates that the condition or event is more likely in the first group. And an odds ratio less than 1 indicates that the condition or event is less likely in the first group. The odds ratio must be greater than or equal to zero. As the odds of the first group approaches zero, the odds ratio approaches zero.  As the  odds of the second group approaches zero, the odds ratio approaches positive infinity.
For example, suppose that in a sample of 100 men, 90 have drunk wine in the previous week, while in a sample of 100 women only 20 have drunk wine in the same period.  The odds of a man drinking wine are 90 to 10, or 9:1, while the odds of a woman drinking wine are only 20 to 80, or 1:4 = 0.25:1. Now, 9/0.25 = 36, so the odds ratio is 36, showing that men are much more likely to drink wine than women. Using the above formula for the calculation yields:
This example also shows how odds ra can sometimes seem to overstate relative positions: in this sample men are 4.5 times more likely to have drunk wine than women, but have 36 times the odds.
Taking the logarithm of the odds ratio ameliorates this effect, and also improves symmetry. For example, using natural logarithms, an odds ratio of 36 maps to 3.584, an odds ratio of one maps to zero, and an odds ratio of 1/36 maps to -3.584.
The logarithm of the odds ratio is the difference of the logits of the probabilities.
The increased use of logistic regression in medical and social science research means that the odds ratio is commonly used as a means of expressing the results in some forms of clinical trials, in survey research, and in epidemiology, such as in case-control studies. It is often abbreviated "OR" in reports. When data from multiple surveys is combined, it will often be expressed as "Pooled OR".
Oleic acid

# Overview
Oleic acid is a monounsaturated omega-9 fatty acid found in various animal and vegetable sources. It has the formula C18H34O2 (or CH3(CH2)7CH=CH(CH2)7COOH). The saturated form of this acid is stearic acid.
Oleic acid makes up 55-80% of olive oil, though there may be only 0.5-2.5% or so as actual free acid, and 15-20% of grape seed oil and Sea buckthorn oil.
Reduction of oleic acid at the carboxyl end yields oleyl alcohol.
Oleic acid is emitted by the decaying corpses of a number of insects, including bees and Pogonomyrmex ants and triggers the instincts of living workers to remove the dead bodies from the hive. If a live bee or ant is daubed with oleic acid, it is dragged off as if it were dead.
Oligomycin
Oligomycins are macrolides created by Streptomyces that can be poisonous to other organisms.

# Function
They have use as antibiotics.
In addition, oligimycin inhibits ATP synthase by blocking its proton channel, which is necessary for oxidative phosphorylation of ADP to ATP (energy production).
Administering oligomycin to an individual can result in very high levels of lactate accumulating in the blood and urine.
hu:Oligomicin
Ophiovirus

# Overview
The viral genus Ophiovirus is characterized by an elongated and highly filamentous and flexible nucleocapsid with helical symmetry.
Virus capsid is not enveloped and have a constant diameter of 1500-2500 nm and a width of 3 nm, or 9 nm.  They form kinked circles, which can collapse to form linear duplex structures, much like a spring.  The entire genome is 1100-1200 nucleotides long.
The best studied species under this genus is the Citrus psorosis virus.
Opsophagos

