Persius/hicric huggingface dataset:
Trematoda

# Overview
The Trematoda is a class within the phylum Platyhelminthes that contains two groups of parasitic worms, commonly referred to as flukes.

# Taxonomy and biodiversity
The Trematoda are estimated to include 18 000 to 24 000 species, and are divided into two subclasses. Nearly all trematodes are parasites of molluscs and vertebrates. The smaller Aspidogastrea, comprising about 100 species, are obligate parasites of molluscs and may also infect turtles and fishes, including cartilaginous fishes. The Digenea, which constitute the majority of trematode diversity, are obligate parasites of both molluscs and vertebrates, but do not occur in cartilaginous fishes.  Crepidostomum sp. do occur in Lake Sturgeon.
Formerly the Monogenea were included in the Trematoda on the basis that these worms are also vermiform parasites, but modern phylogenetic studies have raised this group to the status of a sister class within the Platyhelminthes, along with the Cestoda.

# Etymology
Trematodes are commonly referred to as flukes. This term can be traced back to the Saxon name for flounder, and refers to the flattened, rhomboidal shape of the worms.
The flukes can be classified into two groups, on the basis of the system which they infect in the vertebrate host. Tissue flukes infect the bile ducts, lungs, or other biological tissues. This group includes the lung fluke, Paragonimus westermani, and the liver flukes, Clonorchis sinensis and Fasciola hepatica. Blood flukes inhabit the blood in some stages of their life cycle. Blood flukes include species of the genus Schistosoma.

# Life cycles
All trematodes infect molluscs and most have a complex life cycle involving other  hosts. Most trematodes are monoecious and alternately reproduce sexually and asexually. The two main exceptions to this are the Aspidogastrea, which have no asexual reproduction, and the  schistosomes, which are dioecious.
In the definitive host, in which sexual reproduction occurs, eggs are commonly shed along with host feces. Eggs shed in water release free-swimming larval forms that are infective to the intermediate host, in which asexual reproduction occurs.
Apex beat
The apex beat, also called the point of maximum impulse (PMI), is the furthermost point outwards (laterally) and downwards (inferiorly) from the sternum at which the cardiac impulse can be felt. The cardiac impulse is the result of the heart rotating, moving forward and striking against the chest wall during systole.
The normal apex beat can be palpated in the precordium left 5th intercostal space, at the point of intersection with the left midclavicular line. In children the apex beat occurs in the fourth rib interspace medial to the nipple. The apex beat may also be found at abnormal locations; in many cases of dextrocardia, the apex beat may be felt on the right side.
Lateral and/or inferior displacement of the apex beat usually indicates enlargement of the heart, called cardiomegaly. The apex beat may also be displaced by other conditions:
- Pleural or pulmonary diseases
- Deformities of the chest wall or the thoracic vertebra
Sometimes, the apex beat may not be palpable, either due to a thick chest wall, or conditions where the stroke volume is reduced; such as during ventricular tachycardia or shock.
The character of the apex beat may provide vital diagnostic clues:
- A forceful impulse indicates pressure overload in the heart (as might occur in hypertension)
- An uncoordinated(dyskinetic) apex beat involving a larger area than normal indicates ventricular dysfunction; such as an aneurysm following myocardial infarction
CME Category::Cardiology
Appendage

# Overview
An appendage in the broadest sense is an additional or subsidiary part existing on, or added to, something which can generally still function if the appendage has never existed or is later provided or grown, or will still perform a primary function if the appendage is removed.

# Biological context
An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs.
In invertebrate biology, "appendage" is a general term that covers any of the homologous body parts that may extend from a body segment. These include antennae, mouthparts (including mandibles, maxillae and maxillipeds), wings, elytra, gills, walking legs (pereiopods), swimming legs (pleopods), sexual organs (gonopods), and parts of the tail (uropods). Typically, each body segment carries one pair of appendages.
Appendages may be uniramous, as in insects and centipedes, where each appendage comprises a single series of segments, or it may be biramous, as in many crustaceans, where each appendage branches into two sections. Triramous (branching into three) appendages are also possible.
All arthropod appendages are variations of the same basic structure (homologous), and which structure is produced is controlled by "homeobox" genes. Changes to these genes have allowed scientists to produce animals (chiefly Drosophila melanogaster) with modified appendages, such as legs instead of antennae.

