Persius/hicric huggingface dataset:
Ki-67 (protein)
Antigen KI-67 also known as Ki-67 or MKI67 is a protein that in humans is encoded by the MKI67 gene (antigen identified by monoclonal antibody Ki-67).

# Function
Antigen KI-67 is a nuclear protein that is associated with and may be necessary for cellular proliferation. Furthermore, it is associated with ribosomal RNA transcription.  Inactivation of antigen KI-67  leads to inhibition of ribosomal RNA synthesis.

# Use as a marker of proliferating cells
The Ki-67 protein (also known as MKI67) is a cellular marker for proliferation. It is strictly associated with cell proliferation. During interphase, the Ki-67 antigen can be exclusively detected within the cell nucleus, whereas in mitosis most of the protein is relocated to the surface of the chromosomes. Ki-67 protein is present during all active phases of the cell cycle (G1, S, G2, and mitosis), but is absent in resting (quiescent) cells (G0). Cellular content of Ki-67 protein markedly increases during cell progression through S phase of the cell cycle. In breast cancer Ki67 identifies a high proliferative subset of patients with ER-positive breast cancer who derive greater benefit from adjuvant chemotherapy 

# Antibody labeling
Ki-67 is an excellent marker to determine the growth fraction of a given cell population. The fraction of Ki-67-positive tumor cells (the Ki-67 labeling index) is often correlated with the clinical course of cancer. The best-studied examples in this context are carcinomas of the prostate, brain and the breast and nephroblastoma and neuroendocrine tumours. For these types of tumors, the prognostic value for survival and tumor recurrence have repeatedly been proven in uni- and multivariate analysis.

## MIB-1
Ki-67 and MIB-1 monoclonal antibodies are directed against different epitopes of the same proliferation-related antigen. Ki-67 and MIB-1 may be used on fixed sections. MIB-1 is used in clinical applications to determine the Ki-67 labelling index. One of its primary advantages over the original Ki-67 antibody (and the reason why it has essentially supplanted the original antibody for clinical use) is that it can be used on formalin-fixed paraffin-embedded sections, after heat-mediated antigen retrieval (see next section below).

## Original Ki-67 antibody
The Ki-67 protein was originally defined by the prototype monoclonal antibody Ki-67, which was generated by immunizing mice with nuclei of the Hodgkin lymphoma cell line L428. The name is derived from the city of origin (Kiel, Germany) and the number of the original clone in the 96-well plate.

# Interactions
Ki-67 (protein) has been shown to interact with CBX3.
Kjeldahl method
The Kjeldahl method in analytical chemistry is a method for the quantitative determination of nitrogen in chemical substances developed by Johan Kjeldahl.

# Method
The method consists of heating a substance with sulfuric acid which decomposes the organic nitrogen present to ammonium sulfate. In this step potassium sulfate is added in order to increase the boiling point of the medium (from 337 to 373 C). Chemical decomposition of the sample is complete when the medium has become clear and colorless (initially very dark).
The solution is then distilled with sodium hydroxide (added in small quantities) which converts the ammonium salt to ammonia. The amount of ammonia present (hence the amount of nitrogen present in the sample) is determined by back titration. The end of the condenser is dipped into a solution of hydrochloric acid or sulfuric acid of precisely known concentration. The ammonia reacts with the acid and the remainder of the acid is then titrated with a sodium carbonate solution with a methyl orange pH indicator.
Nowadays, the Kjeldahl method is largely automated and makes use of specific catalysts (mercury oxide or copper sulfate) to speed up the decomposition.

# Applications
The Kjeldahl method's universality, precision and reproducibility have made it the internationally-recognized method for estimating the protein content in foods and it is the standard method against which all other methods are judged. It does not, however, give a measure of true protein content, as it measures non-protein nitrogen in addition to the nitrogen in proteins. Also, different correction factors are needed for different proteins to account for different amino acid sequences. Additional disadvantages, such as the need to use concentrated sulfuric acid at high temperature and the relatively long testing time (an hour or more), compare unfavorably with the Dumas method for measuring crude protein content.
Patellar reflex
The patellar reflex or knee-jerk is a stretch reflex.

