Persius/hicric huggingface dataset:
Dientamoebiasis overview

# Overview
Dientamoebiasis is a medical condition caused by infection with Dientamoeba fragilis. Dientamoeba fragilis is a single-cell parasite that infects the lower gastrointestinal tract of humans. It is an important cause of travelers diarrhea, chronic abdominal pain, chronic fatigue and failure to thrive in children.

# Historical Perspective
Early microbiologists reported that the organism was not pathogenic, even though six of the seven individuals from whom they isolated it were experiencing symptoms of dysentery. Their report, published in 1918, concluded the organism was not pathogenic because it consumed bacteria in culture, but did not appear to engulf red blood cells as was seen in the most well known disease causing amoeba of the time, Entamoeba histolytica. This initial report may still be contributing to the reluctance of physicians to diagnose the infection.

# Causes
A study of Dientamoeba fragilis isolates from 60 individuals with symptomatic infection in Sydney Australia found that all were infected with the same genotype.

# Epidemiology and Demographics
Although Dientamoeba fragilis has been described as an infection that is "emerging from obscurity," it has become one of the most prevalent gastrointestinal infections in industrialized countries, especially among children and young adults.  A Canadian study reported a prevalence of approximately 10% in boys and girls aged 11-15 years, a prevalence of 11.5% in individuals aged 16-20, and over 20 had a lower incidence of 0.3%-1.9%.

# Risk Factors
Anyone can become infected with this parasite. However, the risk for infection might be higher for people who have weak immune systems and those who live in or travel to settings with poor sanitary conditions.
Diethyl azodicarboxylate
Diethyl azodicarboxylate, often abbreviated DEAD, is the organic compound CH3CH2O2CN=NCO2CH2CH3.  As indicated with this formula, the molecule consists of  a central azo functional group, RN=NR, flanked by two ethyl ester groups. This red orange liquid is a valuable reagent but also quite dangerous.

# Preparation
Although widely available, diethyl azodicarboxylate can be prepared in the laboratory. A two-step synthesis starts from hydrazine, first by alkylation with ethyl chloroformate. followed by treating the resulting ethyl hydrazodicarboxylate with chlorine.
Red fuming nitric acid can also be used in the second step.

# Applications
DEAD is an efficient component in Diels-Alder reactions and in click chemistry, for example the synthesis of Bicyclopentane, which originates from Otto Diels.
DEAD is an important reagent in the Mitsunobu reaction where it forms an adduct with phosphines. In one study  the compound together with triphenylphosphine and a chalcone formed a pyrazoline:

# Safety
DEAD is toxic, shock sensitive, and thermally unstable.  It is handled as a solution, rarely as the pure compound.
Digestive system surgery

# Overview
Digestive system surgery can be divided into upper GI surgery and lower GI surgery.

# Subtypes

## Upper gastrointestinal
Upper gastrointestinal surgery, often referred to as upper GI surgery, refers to a practise of surgery that focuses on the upper parts of the gastrointestinal tract. There are many operations relevant to the upper gastrointestinal tract that are best done only by those who keep constant practise, owing to their complexity. Consequently, a general surgeon may specialise in 'upper GI' by attempting to maintain currency in those skills.
Upper GI surgeons would have an interest in, and may exclusively perform, the following operations:
- Pancreaticoduodenectomy
- Esophagectomy
- Liver resection

## Lower gastrointestinal
Lower gastrointestinal surgery surgery includes colorectal surgery as well as surgery of the small intestine.
Academically, it is the fers to a sub-specialisation of medical practise whereby a general surgeon focuses on the lower gastrointestinal tract.
A lower GI surgeon might specialise in the following operations:
- Colectomy
- Low or ultralow resections for rectal cancer, etc.
Dissociation (chemistry)
Dissociation in chemistry and biochemistry is a general process in which ionic compounds (complexes, molecules, or salts) separate or split into smaller molecules, ions, or radicals, usually in a reversible manner. When a Bronsted-Lowry acid is put in water, a covalent bond between an electronegative atom and a hydrogen atom is broken by heterolytic fission, which gives a proton and a negative ion. Dissociation is the opposite of association and recombination. The process is frequently confused with ionization.