# Linguistic context
In British English, depending on the surrounding context, "appendage" might infer that the added words to which it refers give a more precise meaning to a name or description or else it might be used in a derogatory sense to describe an addition which appears to serve no useful function.
Apramycin

# Overview
Apramycin (also Nebramycin II) is an aminoglycoside antibiotic used in veterinary medicine.  It is produced by Streptomyces tenebrarius.

# Pharmacology

## Indication
Apramycin is used for the treatment of bacterial infections in animals.

## Mechanism of action
Apramycin stands out among aminoglycosides for its mechanism of action which is based on blocking translocation and its ability to bind also to the eukaryotic decoding site despite differences in key residues required for apramycin recognition by the bacterial target. The drug binds in the deep groove of the RNA which forms a continuously stacked helix comprising non-canonical C.A and G.A base pairs and a bulged-out adenine. The binding mode of apramycin at the human decoding-site RNA is distinct from aminoglycoside recognition of the bacterial target, suggesting a molecular basis for the actions of apramycin in eukaryotes and bacteria.

# Spectrum of bacterial susceptibility and resistance
Apramycin can be used to treat bacterial infections in animals caused by Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. The following shows susceptibility data on medically significant organisms:
- Escherichia coli - 1 g/mL - >512 g/mL (this large range may be due to resistant organisms, typical MIC values are likely in the range of 2 -8 g/mL.
- Klebsiella pneumoniae - 2 g/mL - >256 g/mL
- Pseudomonas aeruginosa - 4 g/mL
Arabinose
Arabinose is an aldopentose  a monosaccharide containing five carbon atoms, and including an aldehyde (CHO) functional group.  It has chemical formula C5H10O5 and a molar mass of 150.13 g/mol.

# Isomerism
For biosynthetic reasons, saccharides are almost always more abundant in nature as the "D" form, or structurally analogous to D-(+)-glyceraldehyde.  However, L-arabinose is in fact more common than D-arabinose in nature and is found in nature as a component of biopolymers such as hemicellulose and pectin.  The L-arabinose operon is a very important operon in molecular biology and bioengineering.
A classic method for the organic synthesis of arabinose from glucose is the Wohl degradation.
Arbekacin

# Overview
Arbekacin (INN) is a semisynthetic aminoglycoside antibiotic. It is primarily used for the treatment of infections caused by multi-resistant bacteria including methicillin-resistant Staphylococcus aureus (MRSA). Arbekacin was originally synthesized from dibekacin in 1973. It has been registered and marketed in Japan since 1990 under the trade name Habekacin. Arbekacin is no longer covered by patent and generic versions of the drug are also available under such trade names as Decontasin and Blubatosine.

# Pharmacology
Arbekacin is used for the short term treatment of multi-resistant bacterial infections, such as methicillin-resistant Staphylococcus aureus (MRSA).

## Pharmacodynamics
Aminoglycosides, such as Arbekacin, work by binding to the bacterial 30S ribosomal subunit, causing misreading of t-RNA which consequently, leaves the bacterium unable to synthesize proteins vital to its growth. Energy is needed for aminoglycoside uptake into the bacterial cell. Anaerobes have less energy available for this uptake, so aminoglycosides are less active against anaerobes. Aminoglycosides are useful primarily in infections involving aerobic, gram-negative bacteria, such as Pseudomonas, Acinetobacter, and Enterobacter.

## Mechanism of action
Aminoglycosides, such as 'Arbekacin, inhibit protein synthesis in susceptible bacteria by irreversibly binding to bacterial 30S and 16S ribosomal subunits. Specifically Arbekacin binds to four nucleotides of 16S rRNA and a single amino acid of protein S12. This interferes with decoding site in the vicinity of nucleotide 1400 in 16S rRNA of 30S subunit. This region interacts with the wobble base in the anticodon of tRNA. This leads to misreading of mRNA so incorrect amino acids are inserted into the polypeptide leading to nonfunctional or toxic peptides and the breakup of polysomes into nonfunctional monosomes.

