Persius/hicric huggingface dataset:
Omphalocele

# Overview
An omphalocele is a type of abdominal wall defect in which the intestines, liver, and occasionally other organs remain outside of the abdomen in a sac because of a defect in the development of the muscles of the abdominal wall.

# Causes
Some cases of omphalocele are believed to be due to an underlying genetic disorder.

## Congenital conditions
- Pentalogy of Cantrell

## Chromosomal abnormalities
- Wiedemann-Beckwith syndrome

## Mendelian inherited conditions
- Opitz-Frias syndrome
- Osteodysplasty (Melnick-Needles)

## Autosomal recessive conditions
- Donnai-Barrow syndrome
- Manitoba oculotrichoanal syndrome

# Presentation
The sac protrudes in the midline, through the umbilicus (navel).
It is normal for the intestines to protrude from the abdomen, into the umbilical cord, until about the tenth week of pregnancy, after which they return to inside the fetal abdomen.
The omphalocele can be mild, with only a small loop of intestines present outside the abdomen, or severe, containing most of the abdominal organs. In severe cases surgical treatment is made more difficult because the infant's abdomen is abnormally small because it had no need to expand to accommodate the developing organs.

# Screening
An omphalocele is often detected through AFP screening or a detailed fetal ultrasound. Genetic counseling and genetic testing such as amniocentesis is usually offered during the pregnancy. Some cases of omphalocele are due to an underlying genetic disorder.

# Related conditions
Gastroschisis is a similar birth defect, but the umbilical cord is not involved, and parts of organs may be in the amniotic fluid, and not enclosed in a membranous sac.

# Examples
- Omphalocele
Coiled coil

# Overview
A coiled coil is a structural motif in proteins, in which 2-7 alpha-helices are coiled together like the strands of a rope (Dimers and trimers are the most common types). Many coiled coil type proteins are involved in important biological functions such as the regulation of gene expression e.g. transcription factors. Notable examples are the proteins the oncoproteins c-fos and jun, and the muscle protein tropomyosin.

# Molecular structure of coiled coils
Coiled coils usually contain a repeated seven amino acid residue pattern called heptad repeats. The interacting surface between the helices often contain hydrophobic residues, such as leucine arranged in a so called leucine zipper. The most favorable way for such two helices to arrange them selves in the water-filled environment of the cytoplasm is to wrap the hydrophobic strands against each other sandwiched between the hydrophilic amino acids. It is thus the burial of hydrophobic surfaces, that provides the thermodynamic driving force for the dimerization.
The -helices may be parallel or antiparallel, and usually adopt a left-handed super-coil (Figure 1).  Although disfavored, a few right-handed coiled coils have also been observed in nature and in designed proteins.

# Biological roles of coiled coils

## Role of coiled coils in HIV infection
A key step in the entry of HIV into human cells is the exposure of a trimeric, parallel coiled coil known as gp41.  The gp41 trimer is normally covered by another surface glycoprotein known as gp120, which protects it from antibodies.  Upon binding to the target cell, gp120 undergoes a conformational change that exposes the gp41 trimer, whose hydrophobic N-terminal tails enter the target cell membrane.  Three other helices of gp41 fold down into the grooves of the gp41 coiled coil trimer, forming a hexamer, and drawing the viral membrane and target-cell membrane close enough to fuse.  The virus then enters the cell and begins its replication.  Recently, inhibitors that bind in the gp41 grooves have been developed, such as Fuzeon.

## Coiled coils as dimerization tags
Because of their specific interaction coiled coils can be used as a dimerization "tag".

