Persius/hicric huggingface dataset:
Pulmonary circulation
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# Overview
Pulmonary circulation is the portion of the cardiovascular system which carries oxygen-depleted blood away from the heart, to the lungs, and returns oxygenated blood back to the heart. The term is contrasted with systemic circulation.

# Course
In the pulmonary circulation, deoxygenated blood exits the heart through arteries, enters the lungs and comes back through pulmonary veins.

## Right heart
Oxygen-depleted blood from the body leaves the systemic circulation when it enters the right heart, more specifically the right atrium. The blood is then pumped through the tricuspid valve (or right atrioventricular valve), into the right ventricle.

## Arteries
From the right ventricle, blood is pumped through the pulmonary semi-lunar valve into the pulmonary artery. This blood enters the two pulmonary arteries (one for each lung) and travels through the lungs.

## Lungs
The pulmonary arteries carry blood to the lungs, where red blood cells release carbon dioxide and pick up oxygen during respiration.

## Veins
The oxygenated blood then leaves the lungs through pulmonary veins, which return it to the left heart, completing the pulmonary cycle. This blood then enters the left atrium, which pumps it through the bicuspid valve, also called the mitral or left atrioventricular valve, into the left ventricle. The blood is then distributed to the body through the systemic circulation before returning again to the pulmonary circulation.

# History
Pulmonary circulation was first discovered and published by Ibn Nafis in his Commentary on Anatomy in Avicenna's Canon (1242), for which he is considered the father of circulatory physiology. It was later published by Michael Servetus in Christianismi Restitutio (1553).
Since it was a theology work condemned by most of the Christian factions of his time, the discovery remained mostly unknown until the dissections of William Harvey in 1616.

# Embryonic
The pulmonary circulation loop is virtually bypassed in fetal circulation.  The fetal lungs are collapsed, and blood passes from the right atrium directly into the left atrium through the foramen ovale, an open passage between the two atria.  When the lungs expand at birth, the pulmonary pressure drops and blood is drawn from the right atrium into the right ventricle and through the pulmonary circuit.  Over the course of several months, the foramen ovale closes, leaving a shallow depression known as the fossa ovalis in the adult heart.
Stabilizing selection

# Overview
Stabilizing selection, also referred to as purifying selection, is a type of natural selection in which genetic diversity decreases as the population stabilizes on a particular trait value. Put another way, extreme values of the character are selected against. This is probably the most common mechanism of action for natural selection.
A classic example of this is human birth weight. Babies of low weight lose heat more quickly and get ill from infectious disease more easily, whereas babies of large body weight are more difficult to deliver through the pelvis. However, the recent improvements in human nutrition in developed countries has led to rising rates of caesarean sections, since babies are routinely out-growing the female reproductive tract.
Stabilizing selection operates most of the time in most populations.  This type of selection acts to prevent divergence of form and function.  In this way, the anatomy of some organisms, such as sharks and ferns, has remained largely unchanged for millions of years.
Stabilizing selection can sometimes be detected by measuring the fitness of the range of different phenotypes by various direct measures, but it can also be detected by a variety of tests of molecular sequence data, such as Ka/Ks ratios, changes in allele frequency distributions, and the McDonald Kreitman test.
Pyrimidine metabolism
Pyrimidine biosynthesis occurs both in the body and through organic synthesis.

# De novo biosynthesis of pyrimidine
Unlike purines, pyrimidines are assembled before being attached to 5-phosphoribosyl-1-pyrophosphate (PRPP).
The first three enzymes are all coded by the same gene (CAD).

# Pyrimidine catabolism
Pyrimidines are ultimately catabolized (degraded) to CO2, H2O, and urea. Cytosine can be broken down to uracil which can be further broken down to N-carbamoyl--alanine. Thymine is broken down into -aminoisobutyrate which can be further broken down into intermediates eventually leading into the citric acid cycle.
-aminoisobutyrate acts as a rough indicator for rate of DNA turnover.
Ramos-Arroyo syndrome

# Overview
Ramos-Arroyo syndrome is marked by corneal anesthesia, absence of the peripapillary choriocapillaris and retinal pigment epithelium, bilateral sensorineural hearing loss, unusual facial appearance, persistent ductus arteriosus, Hirschsprung disease, and moderate intellectual disability. It appears to be a distinct autosomal dominant syndrome with variable expressivity.

