Persius/hicric huggingface dataset:
NADH dehydrogenase

# Overview
NADH dehydrogenase (EC 1.6.5.3) is an enzyme located in the inner mitochodrial membrane that catalyzes the transfer of electrons from NADH to coenzyme Q (CoQ).
It is also called the NADH:quinone oxidoreductase.

# Reaction
It is the first enzyme (complex I) of the mitochondrial electron transport chain.
In this process, the complex translocates protons across the inner membrane, helping to build the electrochemical potential used to produce ATP. The exact catalytic mechanism remains unknown.

# Composition and structure
It is the largest of the respiratory complexes, the mammalian enzyme containing 42 separate polypeptide chains.  Of particular functional importance are the flavin prosthetic group and eight iron-sulfur clusters.  Of the 42 subunits, seven are encoded by the mitochondrial genome .
The structure is a L shape with a long membrane domain (with around 60 trans-membrane helices) and a hydrophilic peripheral domain which includes the NAD reducing activity. While the structure of the eukaryotic complex is not well characterised the peripheral/hydrophilic domain of the complex from a bacterium (Thermus thermophilus) has been crystallised (PDB: 2FUG) .

# Inhibitor
The best known inhibitor of complex I is Rotenone (used as an organic pesticide). It is thought to bind to the ubiquinone binding site.
Piericidin A is a more potent inhibitor and is a close structural homologue of ubiquinone.

# Pathology
Mutations in the subunits of complex I can cause mitochondrial diseases, including Leigh syndrome.
There is some evidence that complex I defects may play a role in the etiology of Parkinson's disease, perhaps because of reactive oxygen species (complex I can, like complex II, leak electron to oxygen, forming highly toxic superoxide). In fact, recent investigations suggest that reverse electron transfer through Complex I might be the most important site of superoxide production within mitochondria.

# Genes
- NDUFS1 - NADH dehydrogenase (ubiquinone) Fe-S protein 1, 75kDa (NADH-coenzyme Q reductase)
- NDUFS2 - NADH dehydrogenase (ubiquinone) Fe-S protein 2, 49kDa (NADH-coenzyme Q reductase)
- NDUFV1 - NADH dehydrogenase (ubiquinone) flavoprotein 1, 51kDa
- NDUFV2 - NADH dehydrogenase (ubiquinone) flavoprotein 2, 24kDa
- NDUFV3 - NADH dehydrogenase (ubiquinone) flavoprotein 3, 10kDa
- MT-ND4 - mitochondrially encoded NADH dehydrogenase 4
Construct validity
In social science and psychometrics, construct validity refers to whether a scale measures the unobservable social construct (such as "fluid intelligence") that it purports to measure. It is related to the theoretical ideas behind the personality trait under consideration; a non-existent concept in the physical sense may be suggested as a method of organising how personality can be viewed. The unobservable idea of a unidimensional easier-to-harder dimension must be "constructed" in the words of human language and graphics.
A construct is not restricted to one set of observable indicators or attributes.  It is common to a number of sets of indicators. Thus, "construct validity" can be evaluated by statistical methods that show whether or not a common factor can be shown to exist underlying several measurements using different observable indicators. This view of a construct rejects the operationist past that a construct is neither more nor less than the operations used to measure it.
Evaluation of construct validity requires examining the correlation of the measure being evaluated with variables that are known to be related to the construct purportedly measured by the instrument being evaluated or for which there are theoretical grounds for expecting it to be related (Campbell & Fiske, 1959). Correlations that fit the expected pattern contribute evidence of construct validity. Construct validity is a judgment based on the accumulation of correlations from numerous studies using the instrument being evaluated.
There are  variants of construct validity:
- convergent validity,
- discriminant validity, and
- nomological validity.
Context management
Context Management is a dynamic computer process that uses 'subjects' of data in one application, to point to data resident in a separate application also containing the same subject.
Context Management allows users to choose a subject once in one application, and have all other applications containing information on that same subject 'tune' to the data they contain, thus obviating the need to redundantly select the subject in the varying applications.
An example from the healthcare industry where Context Management is widely used, multiple applications operating "in context" through use of a context manager would allow a user to select a patient (i.e., the subject) in one application and when the user enters the other application, that patient's information is already pre-fetched and presented, obviating the need to re-select the patient in the second application.  The further the user 'drills' into the application (e.g., test, result, diagnosis, etc.) all context aware applications continue to drill-down into the data, in context with the user's requests.
Context Management is gaining in prominence in healthcare due to the creation of the Clinical Context Object Workgroup standard committee (CCOW) which has created a standardized protocol enabling applications to function in a 'context aware' state.
Context Management is gaining in the Business Rule market as well.  Knowing the context of any information exchange is critical. For example a seller may need to know such things as: is this shipment urgent, is this a preferred customer,
do they need English or Spanish, what model is the part for? Without context mistakes and run-on costs rapidly ensue.
In automating information integration, knowing and defining context of use is the single most pervasive and important factor.
This context mechanism is at the heart of allowing users to quantify what their context factors are precisely, this removes the guess work from business transaction exchanges between business transaction information management partners and allows them to formulize their collaboration agreements exactly.
Scientific control
A scientific control augments integrity in experiments by isolating variables as dictated by the scientific method in order to make a conclusion about such variables. In a controlled experiment, two virtually identical experiments are conducted. In one of them, the treatment, the factor being tested is applied. In the other, the control, the factor being tested is not applied.
For example, in testing a drug, it is important to carefully verify that the supposed effects of the drug are produced only by the drug itself. Doctors achieve this with a double-blind study in a clinical trial: two (statistically) identical groups of patients are compared, one of which receives the drug and one of which receives a placebo. Neither the patients nor the doctor know which group receives the real drug, which serves both to curb researchers' bias and to isolate the effects of the drug.