# History of coiled coils
The possibility of coiled coils for -keratin was proposed by Francis Crick in 1952 as well as mathematical methods for determining their structure.
 Remarkably this was soon after the structure of the alpha helix was suggested in 1951 by Linus Pauling and coworkers
Coley Fluid

# Overview
Coley Fluid is a modern reformulation of a historical cancer therapy called Coley Vaccine developed by Dr. William B. Coley that was an effective treatment for many forms of cancer including advanced breast cancer.
The authors of a 1982 study concluded five year survival rates of historical Coley Vaccine patients is indistinguishable from five-year survival of modern patients.
In 1999, researchers found ten-year survival was higher in historical Coley Vaccine patients compared to modern sarcoma, kidney and ovarian cancer patients.
Coley Fluid is manufactured by MBVax Bioscience Inc, Ancaster, Canada.
Comminution
Comminution is one of the four main groups of mechanical processing and describes the movement of the particle size distribution (grains, drops, bubbles) into a range of finer particle sizes (The other groups are agglomeration, separation and mixing).
Comminution can be found in daily life in activities such as cutting, crushing, powder metallurgy, grinding and rasping in the preparation of different foods.
Industrial applications are found in biomass processing, preprocessing of cellulosic material to facilitate ethanol production, mineral processing (extraction of raw materials), chemical and ceramic industries, cement production, production of food, processing of waste.
In most of the cases the word comminution is used in referral to solids. Depending on the particle size it is distinguished between crushing (coarse feed material, bigger than appr. 50 to 100 mm) and grinding. Machines used for comminution are jaw crusher, cone and gyratory crushers, roller crusher, impact crusher, tube mills (e.g. ball mills or autogenous mills), vertical roller mills, and roller presses.

# Mining
Comminution refers to a series of mineral processing techniques used in extractive metallurgy to reduce particle sizes of rocks and ores.  Comminution processes are used to crush rocks into powder in preparation for subsequent processing methods which generally require finer particle sizes.  A particle is liberated when the mineral of interest is physically free from any other minerals present (the gangue).
The machinery used for comminution can be divided into classes based on the size of the fragments they produce. Devices that produce coarse chunks are called crushers and those that produce finer particles are called grinders.

# Waste management
Comminution is also used in the mechanical shredding or pulverizing of waste; a process found in solid and water waste treatment.

# Medical
The term "comminution" is also used in medicine when referring to certain types of fracture.
Usually, an impact will cause one fracture, thus breaking the bone into two pieces.
But when the magnitude of the impact is such that it causes a bone to break in more than one place , it will produce
several (i.e. more than two) fragments of bone.
This is termed a "comminuted fracture".
Common bunt
Common bunt, also known as stinking smut and covered smut is a disease of both spring and winter wheats.  It is caused by two very closely related fungi, Tilletia tritici (syn. T. caries) and T. laevis (syn. T. foetida).

# Symptoms
Plants with common bunt may be moderately stunted but infected plants cannot be easily recognized until near maturity and even then it is seldom conspicuous.  After initial infection, the entire kernel is converted into a sorus consisting of a dark brown to black mass of teliospores covered by a modified periderm, which is thin and papery. The sorus is light to dark brown and is called a bunt ball. The bunt balls resemble wheat kernels but tend to be more sperical.  The bunted heads are slender, bluish-green and may stay greener longer than healthy heads.  The bunt balls change to a dull gray-brown at maturity, at which they become conspicuous. The fragile covering of the bunt balls are ruptured at harvest, producing clouds of spores. The spores have a fishy odor. Intact sori can also be found among harvested grain.

# Disease cycle
Millions of spores are released at harvest and contaminate healthy kernels or land on other plant parts or the soil.  The spores persist on the contaminated kernels or in the soil. The disease is initiated when soil-borne, or in particular seed-borne, teliospores germinate in response to moisture and produce hyphae that infect germinating seeds by penetrating the coleoptile before plants emerge.  Cool soil temperatures (5 to 10C) favor infection.  The intercellular hyphae become established in the apical meristem and are maintained systemically within the plant.  After initial infection, hyphae are sparse in plants. The fungus proliferates in the spikes when ovaries begin to form. Sporulation occurs in endosperm tissue until the entire kernel is converted into a sorus consisting of a dark brown to black mass of teliospores covered by a modified periderm, which is thin and papery.

# Pathotypes
Well-defined pathogenic races have been found among the bunt population, and the classic gene-for-gene relationship is present between the fungus and host.