# Epidemiology
As of 2008 this syndrome has only been reported in five individuals within three generations of the same family; two young children, their mother, their uncle and their maternal grandmother.

# Histopathology
This most recent generation to be diagnosed with Ramos-Arroyo syndrome supports the hypothesis that this disease is a distinct autosomal dominant disorder.
Rate-determining step
The rate-determining step (RDS) is a chemistry term for the slowest step in a chemical reaction. The rate-determining step is often compared to the neck of a funnel; the rate at which water flows through the funnel is determined by the width of the neck, not by the speed at which water is poured in. Similarly, the rate of reaction depends on the rate of the slowest step.
For example, the reaction NO_{2(g)}  +  CO_{(g)}  NO_{(g)} + CO_{2(g)} can be thought of as occurring in two elementary steps:
- NO_2 + NO_2  NO + NO_3 (slow step)
- NO_3 + CO  NO_2 + CO_2 (fast step)
As the second step consumes the NO_3 produced in the slow first step, it is limited by the rate of the first step. For this reason, the rate-determining step is reflected in the rate equation of a reaction.
Another example of a rate-determining step is the formation of a carbo-cation from a haloalkane during the second-order nucleophilic substitution reaction of tertiary haloalkanes with sodium hydroxide.
The concept of the rate-determining step is very important to the optimization and understanding of many chemical processes such as catalysis and combustion.
In a reaction coordinate, the transition state with the highest energy is the rate-determining step of the reaction.
Reaction intermediate
The IUPAC Gold Book defines a reaction intermediate or an intermediate a molecular entity (atom, ion, molecule...) with a lifetime appreciably longer than a molecular vibration (corresponding to a local potential energy minimum of depth greater than RT; R being the gas constant and T is temperature) that is formed (directly or indirectly) from the reactants and reacts further to give (either directly or indirectly) the products of a chemical reaction.
Most chemical reactions are stepwise, that is they take more than one elementary step to complete. An intermediate is the reaction product of each of these steps (except for the last one, which forms the final product).
For example in a hypothetical stepwise reaction:
That includes these elementary steps:
The chemical species X and Y are intermediates.
Reactive intermediates are usually short lived and are very seldom isolated

# The main carbon reactive intermediates
- Carbocations and their stabilized equivalents such as oxonium ions
- Carbanions and their stabilized equivalents
- Free radicals
- Carbenes

## Common features of carbon intermediates
- Low concentration with respect to reaction substrate and final reaction product
- With the exception of carbanions, these intermediates do not obey the lewis octet rule hence the high reactivity
- Often generated on chemical decomposition of a chemical compound
- It is often possible to prove the existence of this species  by spectroscopic means
- Cage effects have to be taken into account
- Often stabilisation by conjugation or resonance
- Often difficult to distinguish from a transition state
- Prove existence by means of chemical trapping

# Other reactive intermediates
- Deprotonated or hydrated forms of the compound, such as the tetrahedral intermediate in esterification
- Arynes
- Carbenes
- Carbenoid
- Carbocations
- Carbyne
- Free radicals
- Nitrenes, nitrenium ions
Rectus femoris muscle

# Overview
The Rectus femoris muscle is one of the four quadriceps muscles of the human body. (The others are the vastus medialis, the vastus intermedius (deep to the rectus femoris), and the vastus lateralis. All four combine to form the quadriceps tendon, which inserts into the patella and continues as the patellar ligament.)
The Rectus femoris is situated in the middle of the front of the thigh; it is fusiform in shape, and its superficial fibers are arranged in a bipenniform manner, the deep fibers running straight down to the deep aponeurosis.

# Origin and insertion
It arises by two tendons: one, the anterior or straight, from the anterior inferior iliac spine; the other, the posterior or reflected, from a groove above the brim of the acetabulum.
The two unite at an acute angle, and spread into an aponeurosis which is prolonged downward on the anterior surface of the muscle, and from this the muscular fibers arise.
The muscle ends in a broad and thick aponeurosis which occupies the lower two-thirds of its posterior surface, and, gradually becoming narrowed into a flattened tendon, is inserted into the base of the patella.