# Mechanism
Striking the patellar tendon with a tendon hammer just below the patella stretches the quadriceps tendon. This stimulates stretch sensory receptors (most importantly, muscle spindles) that triggers an afferent impulse in a sensory nerve fiber of the femoral nerve leading to the lumbar region of the spinal cord. There, the sensory neuron synapses directly with a motor neuron that conducts an efferent impulse to the quadriceps femoris muscle, triggering contraction.  This contraction, coordinated with the relaxation of the antagonistic flexor hamstring muscle causes the leg to kick. It has been thought that this type of reflex helps maintain the upright posture.
The patellar reflex is a clinical and classic example of the monosynaptic reflex arc. There is no interneuron in the pathway leading to flexion of the quadriceps muscle. Instead the bipolar sensory neuron synapses directly on a motor neuron in the spinal cord.  However, there is an inhibitory interneuron used to relax the antagonistic hamstring muscle.

# Purpose
The patellar tendon reflex tests the function of the femoral nerve and spinal cord segments L2-L4.
The absence or decrease of this reflex is known as Westphal's sign.

# History
That term knee-jerk was coined by Sir Michael Foster in his textbook of physiology in 1877: "Striking the tendon below the patella gives rise to a sudden extension of the leg, known as the knee-jerk."

# Popular culture
The term began to be used figuratively from the early 20th century onwards. O.O. McIntyre, in his New York Day-By-Day column in The Coshocton Tribune, October 1921, wrote: "Itinerant preacher stemming Broadway on a soap box. And gets only an occasional knee-jerk." 

# Notes
-  William F. Ganong, MD, Review of Medical Physiology, McGraw Hill, 2005, ISBN 0-8385-8282-6
-  Jump up to: 2.0 2.1
Kumada coupling

# Overview
A Kumada coupling or Kumada-Corriu coupling is a cross coupling reaction in organic chemistry between a alkyl or aryl Grignard reagent and an aryl or vinyl halocarbon catalysed by nickel or palladium. This reaction is relevant to organic synthesis because it gives access to styrene compounds. The reaction type was reported independently by two groups in 1972.

# Development
This method builds on earlier work done by Tamura & Kochi in 1971 on couplings of Grignards with catalytical amounts of other metal halide catalysts than nickel for instance silver . Stoichometric Grignard couplings and Grignard homo-couplings have been known well before that time.
The first report by the Kumada group  described the reaction of a Grigard reagent for instance phenylmagnesium bromide with an aryl or vinyl chloride such as vinyl chloride to the coupled product (styrene) catalyzed by a nickel chloride with two dppe ligands (NiCl2dppe2):
In the 1972 Corriu report , beta-bromostyrene is reacted with phenylmagnesium bromide to trans-stilbene in diethylether also with nickel catalysts notably Nickel(II) acetylacetonate.
Palladium was introduced to this chemistry in 1975 by Murahashi  when Tetrakis(triphenylphosphine)palladium(0) was found to catalyze the reaction of (Z)-bromostyrene with methylmagnesium iodide to (Z)-propenylbenzene. With the far more reactive methyl lithium, the palladium catalyst is not recycled fast enough and an elimination reaction to the alkyne predominates.

# Reaction mechanism
The Nickel reaction mechanism for Ni(II) catalysts is a sequence of several steps :
- Transmetallation: the dihalonickel catalyst reacts with the Grignard RMgX to a diorganonickel intermediate NiR2L2 and dihalonickel NiX2
- Reductive elimination: reaction of NiR2L2 with the organohalide R'X forms the coupled product R-R together with the nickelorganohalide  NiR'XL2. In the overall reaction this step is negligible because the active nickel compound is formed in catalytical amounts
- Transmetallation: in the first step of the catalytic cycle nickelorganohalide  NiR'XL2 reacts with another equivalent of RMgX to mixed diorganonickel NiRR'L2 compound and dihalonickel NiX2
- trans-cis isomerization: with substrates trans-dichloroethylene and phenylmagnesium chloride, the resulting stilbene is enriched in the cis isomer.
- Coordination: a new equivalent of organohalide R'-X adds face-on to the mixed dihalonickel complex
- Oxidative addition: The cross-coupled product R-R' is released with regeneration of nickelorganohalide  NiR'XL2
The main steps in the mechanism for Ni(0) or Pd(0) catalysts are oxidative addition of the organohalide, transmetallation of the Grignard and reductive elimination.