## Absorption
Aminoglycosides are not well absorbed from the gastrointestinal tract. Their absorption is markedly improved by parenteral administration.

## Toxicity
Ototoxicity and nephrotoxicity are the most serious adverse effects of aminoglycoside therapy and are more likely to occur in patients with a history of renal impairment or who are receiving other ototoxic and/or nephrotoxic drugs. Normal duration of IM or IV aminoglycoside therapy is 710 days. Although a longer duration may be necessary in some cases, toxicity is more likely to occur when aminoglycoside treatment is continued for longer than 10 days.

### Affected organisms
Enteric bacteria and other eubacteria
Arginemia
Arginemia (also called arginase deficiency) is a congenital disorder where arginase deficiency causes a high level of arginine and ammonia in the blood. Ammonia, which is formed when proteins are broken down in the body, is toxic if levels become too high. The nervous system is especially sensitive to the effects of excess ammonia.
Arginase deficiency usually becomes evident by about the age of 3. It most often appears as stiffness, especially in the legs, caused by abnormal tensing of the muscles (spasticity). Other symptoms may include slower than normal growth, developmental delay and eventual loss of developmental milestones, mental retardation, seizures, tremor, and difficulty with balance and coordination (ataxia). Occasionally, high protein meals or stress caused by illness or periods without food (fasting) may cause ammonia to accumulate more quickly in the blood. This rapid increase in ammonia may lead to episodes of irritability, refusal to eat, and vomiting.
In some affected individuals, signs and symptoms of arginase deficiency may be less severe, and may not appear until later in life.
Mutations in the ARG1 gene cause arginase deficiency. Arginase deficiency belongs to a class of genetic diseases called urea cycle disorders. The urea cycle is a sequence of reactions that occurs in liver cells. This cycle processes excess nitrogen, generated when protein is used by the body, to make a compound called urea that is excreted by the kidneys.
The ARG1 gene provides instructions for making an enzyme called arginase. This enzyme controls the final step of the urea cycle, which produces urea by removing nitrogen from arginine. In people with arginase deficiency, arginase is damaged or missing, and arginine is not broken down properly. As a result, urea cannot be produced normally, and excess nitrogen accumulates in the blood in the form of ammonia. The accumulation of ammonia and arginine are believed to cause the neurological problems and other signs and symptoms of arginase deficiency.
This condition is inherited in an autosomal recessive pattern, which means two copies of the gene in each cell are altered. Most often, the parents of an individual with an autosomal recessive disorder are carriers of one copy of the altered gene but do not show signs and symptoms of the disorder.

# Differential diagnosis
Arginase deficiency must be differentiated from other diseases that cause neurological manifestations in infants.
Argonaute
Argonaute proteins are the catalytic components of the RNA-induced silencing complex (RISC), the protein complex responsible for the gene silencing phenomenon known as RNA interference (RNAi). Argonaute proteins bind small interfering RNA (siRNA) fragments and have endonuclease activity directed against messenger RNA (mRNA) strands that are complementary to their bound siRNA fragment. The proteins are also partially responsible for selection of the guide strand and destruction of the passenger strand of the siRNA substrate.
The structural basis for binding of RNA to the argonaute protein has been examined by X-ray crystallography of the binding domain of an RNA-bound argonaute protein. The phosphorylated 5' end of the RNA strand enters a conserved basic surface pocket and makes contacts through a divalent cation such as magnesium and by aromatic stacking between the 5' nucleotide in the siRNA and a conserved tyrosine residue. This site is thought to form a nucleation site for the binding of the siRNA to its mRNA target.
In eukaryotes, argonaute proteins have been identified in high concentrations in regions of the cell's cytoplasm known as cytoplasmic bodies, to which mRNA decay is also localized. The argonaute protein family is shared among not only eukaryotes, but also archaea and certain bacteria such as Aquifex aeolicus. Based on comparative genomics studies, the argonaute family is thought to have evolved from components of the translation initiation system.
Argonaute proteins are named after the argonaute (AGO) phenotype of Arabidopsis mutants, which itself was named after its resemblance to argonauts.
Arteriole