# Functions
- Hip Flexion
- Knee Extension
The rectus femoris is the only muscle in the quadriceps group that is involved in hip flexion, since it is the only one that originates in the pelvis and not the femur.
The rectus femoris is a weaker hip flexor when the knee is extended because it is already shortened and thus suffers from active insufficiency. In essence: the action of raising a straightened leg will recruit more iliacus, psoas major, tensor fasciae latae, and the remaining hip flexors than it will the rectus femoris.
Similarly, the rectus femoris is not dominant in knee extension when the hip is flexed since it is already shortened and thus suffers from active insufficiency. In essence: the action of extending a leg from a seated position is primarily driven by the vastus lateralis, vastus medialis, and vastus intermedius, and less by the rectus femoris.
The rectus femoris is considered a direct antagonist to the hamstrings. The hamstrings oppkjuose the rectus femoris at the hip joint through extension and at the knee joint through flexion. Simultaneous contraction of the rectus femoris and hamstrings results in simultaneous hip and knee extension due to leverage (Lombard's Paradox.)

# Additional images
- Structures surrounding right hip-joint.
- Cross-section through the middle of the thigh.
- The femoral artery.
- Nerves of the right lower extremity. Front view.
Reverse osmosis plant
A reverse osmosis plant is a manufacturing plant where the process of reverse osmosis takes place. An average modern reverse osmosis plant needs six kilowatt-hours of electricity to desalinate one cubic metre of water. The process also results in an amount of salty briny waste. The challenge for these plants is to find ways to reduce energy consumption, use sustainable energy sources, improve the process of desalination and to innovate in the area of waste management to deal with the waste.

# Examples of reverse osmosis plants
In operation
- In Israel at Ashkelon on the Mediterranean coast, the world's largest reverse osmosis plant is producing 320,000 cubic metres of water a day at around possibly 50 US$ cents per cubic metre.
Under construction
- In China a desalination plant will be built for Tianjin, to produce 100,000 cubic metres of desalinated seawater a day.
- In Spain 20 reverse osmosis plants will be built along the Costas, expecting to meet slightly over 1 per cent of Spain's total water needs.
Reverse transcription

# Overview
Reverse transcription is the process of making a double stranded DNA (deoxyribonucleic acid) molecule from a single stranded RNA (ribonucleic acid) template. It is called reverse transcription as it acts in the opposite or reverse direction to transcription. This idea was very unpopular at first as it contradicted the Central Dogma of Molecular Biology which states DNA is transcribed into RNA which is translated into proteins. However, in 1970 when the scientists Howard Temin and David Baltimore both independently discovered the enzyme responsible for reverse transcription, named reverse transcriptase, the possibility that genetic information could be passed on in this manner was finally accepted.This was the beginning of a resurgence of interest in Jean-Baptiste de Lamarck, a French scientist who in 1809 developed the first theory of evolution, pre-dating Charles Darwin by fifty years. Lamarck proposed that characteristics acquired during a lifetime could be communicated back to the germline (DNA) and passed on the succeeding generations. Reverse transcription was a critical precursor to wider acceptance of Lamarck's theory.

# Reverse transcription in Class VI viruses
Class VI viruses ssRNA-RT, also called the retroviruses are RNA reverse transcribing viruses with a DNA intermediate. Their genomes consist of two molecules of positive sense single stranded RNA with a 5' cap and 3' polyadenylated tail. Examples of retroviruses include the Human Immunodeficiency Virus HIV and Human T-Lymphotropic virus HTLV.  Once the viruses have entered the cell and been uncoated the genome is reverse transcribed into double stranded DNA which can be incorporated into the host cell and subsequently expressed.
Reverse transcription by the enzyme reverse transcriptase occurs in a series of steps:
- A specific cellular tRNA acts as a primer and hybridizes to a complementary part of the virus genome called the primer binding site or PBS
- Complementary DNA then binds to the U5 (non-coding region) and R region (a direct repeat found at both ends of the RNA molecule) of the viral RNA
- A domain on the reverse transcriptase enzyme called RNAse H degrades the 5 end of the RNA which removes the U5 and R region
- The primer then jumps to the 3 end of the viral genome and the newly synthesised DNA strands hybridizes to the complementary R region on the RNA
- The first strand of complementary DNA (cDNA) is extended and the majority of viral RNA is degraded by RNAse H
- Once the strand is completed, second strand synthesis is initiated from the viral RNA
- There is then another jump where the PBS from the second strand hybridizes with the complementary PBS on the first strand
- Both strands are extended further and can be incorporated into the hosts genome by the enzyme integrase
Ribavirin description