# Necessity of controls
Controls are not needed toInsert non-formatted text here eliminate alternate explanations of experimental results.  For example, suppose a researcher feeds an experimental artificial sweetener to sixty four and a half laboratory rats and observes that 0.2 of them subsequently die of dehydration and puke.  The underlying cause of death could be the popcorn itself or something related.  Perhaps the trees were simply  supplied with alot of water; or the water was not contaminated and undrinkable; or the rats were under some psychological or physiological stress that caused them not to drink enough; or a disease dehydrated them; or their cage was kept too hot. Eliminating each of these possible explanations individually would be time-consuming and difficult.  Instead, the researcher can use an experimental control, separating the rats into two groups:  one group that receives the sweetener and one that doesn't.  The two groups are kept in otherwise identical conditions, and both groups are observed in the same ways.  Now, any difference in morbidity between the two groups can be ascribed to the sweetener itself--and no other factor--with much greater confidence.
In other cases, an experimental control is used to prevent the effects of one variable from being drowned out by the known, greater effects of other variables.  For example, suppose a program that gives out free books to children in subway stations wants to measure the effect of the program on standardized test scores.  However, the researchers understand that many other factors probably have a much greater effect on standardized test scores than the free books:  household income, for example, and the extent of parents' education.  In scientific parlance, these are called confounding variables.  In this case, the researchers can either use a control group or use statistical techniques to control for the other variables.
Variables such as independent and dependent.

# Types of controls
Cordial (medicine)
A cordial is any invigorating and stimulating preparation; e.g., peppermint cordial. The term derives from obsolete medicinal usage, as various beverages were concocted which were believed to be beneficial to one's health, especially for the heart (cordialis, Latin). From the Renaissance onwards, cordials were usually based on alcohol in which certain herbs, spices or other ingredients were allowed to steep. Examples of such cordials are Rosa Solis or Rosolio, derived from the carnivorous sundew (Drosera rotundifolia L.) and believed to not only invigorate the heart, but to be an aphrodisiac as well, and Royal Usquebaugh (from  a Celtic word meaning life water which also gave rise to the word whiskey), a spicy concoction containing flecks of gold leaf thought to capture the sun's golden radiance. Precious ingredients like the gold leaf mentioned, as well as pearls and coral were sometimes added. These were believed to revive the spirit and to preclude disease.
Cordials became more and more frequently consumed recreationally as time progressed, eventually evolving into liqueurs.
In the UK cordials are often added to a measure of alcohol to make a "Rum and Black" (Rum with blackcurrent cordial added), "Rum and Pep" (Rum and peppermint cordial), Gin and orange, Vodka and lime, etc.
Corneal epithelium
The corneal epithelium (epithelium corne anterior layer) covers the front of the cornea and consists of several layers of cells.
The cells of the deepest layer are columnar; then follow two or three layers of polyhedral cells, the majority of which are prickle cells similar to those found in the stratum mucosum of the cuticle.
Lastly, there are three or four layers of squamous cells, with flattened nuclei.