# Scope
Recently the scope of this reaction was extended to aryl-aryl couplings with improved functional group tolerance :
In this particular reaction the Grignard is prepared in situ by I/Mg exchange between an aryl iodide and isopropylmagnesium chloride / lithium chloride .
Kussmaul's sign

# Overview
Kussmaul's sign is the observation of a jugular venous pressure (JVP, the filling of the jugular vein) that rises with inspiration. It can be seen in some forms of heart disease.  It is usually indicative of right ventricular dysfunction along with hypotension and "dry lungs" (absence of pulmonary edema).
Ordinarily the JVP falls with inspiration due to reduced pressure in the expanding thoracic cavity. Kussmaul's sign suggests impaired filling of the right ventricle due to either fluid in the pericardial space or a poorly compliant myocardium or pericardium.

# Historical Perspective
Kussmaul's sign is named after the German doctor who first described it, Adolph Kussmaul (1822-1902). He is also credited with describing Kussmaul breathing.

# Causes
Possible causes of Kussmaul's sign include:
- Cardiac tumors
- Constrictive pericarditis
- Pericardial effusion
- Restrictive cardiomyopathy
- Right heart failure
- Right ventricular infarction
- Tricuspid Stenosis

# Videos
Below is the Video Demonstrating Kussumal's sign: Rise in JVP During Inspiration
Leptin receptor
Leptin receptor also known as LEP-R or OB-R is a Type I cytokine receptor, a protein that in humans is encoded by the LEPR gene. LEP-R functions as a receptor for the fat cell-specific hormone leptin.  LEP-R has also been designated as CD295 (cluster of differentiation 295). Its location is the cell membrane, and it has extracellular, trans-membrane, and intracellular sections (protein regions).

# History
After co-discovering the Leptin gene with Jeffrey Friedman et al. in 1994, which involved a reverse genetic/positional cloning strategy to clone ob and db, Rudolph Leibel, working with collaborators at Millennium Pharmaceuticals and colleague Streamson Chua, confirmed cloning of the leptin receptor by demonstrating that an apparent leptin receptor cloned from a choroid plexus library using leptin as ligand, mapped to a physical map that included db and fa.

# Structure
Like other cytokine receptors, Leptin receptor protein has three different regions: i) extracellular, ii) trans-membrane, and iii) intracellular. The extracellular part has 5 functional domains: i) membrane distal 1st cytokine receptor homology (CRH1), ii) Immunoglobulin like (Ig), iii) 2nd cytokine receptor homology (CRH2) and iv) two membrane proximal fibronectine type-III (FNIII) domains. CRH1 domains is not essential for Leptin binding, but may have regulatory roles. Ig domain interacts with Leptin and is essential for conformational change in the receptor upon ligand binding. CRH2 is essential for leptin binding, deletion of this domain abolishes the leptin binding. FNIII domains are essential for receptor activation upon leptin binding.The structure of the quaternary complex of the complete extracellular part in complex with the cognate ligand Leptin (i.e. 2 receptor and 2 ligand) has been solved by both electron microscopy and SAXS.

# Function
The leptin hormone regulates adipose-tissue mass through hypothalamus effects on hunger and energy use. It acts through the leptin receptor (LEP-R), a single-transmembrane-domain receptor of the cytokine receptor family. In hypothalamic neurons, adequate leptin receptor function and subsequent regulation of energy metabolism and body weight depends on interactions of the receptor with gangliosides in the cell membrane.

# Clinical significance
Variations in the leptin receptor have been associated with obesity and with increased susceptibility to Entamoeba histolytica infections.

# Animals models
The db/db mouse is a model of obesity, diabetes, and dyslipidemia wherein leptin receptor activity is deficient because the mice are homozygous for a point mutation in the gene for the leptin receptor.  In db/db mice, induced swimming helped to overcome obesity by upregulating uncoupling proteins.
LIGHT (protein)
LIGHT, also known as tumor necrosis factor superfamily member 14 (TNFSF14), is a secreted protein of the TNF superfamily. It is recognized by herpesvirus entry mediator (HVEM), as well as decoy receptor 3.