# Management
Control of common bunt includes using clean seed, seed treatments chemicals and resistant cultivars.  Historically, seed treatment with organomercury fungicides reduced common bunt to manageable levels. Systemic seed treatment fungicides include carboxin, difenoconazole, triadimenol and others and are highly effective.  However,in Australia and Greece, strains of T. laevis have developed resistance to polychlorobenzene fungicides.
Nephrectomy
Steven C. Campbell, M.D., Ph.D.

# Overview
Nephrectomy is the surgical removal of a kidney.

# Indications
There are various indications for this procedure, such as renal cell carcinoma, a non-functioning kidney (which may cause high blood pressure) and a congenitally small kidney (in which the kidney is swelling, causing it to press on nerves which can cause pain in unrelated areas such as the back).
Nephrectomy for renal cell carcinoma is rapidly being modified to allow partial removal of the kidney.
When one is donating a kidney for a kidney transplant, a nephrectomy is also performed on the patient.

# Procedure
The surgery is performed with the patient under general anesthesia. The surgeon makes an incision in the side of the abdomen to reach the kidney. Depending on circumstances, the incision can also be made midline.  The ureter and blood vessels are disconnected, and the kidney is then removed.
The surgery can be done as open surgery, with one incision, or as a laparoscopic procedure, with three or four small cuts in the abdominal and flank area.
Recently, this procedure is performed through a single incision in the patient's belly-button. This advanced technique is called as Single Port Access Surgery.

# After Care
Pain medication is often given to the patient after the surgery because of the painful location. An IV with fluids is administered.
Electrolyte balace and fluids are carefully monitored, because these are the functions of the kidneys. It is possible that the remaining kidney does not take over all functionality.
A patient has to stay in the hospital between 2 and 7 days depending on the procedure and complications.

# Links and Sources
Drawings of the steps of the procedure
MedlinePlus Medical Encyclopedia: Nephrectomy 
Explanation of the surgery, the risks and the recovery
Cortexolone
Cortexolone or cortodoxone or 11-deoxycortisol or 11-desoxycortisol or 11-deoxyhydrocortisone or 11-desoxyhydrocortisone or Reichstein's Substance S or, most commonly, Compound S, is a steroid that can be oxygenated to cortisol (hydrocortisone). It was first synthesized by Tadeusz Reichstein.
On April 5, 1952, biochemist Durey Peterson and microbiologist Herbert Murray at Upjohn published the first report of a breakthrough fermentation process for the microbial 11-oxygenation of steroids (e.g. progesterone) in a single step by common molds of the order Mucorales. 
11-oxygenation of Compound S produces 11-hydrocortisone, which can be chemically oxidized to cortisone, or converted by further chemical steps to 11-hydrocortisone (cortisol).
Subsequent fermentation processes for the microbial 11-oxygenation of steroids in a single step were developed that could convert Compound S directly to 11-hydrocortisone (cortisol).
Growth cone

# Overview
A growth cone is a dynamic, actin-supported extension of a developing axon seeking its synaptic target. Their existence was originally proposed by Spanish histologist Santiago Ramon y Cajal based upon stationary images he observed under the microscope. Neuronal growth cones are situated on the very tips of nerve cells on structures called axons and dendrites. The most crucial roles of the neuronal growth cone are to explore its surroundings ultimately establishing synaptic contacts.

# Structure
The morphology of the growth cone can be easily described by using the hand as an analogy. The fine extensions of the growth cone are known as "filopodia". The filopodia are like the "fingers" of the growth cone; they contain actin filaments that give them shape and support. In between filopodia--much like the webbing of the hands--are the "lamellipodia". The filopodia contain receptors that are important for axon guidance.

# Movement
The growth cones are continually being built up through construction of the actin microfilaments and extension of the plasma membrane via vesicle fusion. The actin filaments depolymerize and disassamble on one end to allow free monomers to migrate to the leading edge of the actin filament where it can polymerize and thus reattach. Actin filaments thus do not actually grow but rather migrate. The growth capacity of the axons lies in the microtubules which are located just beyond the actin filaments. Laminins of the basal membrane interact with the integrins of the growth cone to promote the forward movement of the growth cone.