# Dissociation constant
For reversible dissociations in a chemical equilibrium
the dissociation constant Kd is the ratio of dissociated to undissociated compound

# Salts
The dissociation of salts by solvation in a solution like water means the separation of the anions and cations. The salt can be recovered by evaporation of the solvent. See also: Solubility equilibrium

# Acids
The dissociation of acids in a solution means the split-off of a proton H+, see Acid-base reaction theories. This is an equilibrium process, meaning that dissociation and recombination takes place at the same time. The acid dissociation constant Ka is an indicator of the acid strength: stronger acids have a higher Ka value (and a lower pKa value).

# Fragmentation
Fragmentation of a molecule can take place by a process of heterolysis or homolysis

# Receptors
Receptors are proteins that bind small ligands. The dissociation constant Kd is used as indicator of the affinity of the ligand to the receptor. The higher the affinity of the ligand for the receptor the lower the Kd value (and the higher the pKd value).
Distal convoluted tubule

# Overview
The distal convoluted tubule (DCT) is a portion of kidney nephron between the loop of Henle and the collecting duct system.

# Physiology
It is partly responsible for the regulation of potassium, sodium, calcium, and pH.
- It regulates pH by absorbing bicarbonate and secreting protons (H+) into the filtrate.
- Sodium and potassium levels are controlled by secreting K+ and absorbing Na+. Sodium absorption by the distal tubule is mediated by the hormone aldosterone. Aldosterone increases sodium reabsorption. Sodium and chlorine (salt) reabsorption is also mediated by a group of kinases called WNK kinases. There are 4 different WNK kinases, WNK1, WNK2, WNK3, and WNK4.
- It also participates in calcium regulation by absorbing Ca2+ in response to parathyroid hormone.
- Arginine vasopressin receptor 2 is also expressed in the DCT.

# Clinical significance
Thiazide diuretics inhibit Na+/Cl- reabsorption from the DCT by blocking the thiazide-sensitive Na-Cl cotransporter.

# Histology
The distal convoluted tubule (DCT)is the final segment of the nephron.  It is lined with simple cuboidal cells that are shorter then those of the PCT.  The lumen appears larger in DCT than the proximal convoluted tubule (PCT) lumen because the PCT has a brush border (microvilli).  DCT can be recognized by its numerous mitochondria, basal infoldings and lateral membrane interdigitations with neighboring cells.
The point where DCT contacts afferent arteriole of renal corpuscle is called macula densa.  It has tightly packed columnar cells which display reversed polarity and may monitor the osmolarity of blood.
Histologically, cells of the DCT can be differentiated from cells of the proximal convoluted tubule:

# Additional images
- 1 Glomerulus, 2 proximal tubule, 3 distal tubule
- Transverse section of pyramidal substance of kidney of pig, the bloodvessels of which are injected.
Doppler echocardiography

# Overview
Doppler echocardiography is a procedure which uses ultrasound technology to examine the heart by creating an image of it and measuring the speed and direction of blood flow. This procedure is frequently used to examine children's hearts for heart disease because there is no age or size requirement.
- Continuous generation of ultrasound waves coupled with continuous reception Two crystal transducer with dual function: one crystal devoted to generation, one for receiving
- Measures all velocities along transducer beam
- Density of signal can be compared to forward flow
- Shape of flow curve gives information about pressure gradient across the valve
- Advantage:  ability to measure high blood flow velocities accurately
- Disadvantage:  lack of selectivity or depth discrimination

# Resources
- Echocardiography (Ultrasound of the heart)
- Doppler Examination - Introduction
Dorsal respiratory group
The dorsal respiratory group (DRG) is located in the dorsomedial region of the medulla, and is composed of cells in the solitary tract nucleus.  The DRG is found in many types of fish and mammals.