# Description
REBETOL (ribavirin), is a synthetic nucleoside analogue (purine analogue). The chemical name of ribavirin is 1--D-ribofuranosyl-1H-1,2,4-triazole-3-carboxamide and has the following structural formula (see Figure 1).
Ribavirin is a white, crystalline powder. It is freely soluble in water and slightly soluble in anhydrous alcohol. The empirical formula is C8H12N4O5 and the molecular weight is 244.21.
REBETOL capsules consist of a white powder in a white, opaque, gelatin capsule. Each capsule contains 200 mg ribavirin and the inactive ingredients microcrystalline cellulose, lactose monohydrate, croscarmellose sodium, and magnesium stearate. The capsule shell consists of gelatin, sodium lauryl sulfate, silicon dioxide, and titanium dioxide. The capsule is printed with edible blue pharmaceutical ink which is made of shellac, anhydrous ethyl alcohol, isopropyl alcohol, n-butyl alcohol, propylene glycol, ammonium hydroxide, and FD&C Blue #2 aluminum lake.
REBETOL oral solution is a clear, colorless to pale or light yellow bubble gum-flavored liquid. Each milliliter of the solution contains 40 mg of ribavirin and the inactive ingredients sucrose, glycerin, sorbitol, propylene glycol, sodium citrate, citric acid, sodium benzoate, natural and artificial flavor for bubble gum #15864, and water.
Rickettsia prowazekii
Rickettsia prowazekii is a species of gram negative, rod shaped, aerobic bacteria that is the etiologic agent of epidemic typhus, transmitted in the feces of lice and fleas.  R. prowazekii is often surrounded by a protein microcapsular layer and slime layer; the natural life cycle of the bacteria generally involves a vertebrate and an invertebrate host, usually an arthropod, typically a louse. A form of R. prowazekii that exists in the feces of arthropods remains stably infective for months.
Henrique da Rocha Lima , a brazilian doctor discovered this bacteria, in 1916.
Vaccines against R. prowazekii were developed in the 1940s, and were highly effective in reducing typhus deaths among U.S. soldiers during World War II.  Immunity following recovery from infection with, or by immunization against, R. prowazekii is lifelong in most cases. However, R. prowazekii can establish a latent infection, which can reactivate after years or decades.

# Gallery
- Dorsal view of a female head louse, Pediculus humanus var. capitis. From Public Health Image Library (PHIL). 
- Adult female body louse, Pediculus humanus, and two larval young. From Public Health Image Library (PHIL). 
- Photomicrographic view of a culture specimen revealing the presence of numerous Borrelia recurrentis bacteria, which causes European relapsing fever and is transmitted from person-to-person by way of the human body louse. From Public Health Image Library (PHIL).
Rifabutin description

# Description
MYCOBUTIN Capsules contain the antimycobacterial agent rifabutin, which is a semisynthetic ansamycin antibiotic derived from rifamycin S. MYCOBUTIN Capsules for oral administration contain 150 mg of rifabutin, USP, per capsule, along with the inactive ingredients microcrystalline cellulose, magnesium stearate, red iron oxide, silica gel, sodium lauryl sulfate, titanium dioxide, and edible white ink.
The chemical name for rifabutin is 1',4-didehydro-1-deoxy-1,4-dihydro-5'-(2-methylpropyl)-1-oxorifamycin XIV (Chemical Abstracts Service, 9th Collective Index) or (9S, 12E, 14S, 15R, 16S, 17R, 18R, 19R, 20S, 21S, 22E, 24Z)-6,16,18,20-tetrahydroxy-1'-isobutyl-14-methoxy-7,9,15,17,19,21,25-heptamethyl-spiro trienimino)-2H-furonaphth imidazole-2,4'-piperidine]-5,10,26-(3H,9H)-trione-16-acetate. Rifabutin has a molecular formula of C46H62N4O11, a molecular weight of 847.02 and the following structure:
Rifabutin is a red-violet powder soluble in chloroform and methanol, sparingly soluble in ethanol, and very slightly soluble in water (0.19 mg/mL). Its log P value (the base 10 logarithm of the partition coefficient between n-octanol and water) is 3.2 (n-octanol/water).
Rifampin how supplied