# Background
Opsophagos was an ancient Greek term used to describe one who exhibited a seemingly uncontrollable desire for fish. This term had extremely negative connotations, as it was a criticism not of one's tastes, but rather of one's character.
To be labeled an opsophagos was to be accused of obsessive and over-indulgent behavior, and this was no small charge in ancient Greek society, since such behavior was understood to imply the corruption of the soul. Proper humans were expected to be rational and exercise moderation, so those who could not control their desires were seen as barbaric and uncivilized.
Tales of infamous opsophogoi (plural form) depicted men who took their obsession and greed to unbelievable levels, training their bodies in various ways to be able to consume massive quantities of fish immediately after they had been prepared, ensuring that they would have the fish to themselves, since they would be too hot for others to even touch, let alone eat. These tales of men with heat-resistant throats and padded fingertips were likely fictional, but they served as reminders to all who heard them that letting the pleasure-driven body overcome the rational soul was not the way to become an ideal human. One could enjoy fish, but one had to be careful not to take this enjoyment too far and become an opsophagos.
Source: Davidson, James (1997). Courtesans and Fishcakes: The Consuming Passions of Classical Athens. Great Britain:  Harper Collins. Retrieved 2007-02-10..mw-parser-output cite.citation{font-style:inherit}.mw-parser-output q{quotes:"\"""\"""'""'"}.mw-parser-output code.cs1-code{color:inherit;background:inherit;border:inherit;padding:inherit}.mw-parser-output .cs1-lock-free a{background:url("")no-repeat;background-position:right .1em center}.mw-parser-output .cs1-lock-limited a,.mw-parser-output .cs1-lock-registration a{background:url("")no-repeat;background-position:right .1em center}.mw-parser-output .cs1-lock-subscription a{background:url("")no-repeat;background-position:right .1em center}.mw-parser-output .cs1-subscription,.mw-parser-output .cs1-registration{color:#555}.mw-parser-output .cs1-subscription span,.mw-parser-output .cs1-registration span{border-bottom:1px dotted;cursor:help}.mw-parser-output .cs1-hidden-error{display:none;font-size:100%}.mw-parser-output .cs1-visible-error{display:none;font-size:100%}.mw-parser-output .cs1-subscription,.mw-parser-output .cs1-registration,.mw-parser-output .cs1-format{font-size:95%}.mw-parser-output .cs1-kern-left,.mw-parser-output .cs1-kern-wl-left{padding-left:0.2em}.mw-parser-output .cs1-kern-right,.mw-parser-output .cs1-kern-wl-right{padding-right:0.2em}
Optineurin
Optineurin is a protein that in humans is encoded by the OPTN gene.

# Function
This gene encodes the coiled-coil containing protein optineurin. Optineurin may play a role in normal-tension glaucoma and adult-onset primary open angle glaucoma. Optineurin interacts with adenovirus E3-14.7K protein and may utilize tumor necrosis factor-alpha or Fas-ligand pathways to mediate apoptosis, inflammation or vasoconstriction. Optineurin may also function in cellular morphogenesis and membrane trafficking, vesicle trafficking, and transcription activation through its interactions with the RAB8, huntingtin, and transcription factor IIIA proteins. Alternative splicing results in multiple transcript variants encoding the same protein.

# Model organisms
Model organisms have been used in the study of OPTN function. A conditional knockout mouse line, called Optntm1a(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  at the Wellcome Trust Sanger Institute.
Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Twenty one tests were carried out on mutant mice, however no significant abnormalities were observed.

# Interactions
Optineurin has been shown to interact with Huntingtin and RAB8A.
Oral torus

# Overview
Oral Torus is a legion made of compact bone and occurs along the palate or the mandible inside the mouth.  The palatal torus or torus palatinus occurs along the palate, close to the midline, where as the mandibular torus or torus mandibularis occur along the lingual side of the mandible.
Occurrences of tori are more frequent in women then they are in men.  Tori are associated with adulthood and rarely appear before the age of 15.  The palatal version of tori have a higher occurrence in Native American and Inuit populations.
Treatment is not necessary unless they become an obstruction to chewing or prosthetic appliances.
Orange oil
Orange oil is an essential oil produced by glands inside the rind of an orange fruit.  It is extracted or steam distilled as a by-product of orange juice production.  It is composed mostly of d-limonene, and is therefore often used in place of pure lemon, which can be further extracted from the oil by distillation.

# Limonene
Limonene is what gives citrus fruit their familiar aroma, and is therefore used in perfume and household cleaners for its fragrance.  It is also an effective, environmentally friendly, and relatively safe solvent, which makes it an active ingredient of choice in many applications, such as, but not limited to, adhesive and stain removers, cleaners of various sorts, and strippers.