# Overview
An arteriole is a small diameter blood vessel that extends and branches out from an artery and leads to capillaries.
Arterioles have thin muscular walls (usually only one to two layers of smooth muscle) and are the primary site of vascular resistance.
This means blood pressure in the arteries supplying the body is a result of the interaction between the cardiac output (the volume of blood the heart is pumping per minute) and the vascular resistance, usually termed total peripheral resistance by physicians and researchers.

# Natural fluctuation
The up and down fluctuation of the arterial blood pressure is due to the pulsatile nature of the cardiac output and determined by the interaction of the stroke volume versus the volume and elasticity of the major arteries.
In a healthy vascular system the endothelium, inner lining of arterioles and other blood vessels, is smooth and the vessel is relaxed.
This healthy condition is promoted by the ample production of nitric oxide in the endothelium, which biochemical reaction is regulated by a complex balance of polyphenols, various nitric oxide synthase enzymes and L-arginine.  In addition there is direct communication via gap junctions between the endothelial cells and the vascular smooth muscle

# Pathology
Any pathogen which constricts blood flow, such as stenosis, will increase total peripheral resistance and lead to hypertension.

# Medication
The muscular contraction of arterioles is targeted by drugs that lower blood pressure (antihypertensives), for example the dihydropyridines (nifedipine and nicardipine), which block the calcium conductance in the muscular layer of the arterioles, causing relaxation.
This decreases the resistance to flow into peripheral vascular beds, lowering overall systemic pressure.

# Metarterioles
A "metarteriole" is an arteriole which bypasses capillary circulation.
Atrial MI

# Overview
In approximately 10% of patients with acute myocardial infarction involving the ventricular territory, an atrial infarct also occurs. An atrial infarct can manifest itself in atrial rhytm disturbances such as atrial fibrillation. Because the atria may be of minor consequences hemodynamically, an atrial infarct may be missed.
On the ECG, an atrial infarct manifests by rhythm changes and/or change of the P-Ta segment (sometimes called PTA (P - atriale T) segment or PR or PQ or PTp (P - T wave of P wave) segment). This is the part between the end of the P wave and the Q. The ST segment indicates an infarct in the ventricle, the P-Ta segment indicates an infarct in the atria.
Diagnostic criteria for an atrial infarct include:
- P-Ta elevation >0.5mm in V5 and V6 with reciprocal depression in V1 and V2
- P-Ta elevation >0.5mm in I and depression in II and III
- >1.5mm P-Ta depression in precordial leads
- >1.2mm P-Ta depression in I,II or III in combination with atrial arrhytmias
Several diagnostic criteria are in use, and this is just an example of one. An important differential diagnosis of PTa segment elevation or depression is pericarditis.
Austenite
Austenite (or gamma phase iron) is a metallic non-magnetic solid solution of iron and an alloying element.  In plain-carbon steel, austenite exists above the critical eutectoid temperature of 1000 K (about 727 C); other alloys of steel have different eutectoid  temperatures.  It is named after Sir William Chandler Roberts-Austen (1843-1902).

# Behavior in Plain-Carbon Steel
As austenite cools, it often transforms into a mixture of ferrite and cementite as dissolved carbon falls out of solution. Depending on alloy composition and rate of cooling, pearlite may form.  If the rate of cooling is very fast, the alloy may experience a slight lattice distortion known as martensitic transformation, instead of transforming into a mixture. In this industrially very important case, the carbon is not allowed to blend out in the remaining melt due to the cooling speed, but is captured inside the FCC-structure of austenite, creating tension in the crystal when the alloy cools. The result is hard martensite. The rate of cooling determines the relative proportions of these materials and therefore the mechanical properties (e.g. hardness, tensile strength) of the steel. Quenching (to induce martensitic transformation), followed by tempering will transform some of the brittle martensite into bainite. If a low-hardenability steel is quenched, a significant amount of austenite will be retained in the microstructure.