# Respiratory effects
The DRG is involved in the generation of respiratory rhythm, and is primarily responsible for the generation of inspiration. It is a part of the solitary tract, which is responsible for appropriating responses to sensory information from chemoreceptors and mechanoreceptors in humans.
Inspiration begins when cells of the solitary tract nucleus (along with cells of the ventral respiratory group) begin a steady increase in firing, leading to contraction of the respiratory muscles.  When neurons in the DRG fire, impulses travel down the phrenic and intercostal nerves to stimulate the diaphragm and external intercostal muscles.  The thoracic cavity expands and air rushes into the lungs due to the negative pressure, producing inspiration.  When the cells stop firing, the inspiratory muscles relax, inspiration ceases, and exhalation begins.
The rhythm of the DRG produces a respiratory rate of 12-16 breaths per minute in humans.  Inspiration usually lasts approximately 2 seconds, and expiration lasts about 3 seconds.  The normal inspiration rate and rhythm is called eupnea, and difficult respiration is termed dyspnea.
Dystrophic calcification

# Overview
Dystrophic Calcification (D.C.) is the mineralization of soft tissue without a systemic mineral imbalance. A systemic imbalance would elevate calcium levels in the blood and all tissues: metastatic calcification. This occurs as a reaction to tissue damage, including as a consequence of medical device implantation.
Dystrophic calcification can occur in a eucalcemic state.  Basophilic calcium salt deposits aggregate, first in the mitochondria, and progressively throughout the cell.  These calcifications are an indication of previous cell injury on the microscopic level.
Calcification can occur in dead or degenerated tissue

# Calcification in dead tissue
- Caseous necrosis in T.B. is most common site of dystrophic calcification.
- Liquefactive necrosis in chronic abscesses may get calcified.
- Fat necrosis following acute pancreatitis or traumatic fat necrosis in breasts results in deposition of calcium soaps.
- Infarcts may undergo D.C.
- Thrombi, esp. in veins, may produce phleoboliths.
- Haematomas in the vicinity of bones may undergo D.C.
- Dead parasites like schistostoma eggs show D.C.
- Congenital toxoplasmosis involving CNS visualised by calcification in infaract brain.

# Calcification in degenerated tissue
- Dense scars may undergo hyaline degeneration and calcification.
- Atheroma in aorta and coronaries frequently undergo calcification.
- Cysts can show calcifcation.
- Calcinosis cutis is condition in which there are irregular nodular deposits of calcium salts in skin and subcutaneous tissue.
- Senile degenerative changes may be accompanied by calcification.

# Pathological Findings
Image courtesy of Professor Peter Anderson DVM PhD and published with permission  PEIR, University of Alabama at Birmingham, Department of Pathology
- Metastatic calcification is only one of two forms of pathologic calcification. Unlike metastatic calcification, dystrophic calcification does not require an increase in serum calcium levels. This is a gross specimen of a heart with dystrophic calcification of the aortic valve (arrow).
- A closer view of this same aortic valve (arrow) illustrates the nodularity and thickening of this valve. This valve would be extremely stiff and almost entirely immobile. This particular example of dystrophic calcification is associated with a degenerative change of the aortic valve due to an unknown cause.
- This gross photograph affords a closer view of the same aortic valve. Note the nodularity and thickening of this valve due to fibrosis and dystrophic calcification.

# Related Chapters
- Calcinosis
Ectodysplasin A receptor
Ectodysplasin A receptor (EDAR) is a protein that in humans is encoded by the EDAR gene. EDAR is a cell surface receptor for ectodysplasin A which plays an important role in the development of ectodermal tissues such as the skin. It is structurally related to members of the TNF receptor superfamily.

# Function
EDAR and other genes provide instructions for making proteins that work together during embryonic development. These proteins form part of a signaling pathway that is critical for the interaction between two cell layers, the ectoderm and the mesoderm. In the early embryo, these cell layers form the basis for many of the body's organs and tissues. Ectoderm-mesoderm interactions are essential for the proper formation of several structures that arise from the ectoderm, including the skin, hair, nails, teeth, and sweat glands.

# Clinical significance
Mutation in this gene have been associated with hypohidrotic ectodermal dysplasia, a disorder characterized by a lower density of sweat glands.