# Axon guidance
Movement of the axons is controlled by an integration of its sensory and motor function (described above) which is established through second messengers such as calcium and cyclic nucleotides. The sensory function of axons is dependent on cues from the extracellular matrix which can be either attractive or repulsive, thus helping to guide the axon away from certain paths and attracting them to their proper target destinations. Attractive cues inhibit retrograde flow of the actin filaments and promote their assembly whereas repulsive cues have the exact opposite effect. Growth cone receptors detect the presence of axon guidance molecules such as Netrin, Slit, Ephrins, and Semaphorins. It has more recently been shown that cell fate determinants such as Wnt can also act as guidance cues. Quite interestingly, the same guidance cue can act as an attractant or a repellent, depending on context. A prime example of this is Netrin-1, which signals attraction through the DCC receptor and repulsion through the Unc-5 receptor. Furthermore, it has been discovered that these same molecules are involved in guiding vessel growth. Axon guidance directs the initial wiring of the nervous system and is also important in axonal regeneration following an injury.
Conjunctiva
The conjunctiva is a membrane that covers the sclera (white part of the eye) and lines the inside of the eyelids.

# Function
It helps lubricate the eye by producing mucus and tears, although a smaller volume of tears than the lacrimal gland.
It also contributes to  immune surveillance and helps to prevent the entrance of microorganisms into the eye.

# Histology
The conjunctiva is typically divided into three parts:
- Palpebral or tarsal conjunctiva: The conjunctiva lining the eyelids.
- Fornix conjunctiva: The conjunctiva where the inner part of the eyelids and the eyeball meet, the palpebral conjunctiva is reflected at the superior fornix and the inferior fornix to become the bulbar conjunctiva.
- Bulbar or ocular conjunctiva: The conjunctiva covering the eyeball, over the sclera. This region of the conjunctiva is bound tightly and moves with the eyeball movements.

# Diseases and disorders
Disorders of the conjunctiva and cornea are a common source of eye complaints.
The surface of the eye is exposed to various external influences and is especially suspectible to trauma, infections, and allergic reactions.
The conjunctiva is best known because of its inflamed state, conjunctivitis (more commonly known as pinkeye).
Conjunctival irritation is one of the adverse health effects that can take place after overexposure to VOCs (Volatile organic compounds).
Contactin 4
Contactin-4 is a protein that in humans is encoded by the CNTN4 gene.
The protein encoded by this gene is a member of the immunoglobulin superfamily. It is a glycosylphosphatidylinositol (GPI)-anchored neuronal membrane protein that functions as a cell adhesion molecule. It may play a role in the formation of axon connections in the developing nervous system. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined.

# Genomics
The gene is located on the short arm of chromosome 3 (3p26.3). It is a single copy gene within the Watson (plus) strand, 957,399 bases in length and encodes a protein of  1026 amino acids (molecular weight 113.454 kDa)

# Clinical relevance
Abnormal expression of this gene has been implicated in some cases of autism. It has also been associated with cerebellar degeneration in spinocerebellar ataxia type 16.
Contrayerva
In botany, the contrayerva, or contrajerva, is the root and scaly rhizome of various tropical American species of Dorstenia in the family Moraceae (D. contrayerva and D. braziliensis), a South American plant, the aromatic root of which is sometimes used in medicine as a gentle stimulant and tonic. It was previously used as an antidote to snake bites.
The name is used in Jamaica to refer to a species of Birthwort (Aristolochia odoratissima) still believed to have antidotal properties.
The root is smaller than that of the iris, reddish outside and white inside, knotty, and fibrous. To be of use, it must be new, heavy, and of a dusky red color. Its odor resembles that of fig leaves. Its taste is aromatic, accompanied with some acrimony.
The contrayerva root was formerly considered by many writers to be one of the best anti-epidemics known. Dr. Nathaniel Hodges (16291688), in his treatise of the Great Plague of London (Loimologia; published in 1672), had a recipe which he said was very successful, and of which this root was one of the chief ingredients.
Cor bovinum
Cor bovinum refers to a massive hypertrophy of the left ventricle of the heart due to volume overload, usually in the context of syphilis infection.