# How Supplied
150 mg maroon and scarlet capsules imprinted "RIFADIN 150."
Bottles of 30 (NDC 0068-0510-30)
300 mg maroon and scarlet capsules imprinted "RIFADIN 300."
Bottles of 60 (NDC 0068-0508-60)
Bottles of 100 (NDC 0068-0508-61)

## Storage
Store at 25C (77F); excursions permitted to 1530C (5986F) . Keep tightly closed. Store in a dry place. Avoid excessive heat.
RIFADIN IV (rifampin for injection USP) is available in glass vials containing 600 mg rifampin (NDC 0068-0597-01).
Storage: Store at 25C (77F); excursions permitted to 1530C (5986F) . Avoid excessive heat (temperatures above 40C or 104F). Protect from light.
Rifaximin description

# Description
XIFAXAN tablets contain rifaximin, a non-aminoglycoside semi-synthetic, nonsystemic antibiotic derived from rifamycin SV. Rifaximin is a structural analog of rifampin.  The chemical name for rifaximin is (2S,16Z,18E,20S,21S,22R,23R,24R,25S,26S,27S,28E)-5,6,21,23,25-pentahydroxy-27-methoxy-2,4,11,16,20,22,24,26-octamethyl-2,7-(epoxypentadeca-trienimino)benzofuropyrido-benzimidazole-1,15(2H)-dione,25-acetate. The empirical formula is C43H51N3O11 and its molecular weight is 785.9.  The chemical structure is represented below:
XIFAXAN Tablets for oral administration are film-coated and contain 200 mg or 550 mg of rifaximin.

## Inactive ingredients
Each 200 mg tablet contains colloidal silicon dioxide, disodium edetate, glycerol palmitostearate, hypromellose, microcrystalline cellulose, propylene glycol, red iron oxide, sodium starch glycolate, talc, and titanium dioxide.
Each 550 mg tablet contains colloidal silicon dioxide, glycerol palmitostearate, microcrystalline cellulose, polyethylene glycol/macrogol, polyvinyl alcohol, red iron oxide, sodium starch glycolate, talc, and titanium dioxide.
Right border of heart

# Overview
The right margin of the heart (right border of heart) is long, and is formed by the right atrium above and the right ventricle below.
- The atrial portion is rounded and almost vertical; it is situated behind the third, fourth, and fifth right costal cartilages about 1.25 cm. from the margin of the sternum.
- The ventricular portion, thin and sharp, is named the acute margin; it is nearly horizontal, and extends from the sternal end of the sixth right coastal cartilage to the apex of the heart.
Ritonavir description

# Description
NORVIR (ritonavir) is an inhibitor of HIV-1 protease with activity against the Human Immunodeficiency Virus (Hiv) type 1.
Ritonavir is chemically designated as 10-Hydroxy-2-methyl-5-(1-methylethyl)-1- -3,6-dioxo-8,11-bis(phenylmethyl)-2,4,7,12- tetraazatridecan-13-oic acid, 5-thiazolylmethyl ester, . Its molecular formula is C37H48N6O5S2, and its molecular weight is 720.95. Ritonavir has the following structural formula:
Ritonavir is a white-to-light-tan powder. Ritonavir has a bitter metallic taste. It is freely soluble in methanol and ethanol, soluble in isopropanol and practically insoluble in water.
NORVIR soft gelatin capsules are available for oral administration in a strength of 100 mg ritonavir with the following inactive ingredients: Butylated hydroxytoluene, ethanol, gelatin, iron oxide, oleic acid, polyoxyl 35 castor oil, and titanium dioxide.