# Stabilization
The addition of certain alloying elements, such as manganese and nickel, can stabilize the austenitic structure, facilitating heat-treatment of low-alloy steels.  In the extreme case of austenitic stainless steel, much higher alloy content makes this structure stable even at room temperature.  On the other hand, such elements as silicon, molybdenum, and chromium tend to de-stabilize austenite, raising the eutectoid temperature.

# Austenite transformation and Curie point
In many magnetic alloys, the Curie point, the temperature at which magnetic materials cease to behave magnetically, occurs at nearly the same temperature as the austenite transformation.  This behavior is attributed to the paramagnetic nature of austenite, while both martensite and ferrite are strongly ferromagnetic.

# Thermo-optical emission
A blacksmith causes phase changes in the iron-carbon system in order to control the material's mechanical properties, often using the annealing, quenching, and tempering processes. In this context, the color of light emitted by the workpiece is an approximate gauge of temperature, with the transition from red to orange corresponding to the formation of austenite in medium- and high-carbon steel.
Maximum carbon solubility in austenite is 2.03% C at 1420 K (1147 C).
Autotaxin
Autotaxin, also known as ectonucleotide pyrophosphatase/phosphodiesterase family member 2 (E-NPP 2), is an enzyme that in humans is encoded by the ENPP2 gene.

# Function
Autotaxin, also known as ectonucleotide pyrophosphatase/phosphodiesterase 2 (NPP2 or ENPP2), is a secreted enzyme important for generating the lipid signaling molecule lysophosphatidic acid (LPA).  Autotaxin has lysophospholipase D activity that converts lysophosphatidylcholine into LPA.
Autotaxin was originally identified as a tumor cell-motility-stimulating factor; later it was shown to be LPA (which signals through lysophospholipid receptors), the lipid product of the reaction catalyzed by autotaxin, which is responsible for its effects on cell-proliferation.
The protein encoded by this gene functions as a phosphodiesterase. Autotaxin is secreted and further processed to make the biologically active form. Several alternatively spliced transcript variants have been identified. Autotaxin is able to cleave the phosphodiester bond between the  and the  position of triphosphate nucleotides, acting as an ectonucleotide phosphodiesterase producing pyrophosphate, as most members of the ENPP family. Importantly, autotaxin also acts as phospholipase, catalyzing the removal of the head group of various lysolipids. The physiological function of autotaxin is the production of the signalling lipid  lysophosphatidic acid (LPA) in extracellular fluids. LPA evokes growth factor-like responses including stimulation of cell proliferation and chemotaxis. This gene product stimulates the motility of tumor cells, has angiogenic properties, and its expression is up-regulated in several kinds of tumours. Also, autotaxin and LPA are involved in numerous inflammatory-driven diseases such as asthma and arthritis. Physiologically, LPA helps promote wound healing responses to tissue damage. Under normal circumstances, LPA negatively regulates autotaxin transcription, but in the context of wound repair, cytokines induce autotaxin expression to increase overall LPA concentrations.
It has been shown that autotaxin's function can be regulated by certain steroids, namely bile acids.

# As a drug target
Various small molecule inhibitors of autotaxin have been developed for clinical applications. A specific inhibitor against idiopathic pulmonary fibrosis showed promising results in a phase II trial that ended in May 2018. A DNA aptamer inhibitor of Autotaxin has also been described.

# Structure
The crystal structures rat and mouse autotaxin have been solved. In each case, the apo structure have been solved along with product or inhibitor bound complexes. Both proteins consist of 4 domains, 2 N-terminal somatomedin-B-like (SMB) domains which may be involved in cell-surface localisation. The catalytic domain follows and contains a deep hydrophobic pocket in which the lipid substrate binds. At the C-terminus is the inactive nuclease domain which may function to aid protein stability.