# Cornea Cell LASIK Complication
Epithelial ingrowth is a LASIK complication in which cells from the cornea surface layer (epithelial cells) begin to grow underneath the corneal flap.
Epithelial ingrowth is a rarely occurring LASIK complication, appearing in less than one percent of LASIK procedures. However, the incidence of epithelial ingrowth appears to be higher after subsequent enhancement LASIK procedures.
Golgi tendon organ

# Overview
The Golgi organ (also called Golgi tendon organ, neurotendinous organ or neurotendinous spindle), is a proprioceptive sensory receptor organ that is located at the insertion of skeletal muscle fibres into the tendons of skeletal muscle.
The Golgi organ should not be confused with the Golgi Apparatus, which is an organelle in the eukaryotic cell, or the Golgi stain, which is an histologic stain for neuron cell bodies.

# Anatomy
The body of the organ is made up of strands of collagen that are connected at one end to the muscle fibres and at the other merge into the tendon proper. Each tendon organ is innervated by a single afferent type Ib sensory fiber that branches and terminates as spiral endings around the collagen strands. The Ib afferent axon is a large diameter, myelinated axon. Each neurotendinous spindle is enclosed in a fibrous capsule which contains a number of enlarged tendon fasciculi (intrafusal fasciculi). One or more nerve fibres perforate the side of the capsule and lose their medullary sheaths; the axis-cylinders subdivide and end between the tendon fibers in irregular disks or varicosities (see figure).

# Function
During muscle contraction the strands of collagen are stretched as the muscle shortens. This stretching deforms the terminals of the Ib afferent axon, opening stretch-sensitive cation channels. As a result, the axon is depolarized and fires nerve impulses up to the central nervous system via the spinal cord. The action potential frequency signals the force being developed within the muscle.
This sensory feedback plays an important role in spinal reflexes and in the central control of muscle contraction. Specifically, it is postulated that because a Golgi tendon organ exists in serial connection with muscle fibers, it can measure the tension that each muscle contraction builds up. The Ib afferent axon synapses with interneurons within the spinal cord and also relays information to the brain. One of the main spinal reflexes receiving an input from the Ib afferent is the autogenic inhibition reflex, which is involved with the regulation of the force profile of on-going muscle contractions.
The ascending or afferent pathways to the cerebellum are the dorsal and ventral spinocerebellar tracts and are involved in the cerebellar regulation of movement.

# History
It was once believed that Golgi tendon organs were responsible for the clasp-knife reflex observed in spinal cord-injured patients.  This theory has been rejected in favor of one that explains the reflex with free nerve endings.
Creeping buttercup
The Creeping buttercup (Ranunculus repens) is a flowering plant in the Buttercup family, native to Europe and the Pacific Northwest. It has attractive yellow flowers and stolons, running stems, which produce roots and new plants at the nodes. Creeping buttercup has three-lobed dark green, white-spotted leaves that grow out of the node.   The stems also grow out of the nodes, and are quite hairy.
Creeping buttercup can be differentiated from other buttercups because the flowers produced are often   larger than many  other Ranuncules (although in poor conditions the flowers may be as small as 10 mm diameter), there are stolons, and it is very low-lying.

# Cultivation and uses
Creeping buttercup is native to Europe and the Pacific Northwest but was sold in many parts of the world as an ornamental flower.
It has now become an invasive species in many parts of the world.  The plant grows in fields and pastures and prefers wet soil.
Like most buttercups R. repens is poisonous, although when dried with hay these poisons are lost.  The taste of buttercups is acrid, so cattle avoid eating them.  The plants then take advantage of the cropped ground around it to spread their stolons. Creeping buttercup also is spread through the transportation of hay. Contact with the sap of the plant can cause skin and mucus membrane irritation.
Cremasteric reflex
The cremasteric reflex is a cutaneous reflex observed in human males.
This reflex is elicited by lightly stroking the superior and medial part of the thigh in a downward direction. The normal response is a contraction of the cremaster muscle that pulls up the scrotum and testis on the side stroked.
More specifically, the reflex utilizes sensory and motor fibers of the L1 spinal nerve. When the inner thigh is stroked, sensory fibers of the ilioinguinal nerve are stimulated. These synapse in the spinal cord and activate the motor fibers of the genital branch of the genitofemoral nerve which causes the cremaster muscle to contract and elevate the testis.
In children, this reflex may be exaggerated, and this can lead to the mistaken diagnosis of undescended testes.
Upper and lower motor neuron disorders, as well as a spine injury of L1-L2, can cause an absence of the cremasteric reflex. It has also been reported to be absent in 100% of cases of testicular torsion, making it a useful sign in this difficult diagnosis.