# Safety
The limonene which is the main component of the oil is a mild hand irritant, by virtue of dissolving the protective oils in the skin.  It is wise to wear solvent-resistant gloves when handling limonene solutions.
Limonene is also combustible.  If you squeeze an orange peel in front of a flame, the glands will burst with an aerosol that will ignite on contact with the flame.
Limonene has been observed to cause cancer in male rats, by reacting with 2U-globulin, which is not produced by female rats.  There is no evidence for carcinogenicity or genotoxicity in humans.  The IARC classifies d-limonene under Class 3: not classifiable as to its carcinogenicity to humans. 
For more details of the regulatory status and toxicity, see limonene.

# Insecticide
d-Limonene serves as a natural insect repellent for citrus fruits.  Direct contact with d-Limonene can act as an organic insecticide.  Experiments with fruit flies have shown that they by-pass this problem by laying eggs between the oil-producing glands.
Also effective on Drywood Termites
Orchialgia
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# Overview
Orchialgia is chronic pain of the testicles or scrotum that typically lasts for more than three months.

# Causes

## Common Causes
- Cancer
- Injury
- Orchialgia is a possible complication after vasectomy.
- Surgery
- Testicular torsion

# Diagnosis

## History and Symptoms
Patient usually complaints of deep aching pain in the testes. Following history has to be taken from a patient presenting with complaints of testicular pain:
- Onset can be sudden or gradual
- Site location: Unilateral or bilateral (bilateral testicular pain is more commonly seen)
- Intermittent or constant: Pain is usually intermittent and can shift from one side to the other.
- Type of pain: Patients usually have deep aching pain.
- Associated symptoms:
Local area redness, warmth and swelling can be seen in case of testicular torsion or infections.
Associated back pain and pain in inguinal area may be seen.
Epididymitis is often accompanied by symptoms of a urinary tract infection, fever, and in over half of cases it presents in combination with orchitis.
- Local area redness, warmth and swelling can be seen in case of testicular torsion or infections.
- Associated back pain and pain in inguinal area may be seen.
- Epididymitis is often accompanied by symptoms of a urinary tract infection, fever, and in over half of cases it presents in combination with orchitis.
- Recent history of surgery and trauma to the local area needs to be elicited to know the cause of the pain.

## Laboratory Findings
Testing for gonorrhea and chlamydia should be routinely performed.

# Treatment

## Medical Therapy
Treatment is often with NSAIDs and antibiotics. However, this  is not always effective.

# Related Chapters
- Post-vasectomy pain syndrome
Osteoblast

# Overview
An osteoblast (from the Greek words for "bone" and "germ" or embryonic) is a mononucleate cell that is responsible for bone formation. Osteoblasts produce osteoid, which is composed mainly of Type I collagen. Osteoblasts are also responsible for mineralization of the osteoid matrix. Bone is a dynamic tissue that is constantly being reshaped by osteoblasts, which build bone, and osteoclasts, which resorb bone.

# Osteogenesis
Osteoblasts arise from osteoprogenitor cells located in the periosteum and the bone marrow. Osteoprogenitors are immature progenitor cells that express the master regulatory transcription factor Cbfa1/Runx2.
Osteoprogenitors are induced to differentiate under the influence of growth factors, in particular the bone morphogenetic proteins (BMPs). Aside from BMPs, other growth factors including fibroblast growth factor (FGF), platelet-derived growth factor (PDGF), transforming growth factor beta (TGF-) may promote the division of osteoprogenitors and potentially increase osteogenesis.
Once osteoprogenitors start to differentiate into osteoblasts, they begin to express a range of genetic markers including Osterix, Col1, ALP, osteocalcin, osteopontin, and osteonectin. Although the term osteoblast implies an immature cell type, osteoblasts are in fact the mature bone cells entirely responsible for generating bone tissue in animals and humans.

# Morphology and histological staining
The cytoplasm of osteoblasts appears to be basophilic via normal H&E stain due to presence of large amount of rough endoplasmic reticulum. A large Golgi apparatus is also present in the centre. The nucleus is spherical and large. Osteoblasts can be stained for type 1 collagen or for the production of alkaline phosphatase.

# Osteoblasts and osteocytes
Osteoblasts   that become trapped in the bone matrix become osteocytes. They cease to generate osteoid and mineralized matrix, and instead act in a paracrine manner on active osteoblasts. They are believed to act in a mechanosensory manner.