# Derived EDAR allele
A derived G-allele point mutation (SNP) with pleiotropic effects in EDAR, 370A or rs3827760, found in most modern East Asians and Native Americans but not common in African or European populations, is thought to be one of the key genes responsible for a number of differences between these populations, including the thicker hair, more numerous sweat glands, smaller breasts, and the Sinodont dentition (so-called shovel incisors) characteristic of East Asians. It has been hypothesized that natural selection favored this allele during the last ice age in a population of people living in isolation in Beringia, as it may play a role in the synthesis of breast milk under Vitamin D-poor conditions. The 370A mutation arose in humans approximately 30,000 years ago, and now is found in 93% of Han Chinese and in the majority of people in nearby Asian populations. This mutation is also implicated in ear morphology differences and reduced chin protrusion. The derived G-allele is a mutation of the ancestral A-allele, the version found in most modern non-East Asian and non-Native American populations.
In a 2015 study, three (of six) ancient DNA samples (7,900-7,500 BP) from Motala, Sweden; two (33003000 BC) from the Afanasevo culture and one (400200 BC) Scythian sample were found to carry the rs3827760 mutation.
In a 2018 study, several ancient DNA samples from the Americas, including USR1 from the Upward Sun River site, Anzick-1, and the 9,600 BP individual from Lapa do Santo, were found to not carry the derived allele. This suggests that the increased frequency of the derived allele occurred independently in both East Asia and the Americas.
Epigallocatechin gallate
Epigallocatechin gallate (EGCG) is a type of catechin and is the most abundant catechin in tea.
According to one researcher epigallocatechin-3-gallate is an antioxidant that helps protect the skin from UV radiation-induced damage and tumor formation.
It is currently under study for multiple sclerosis
It can be found in many nutritional supplements.

# EGCG and HIV
There has been some research investigating the benefit of EGCG from green tea in the treatment of HIV infection.  One study examined the molecular binding of ECGC to the CD4 receptor molecule on human lymphocytes.  The CD4 receptor is the site where the HIV virus attaches to a cell before infecting it.  To bind to CD4, HIV uses its own receptor gp120.  The study found "clear evidence of high-affinity binding of EGCG to the CD4 molecule" and "inhibition of gp120 binding to human CD4+ T cells."   The mechanism is very similar to a new class of anti-HIV medications, the entry inhibitors.  For reasons not yet understood, EGCG seems to have an inhibitory effect on other steps of the HIV lifecycle, including suppression of reverse-transcriptase concentration and decreased protease kinetics.  These effects have only been observed in laboratory studies, not in HIV+ individuals.  The concentrations  of EGCG used in the studies could not be reached by drinking green tea.  More study into EGCG and HIV is currently underway.
Right atrial enlargement
Synonyms and keywords: Himalayan P waves, Himalayan P-wave, giant P waves, P pulmonale, right atrial abnormality,  RAE

# Overview
Right atrial enlargement can result from increased pressure in the pulmonary artery.   A P wave >2.5 mm in leads II, III and aVF 
-r a P wave >1.5 mm in lead V1 indicates right atrial enlargement. Despite the increase in the height of the P wave, the width of the P wave does not change.  Sometimes these large P waves can be referred to as Himalayan P waves.

# Causes of Right Atrial Enlargement
In alphabetical order:
- Atrial aneurysm
- Atrial septal defect
- Cor pulmonale or right heart failure
- Ebstein's anomaly
- Pulmonic stenosis
- Tricuspid prolapse
- Tricuspid regurgitation
- Tricuspid stenosis
- Tumor

# The EKG in Right Atrial Enlargement
Right atrial enlargement is defined as either:
- A P wave >2.5 mm in leads II, III and aVF
- A P wave >1.5 mm in lead V1
Shown below is an illustration of right atrial enlargement:
Shown below is an EKG demonstrating large P waves in leads to 2,3, and aVF which have a P-wave height greater than 2.5 mm consistent with right each one enlargement:

# Chest X-Ray
Shown below is the chest x-ray of a patient with Ebstein's anomaly in whom the right atrium is markedly enlarged as demonstrated by the convex curvature to the right border the heart.
Electrophysiologic study

# Overview
An electrophysiologic study (EPS) is one of a number of tests of the electrical conduction system of the heart performed by a cardiac electrophysiologist, a specialist in the electrical conduction system of the heart.  These tests are performed using catheters situated within the heart.