# Urban legends
According to the Straight Dope, it is a classic urban legend that Sumo wrestlers raise their testicles in preparation for training and/or combat. While it may be possible to do this via the pubococcygeal muscle or acquired control over the cremaster muscle, it is not practiced by Sumo wrestlers and Sumo does not allow contact with this region.
it:Riflesso cremasterico
Cryptogenic stroke
In neurology, Cryptogenic stroke is stroke of undetermined source.

# Causes

## Patent foramen ovale
One cause is paradoxical embolism that may be treated with patent foramen ovale closure.

## Atrial fibrillation
One cause is atrial fibrillation which may be detected by prolonged event monitors or prolonged, implantable recorders such as the LINQ, or even smartphones.
The various methods of diagnosis have been compared by a systematic reviews which:
- recommends" sequentially combining cardiac monitoring methods". An example of a phase 4 (second ambulatory period) consisted of mobile cardiac outpatient telemetry, external loop recording, and implantable loop recording is the 
- "evidence for a potential impact of PCM on secondary stroke prevention"
Clinical practice guidelines address the diagnosis strategy:
- The 2019 AHA/ACC/HRS Focused Update of atrial fibrillation guidelines contain a new section, "7.12. Device Detection of AF and Atrial Flutter," which states "In patients with cryptogenic stroke (ie, stroke of unknown cause) in whom external ambulatory monitoring is inconclusive, implantation of a cardiac monitor (loop recorder) is reasonable to optimize detection of silent AF". However, the guidelines do not address alternative methods to detect atrial fibrillation.
- 2016 Guidelines by the ESC state "In stroke patients, additional ECG monitoring by long-term noninvasive ECG monitors or implanted loop recorders should be considered to document silent atrial fibrillation."
The benefit of anticoagulation based on long-term monitoring is uncertain.

## Unknown source
For cryptogenic stroke on unknown source, anticoagulation may not help over aspirin.
Currarino syndrome

# Overview
Currarino syndrome is a condition where the sacrum (the fused vertebrae forming the back of the pelvis) is not formed properly, there is a mass in the presacral space in front of sacrum, and there are malformations of the anus or rectum.
The condition is an autosomal dominant genetic trait caused by a mutation in the HLXB9 homeobox gene.
Currarino syndrome may cause an anterior meningocele or presacral teratoma, or both.
Cytidine deaminase
Cytidine deaminase is an enzyme that in humans is encoded by the CDA gene.
This gene encodes an enzyme involved in pyrimidine salvaging. The encoded protein forms a homotetramer that catalyzes the irreversible hydrolytic deamination of cytidine and deoxycytidine to uridine and deoxyuridine, respectively. It is one of several deaminases responsible for maintaining the cellular pyrimidine pool. Mutations in this gene are associated with decreased sensitivity to the cytosine nucleoside analogue cytosine arabinoside used in the treatment of certain childhood leukemias.
A related activation-induced (cytidine) deaminase (AID) regulates antibody diversification, especially the process of somatic hypermutation.

# Interactive pathway map
Click on genes, proteins and metabolites below to link to respective articles.
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DNA polymerase eta
DNA polymerase eta (Pol ), is a protein that in humans is encoded by the POLH gene.
DNA polymerase eta is a eukaryotic DNA polymerase involved in the DNA repair by translesion synthesis. The gene encoding DNA polymerase eta is POLH, also known as XPV, because loss of this gene results in the disease xeroderma pigmentosum.  Polymerase eta is particularly important for allowing accurate translesion synthesis of DNA damage resulting from ultraviolet radiation or UV.

# Function
This gene encodes a member of the Y family of specialized DNA polymerases. It copies undamaged DNA with a lower fidelity than other DNA-directed polymerases. However, it accurately replicates UV-damaged DNA; when thymine dimers are present, this polymerase inserts the complementary nucleotides in the newly synthesized DNA, thereby bypassing the lesion and suppressing the mutagenic effect of UV-induced DNA damage. This polymerase is thought to be involved in hypermutation during immunoglobulin class switch recombination.

## Bypass of 8-oxoguanine
During DNA replication of the Saccharomyces cerevisiae chromosome, the oxidative DNA damage 8-oxoguanine triggers a switch to translesion synthesis by DNA polymerase eta.  This polymerase replicates 8-oxoguanine with an accuracy (insertion of a cytosine opposite the 8-oxoguanine) of approximately 94%.  Replication of 8-oxoguanine in the absence of DNA polymerase eta is less than 40%.

# Clinical significance
Mutations in this gene result in XPV, a variant type of xeroderma pigmentosum, characterized by sun sensitivity, elevated incidence of skin cancer, and at the cellular level, by delayed replication and hypermutability after UV-irradiation

# Interactions
POLH has been shown to interact with PCNA.