# Nomenclature
LIGHT stands for "homologous to lymphotoxin, exhibits inducible expression and competes with HSV glycoprotein D for binding to herpesvirus entry mediator, a receptor expressed on T lymphocytes". In the cluster of differentiation terminology it is classified as CD258.

# Function
The protein encoded by this gene is a member of the tumor necrosis factor (TNF) ligand family. This protein is a ligand for TNFRSF14, which is a member of the tumor necrosis factor receptor superfamily, and which is also known as a herpesvirus entry mediator ligand (HVEML). This protein may function as a costimulatory factor for the activation of lymphoid cells and as a deterrent to infection by herpesvirus. This protein has been shown to stimulate the proliferation of T cells, and trigger apoptosis of various tumor cells. This protein is also reported to prevent tumor necrosis factor alpha mediated apoptosis in primary hepatocyte. Two alternatively spliced transcript variant encoding distinct isoforms have been reported.

# Interactions
LIGHT has been shown to interact with TNFRSF14, TNFRSF6B, BIRC2, TRAF2 and TRAF3.

# Role in herpes simplex virus
Similar to how CD4 is the primary mediating receptor in HIV infection, the HSV glycoprotein (gD) binds to the HVEM receptor which is demanded by TNFSF14/LIGHT lowering the ability for LIGHT to activate the NFB pathway. NFB is a survival factor helping to inhibit apoptosis which triggers a pathway inhibiting caspase 8. When gD from HSV binds to HVEM, LIGHT is non-competitively inhibited from binding, encouraging apoptosis in the infected cell.
Lacrimal artery
The lacrimal artery arises close to the optic foramen, and is one of the largest branches derived from the ophthalmic artery: not infrequently it is given off before the artery enters the orbit.
It accompanies the lacrimal nerve along the upper border of the Lateral Rectus, supplies the lacrimal gland.
Its terminal branches, escaping from the gland, are distributed to the eyelids and conjunctiva: of those supplying the eyelids, two are of considerable size and are named the lateral palpebral arteries; they run medially in the upper and lower lids respectively and anastomose with the medial palpebral arteries, forming an arterial circle in this situation.
The lacrimal artery give off one or two zygomatic branches, one of which passes through the zygomatico-temporal foramen, to reach the temporal fossa, and anastomoses with the deep temporal arteries; another appears on the cheek through the zygomatico-facial foramen, and anastomoses with the transverse facial.
A recurrent branch passes backward through the lateral part of the superior orbital fissure to the dura mater, and anastomoses with a branch of the middle meningeal artery.
The lacrimal artery is sometimes derived from one of the anterior branches of the middle meningeal artery.