# Pathophysiology
Due to Syphilitic aortitis (a complication of tertiary syphilis) the aortic valve ring becomes dilated.  The free margins of ] no longer approximate leading to aortic valve insufficiency.  As blood regurgitates into the left ventricle between each systole, volume overload ensues and the ventricular wall hypertrophies in an attempt to maintain cardiac output and blood pressure.  The massive ventricle can lead to a heart weighing over 1000 grams (the weight of a normal heart is about 350 grams), referred to as "Cor Bovinum" 
A Medline search of articles published since 1950 revealed seven articles on "cor bovinum" (in the earlier part of this period only the titles could be searched), of which only one is in English. Searching for the synonyms revealed no mention of "bucardia," and all 101 articles mentioning "ox heart" related to oxen.
Fluri and Gebbers define cor bovinum as a heart exceeding 500 g in weight. Looking through autopsies on Internal Medicine patients at the Kantonsspital Luzern, they found 415 cases out of 1181 autopsies in the two periods 1978-81 and 1997-2000. Cor bovinum was found in 25.3% of cases in the earlier period, with mean age at death 67.7 years, and in the later period 20.6% with mean age 74.3 years. The male female ratio was 4:1. "In 93% of all patients with CB, we found coronary atherosclerosis as a sign of high blood pressure and in 79% a COPD."
In 84% of cases the cause of death was directly related to the cor bovinum, but in 37% the cause of death was still unclear. They concluded that cor bovinum was a decreasing but still frequent autopsy finding. High blood pressure, COPD and male sex were the main risk factors. The decreasing incidence was ascribed to improved medical management: they mention treatments for high blood pressure and coronary artery disease, which suggests that "COPD" in their abstract refers to the latter.
Glans penis
The glans penis (or simply glans) is the sensitive tip of the penis. It is also commonly referred to as the "head" of the penis. Slang terms include "helmet" and "bell end". When the penis is flaccid it is wholly or partially covered by the foreskin, except in men who have been circumcised.

# Medical considerations
The meatus (opening) of the urethra is at the tip of the glans penis. In circumcised infants who wear diapers, the meatal area of the glans penis is without the protection of the foreskin and at slight risk of meatitis, meatal ulceration, and meatal stenosis.
The epithelium of the glans penis is mucocutaneous tissue. Birley et al. report that excessive washing with soap may dry the mucous membrane that covers the glans penis and cause non-specific dermatitis.
Inflammation of the glans penis is known as balanitis. It occurs in 311% of males, and up to 35% of diabetic males. It has many causes, including irritation, or infection with a wide variety of pathogens. Careful identification of the cause with the aid of patient history, physical examination, swabs and cultures, and biopsy are essential in order to determine the proper treatment.

# Anatomical details
The glans penis is the expanded cap of the corpus spongiosum. It is moulded on the rounded ends of the Corpora cavernosa penis, extending farther on their upper than on their lower surfaces. At the summit of the glans is the slit-like vertical external urethral orifice. The circumference of the base of the glans forms a rounded projecting border, the corona glandis, overhanging a deep retroglandular sulcus (the coronal sulcus), behind which is the neck of the penis. The proportional size of the glans penis can vary greatly.
The foreskin maintains the mucosa in a moist environment. In males who have been circumcised, but have not undergone restoration, the glans is permanently exposed and dry. Szabo and Short found that the glans of the circumcised penis does not develop a thicker keratinization layer. Studies have suggested that the glans is equally sensitive in circumcised and uncircumcised males. 
Halata & Munger (1986) report that the density of genital corpuscles is greatest in the corona glandis, while Yang & Bradley (1998) report that their study "showed no areas in the glans to be more densely innervated than others."
Halata & Spathe (1997) reported that "the glans penis contains a predominance of free nerve endings, numerous genital end bulbs and rarely Pacinian and Ruffinian corpuscles. Merkel nerve endings and Meissner corpuscles are not present."
Yang & Bradley argue that "The distinct pattern of innervation of the glans emphasizes the role of the glans as a sensory structure".
An anatomycal variant of glans is showed: Hirsuties papillaris genitalis

# Additional images
- Diagram of the arteries of the penis.
- Penis
- An uncircumcised glans penis
- Side view circumcised glans penis
- An anterior view of a flaccid uncircumcised glans penis