# Overview
There are a number of different tests that fall under the heading of an electrophysiologic study (EP study).  If the heart is electrically stimulated via the intracardiac catheter it is known as programmed electrical stimulation (PES).  PES is used to help diagnose and risk stratify individuals with a number of rhythm disturbances of the heart.  Other studies that do not require extrinsic stimulation of the heart include conduction studies to determine if the individual's heart block is at risk of progressing to complete heart block.
EP studies also allow the ablation of ectopic electrical foci causing supraventricular arrythmias

# Method
In order to perform an EP study, one or more catheters must be placed within the heart.  The catheters are typically placed in the right atrium and/or right ventricle via one or more incisions made in the central venous system.  The incisions are typically made in either the internal jugular vein, subclavian vein, or common femoral vein.
Catheters placed via the venous system enter the heart via the right atrium.  The advantage of this is that the right atrium is where the SA node is located.  The right atrium is also the location of most of the common re-entrant pathways associated with atrial flutter.  If a catheter is placed with the distal tip in the right ventricle, it may be possible to measure conduction through the bundle of His, which is useful to determine the level of heart block.  If the catheter is placed in the coronary sinus, it is possible to measure electrical activity in both the left atrium and the left ventricle without entering the high pressure arterial system associated with the left side of the heart.
Additional advantages of using these veins is that they are all part of the central venous system and do not have the valves that peripheral veins contain.  The advantage of approaching the heart via the venous system as opposed to via the arterial system is that the risk of stroke is dramatically less if the arterial system is not used.  Also, since the venous system is lower pressure, complications such as hematomas are typically easier to manage.
Therapeutic embolization

# Overview
Embolization is a non-surgical, minimally-invasive procedure performed by an interventional cardiologist or interventional radiologist and interventional neuroradiologists. It involves the selective occlusion of blood vessels, by purposely introducing emboli.

# Therapeutic Applications
Embolization is used to treat a wide variety of conditions affecting different organs of the human body.

## Hemorrhage
The treatment is used to occlude:
- AVMs
- Cerebral aneurysm
- Gastrointestinal bleeding
- Epistaxis

## Growths
- In the liver, typically HCC lesions.  Either by infarction or TACE (Transcatheter arterial chemoembolization).
- Kidney lesions
- Uterine fibroids

# The Procedure
The procedure is a minimally-invasive alternative to surgery. The purpose of therapeutic embolization is to prevent blood flow to an area of the body, which effectively can shrink a tumor or block an aneurysm.
The procedure is carried out as an endovascular procedure, by an Interventional Cardiologist or a Consultant Radiologist in an Interventional Suite. It is common for most patients to have the treatment carried out with little or no sedation, although this depends largely on the organ to be embolized. Patients who undergo Cerebral Embolization or Portal Vein Embolization are usually given a general anesthetic.
Access to the organ in question is acquired by means of a guide wire and catheter(s). Depending on the organ this can be very difficult and time consuming. The position of the correct artery or vein supplying the pathology in question is located by Digital subtraction angiography or DSA. These images are then used as a map for the radiologist to gain access to the correct vessel by selecting an appropriate catheter and or wire, depending on the 'shape' of the surrounding anatomy.
Once in place, the treatment can begin. The artificial embolus used is usually one of three things:
- Coils: Guglielmi Detachable Coil or Hydrocoil
- Particles
- Foam
Once the artificial emboli have been successfully introduced, another set of DSA images are taken to confirm a successful deployment.

# Advantages
- Minimally invasive
- No scarring
- Minimal risk of infection
- No or rare use of general anaesthetic
- Faster recovery time

# Disadvantages
- User dependent success rate
- Risk of emboli reaching healthy tissue
- Not suitable for everyone
Emtricitabine overdosage

# Overdosage
There is no known antidote for EMTRIVA. Limited clinical experience is available at doses higher than the therapeutic dose of EMTRIVA. In one clinical pharmacology trial single doses of emtricitabine 1200 mg were administered to 11 subjects. No severe adverse reactions were reported.
The effects of higher doses are not known. If overdose occurs the patient should be monitored for signs of toxicity, and standard supportive treatment applied as necessary.
Hemodialysis treatment removes approximately 30% of the emtricitabine dose over a 3-hour dialysis period starting within 1.5 hours of emtricitabine dosing (blood flow rate of 400 mL/min and a dialysate flow rate of 600 mL/min). It is not known whether emtricitabine can be removed by peritoneal dialysis.