# Additional images
- Bloodvessels of the eyelids, front view.
Laminin, beta 1
Laminin subunit beta-1 is a protein that in humans is encoded by the LAMB1 gene.
Laminins, a family of extracellular matrix glycoproteins, are the major noncollagenous constituent of basement membranes.  They have been implicated in a wide variety of biological processes including cell adhesion, differentiation, migration, signaling, neurite outgrowth and metastasis.  Laminins are composed of 3 non identical chains: laminin alpha, beta and gamma (formerly A, B1, and B2, respectively) and they form a cruciform structure consisting of 3 short arms, each formed by a different chain, and a long arm composed of all 3 chains.  Each laminin chain is a multidomain protein encoded by a distinct gene.  Several isoforms of each chain have been described.  Different alpha, beta and gamma chain isomers combine to give rise to different heterotrimeric laminin isoforms, which are designated by Arabic numerals in the order of their discovery, i.e. alpha1beta1gamma1 heterotrimer is laminin 1.  The biological functions of the different chains and trimer molecules are largely unknown, but some of the chains have been shown to differ with respect to their tissue distribution, presumably reflecting diverse functions in vivo.  This gene encodes the beta chain isoform laminin, beta 1.  The beta 1 chain has 7 structurally distinct domains, which it shares with other beta chain isomers.  The C-terminal helical region containing domains I and II are separated by domain alpha, domains III and V contain several EGF-like repeats, and domains IV and VI have a globular conformation.  Laminin, beta 1 is expressed in most tissues that produce basement membranes, and is one of the 3 chains constituting laminin 1, the first laminin isolated from Engelbreth-Holm-Swarm (EHS) tumor.  A sequence in the beta 1 chain that is involved in cell attachment, chemotaxis, and binding to the laminin receptor was identified and shown to have the capacity to inhibit metastasis.
5-UTR of Laminin-B1 harbors IRES (internal ribosome entry site) between 293 and 1 upstream of the start codon.  IRES are involved in cancer malignancy.
Lanai Hookbill
The Lana'i Hookbill (Dysmorodrepanis munroi) was a species of finch in the Fringillidae family. It was endemic to the island of Lana'i, Hawaii. Last seen in Kaiholeua Valley and Waiakeakua area of the island. It became extinct due to habitat loss. G.C. Munro collected a single specimen of this species on the island of Lanai in 1913. No specimens have been seen and or collected since. The specimen is housed in the Bishop Museum in Honolulu.  Adults: Light gray with a tinge of green, the underparts were paler and almost white. A light band ran along the wing and there was a light mark over the eye. the mandibles curved towards each other and so the tip of the lower mandible was the only part that touched the upper, therefore leaving a gap in the middle. (6 inches) No one has ever weighed this bird so no one knows how much about weight.
Only seen a few times ever, and all between c. 1912 and 1918. Some naturalists consider that the Lana'i Hookbill was actually just a deformed individual of another species and because so few were ever seen (probably only three) there is some doubt as to the validity of these records.It was thought by some to be the same species as the O`u (Psittirostra psittacea), however, recent study by James et al., 1989 has shown that it is a species all of its own. Its preferred food is unknown because the birds were never seen feeding, though dissection of the stomach showed it had fed on native berries from the island. However, it is possible, based on its uniquely shaped bill and relatively weak jaw muscles, that it may have fed on endemic landsnails. The extinction of snails through human intervention no doubt then led to the reduction in numbers and ultimately, the extinction of this species. First seen alive February 22, 1913, when Munro collected a single specimen in the Kaiholena Valley of Lanai. Munro was the only person to see the species, so nearly everything known about it is in his book The Birds of Hawaii (1960). The only existing specimen (Munro's) is in Bishop Museum in Honolulu. After 1913, Munro saw the bird on March 16, 1916, in the Kaiholena Valley, and on August 12, 1918, at Waiakeakua. The 1918 sighting was the last, by that time most of the native akoko forest on Lanai had been replaced by pineapple plantations.
Lana'i Hookbill or Dysmorodrepanis munroi is now listed on the IUCN Red list as Extinct in 1996.
Langerhans cell
Langerhans' cells are dendritic cells abundant in epidermis, containing large granules called Birbeck granules. They are normally present in lymph nodes, and can be found in other organs in the condition Histiocytosis.
Named after German anatomist and physician Paul Langerhans (1847-1888) who described it in skin while a medical student.

# Function
On infection of an area of skin, the local Langerhans' cells will take up and process microbial antigens to become fully-functional antigen-presenting cells.
Generally, dendritic cells in tissue are active in the capture, uptake and processing of antigens. Once dendritic cells arrive in secondary lymphoid tissue however, they lose these properties while gaining the capacity to interact with naive T-cells.
Langerhans' cells are derived from the cellular differentiation of monocytes with the marker "Gr-1" (also known as "Ly-6c/G").  The differentiation requires stimulation by colony stimulating factor-1. They are similar in morphology and function to macrophages.

# Clinical significance

## LCH
In the rare disease Langerhans' cell histiocytosis (LCH), an excess of these cells is produced, which can cause damage to skin, bone and other organs.

## HIV
Langerhans' cells capture HIV-1 virions by way of Fc receptor binding to antibody-coated virus. Langerhans' cells act as reservoirs for the HIV-1 virus, serving as a site of replication when T-cells become depleted (Robbins Pathology).
Langerhans' cells have been observed in foreskin, vaginal, and oral mucosa of humans; the lower concentrations in oral mucosa suggest that it is not a likely source of HIV infection relative to foreskin and vaginal mucosa.
On March 4, 2007 the online Nature Medicine magazine published the letter "Langerin is a natural barrier to HIV-1 transmission by Langerhans cells", written by Dutch scientists which claims "that Langerin is able to scavenge viruses from the surrounding environment, thereby preventing infection", as lead researcher Teunis Geijtenbeek of Vrije University Medical Center in Amsterdam told to YahooNews-HealthDay reporter.