Persius/hicric huggingface dataset:
Mycobacterium canariasense
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Mycobacterium canariasense is a rapidly growing, non-pigmented mycobacterium first isolated from blood samples obtained from 17 patients with febrile syndrome.  Etymology: canariasense; referring to the Latin adjective of the Spanish
islands where all strains were isolated.

# Description
Microscopy
- Weakly acid-fast rods.
Colony characteristics
- Visible growth appears in 23 days as smooth, moist, shiny, non-pigmented colonies on Lowenstein-Jensen medium.  Growth later develops a more yellowish, smooth, moist and shiny appearance.
Physiology
- Growth occurs at 30 and 37C, but not at 22, 42 or 45C.
- Grows on MacConkey agar without crystal violet, but does not grow in the presence
-f 5% NaCl.
- Positive for arylsulfatase activity (3 days) and Tween 80 hydrolysis.
- Produces a low level of heatstable catalase and is negative for reduction of nitrates.
Differential characteristics
- The 16S rRNA and hsp65 gene sequences of M. canariasense are unique.
- Most closely related to Mycobacterium diernhoferi and Mycobacterium mucogenicum.

# Pathogenesis
- First isolated from blood samples obtained from 17 patients with febrile syndrome in the Canary Islands.

# Type Strain
- Strain 502329T =CIP 107998T =CCUG 47953T
Mycobacterium farcinogenes
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Mycobacterium farcinogenes

# Description
Gram-positive, nonmotile and strongly acid-fast rods. Short or long filaments, bent and branched, in clumps or tangled, lacy network.
Colony characteristics
Rough, yellow and convoluted colonies. Firmly adherent to medium and surrounded by an iridescent halo.
Physiology
- Slow growth after 15-20 days on Lowenstein-Jensen medium.
Differential characteristics
- On the basis of characteristic lipids this species belongs to the genus Mycobacterium and not to the genus Nocardia.
- DNA homology to the closely related species M. senegalense. Both species, share an identical 5' 16S rDNA sequence.  However, the ITS sequences are different

# Pathogenesis
- Causes farcy in African cattle.
- Distinctive pathogenicity for guinea pigs: on subcutaneous inoculation, M. farcinogenes produces draining and slow healing abscesses after 8 days

# Type Strain
- First isolated from lesions of farcy in African bovines (Chad).
Strain IEMVT 75 = ATCC 35753 = CCUG 21047 = DSM 43637 = NCTC 10955.
National Influenza Centers
National Influenza Centers (also called National Influenza Centres) are institutions which are formally recognized as such by the World Health Organization (WHO).
"The WHO Global Influenza Surveillance Network was established in 1952. The network comprises 4 WHO Collaborating Centres (WHO CCs) and 112 institutions in 83 countries, which are recognized by WHO as WHO National Influenza Centres (NICs). These NICs collect specimens in their country, perform primary virus isolation and preliminary antigenic characterization. They ship newly isolated strains to WHO CCs for high level antigenic and genetic analysis, the result of which forms the basis for WHO recommendations on the composition of influenza vaccine for the Northern and Southern Hemisphere each year."
Among the more than 110 National Influenza Centers are the  WHO collaborating centres and reference laboratories that are involved in annual influenza vaccine composition recommendations.

# Sources and notes
-   WHO article Global influenza surveillance
- WHO Collaborating Centres and Reference Laboratories
- World Health Organization's Guide on How to become a National Influenza center
Neomycin contraindications

# Contraindications
Neomycin sulfate oral preparations are contraindicated in the presence of intestinal obstruction and in individuals with a history of hypersensitivity to the drug.
Patients with a history of hypersensitivity or serious toxic reaction to other aminoglycosides may have a cross-sensitivity to neomycin.
Neomycin sulfate oral solution is contraindicated in patients with inflammatory or ulcerative gastrointestinal disease because of the potential for enhanced gastrointestinal absorption of neomycin.
Neomycin drug interactions

# Drug Interactions
Caution should be taken in concurrent or serial use of other neurotoxic and/or nephrotoxic drugs because of possible enhancement of the nephrotoxicity and/or ototoxicity of neomycin (see boxed WARNINGS ).
Caution should also be taken in concurrent or serial use of other aminoglycosides and polymyxins because they may enhance neomycin's nephrotoxicity and/or ototoxicity and potentiate neomycin's neuromuscular blocking effects.
Oral neomycin inhibits the gastrointestinal absorption of penicillin V, oral vitamin B12, methotrexate and 5-fluorouracil. The gastrointestinal absorption of digoxin also appears to be inhibited. Therefore, digoxin serum levels should be monitored.
Oral neomycin may enhance the effect of coumarin in anticoagulants by decreasing vitamin K availability.
Neuropathy target esterase
Neuropathy target esterase also known as patatin-like phospholipase domain-containing protein 6 (PNPLA6) is a neuropathy target esterase enzyme that in humans is encoded by the PNPLA6 gene.
Neuropathy target esterase is a phospholipase that deacetylates intracellular phosphatidylcholine to produce glycerophosphocholine. It is thought to function in neurite outgrowth and process elongation during neuronal differentiation. The protein is anchored to the cytoplasmic face of the endoplasmic reticulum in both neurons and non-neuronal cells.

# Function
Neuropathy target esterase is an enzyme with phospholipase B activity:  It sequentially hydrolyses both fatty acids from the major membrane lipid phosphatidylcholine, which generates water-soluble glycerophosphocholine. In cells of eukaryotes from yeast to humans, NTE is anchored to the cytoplasmic face of the endoplasmic reticulum membrane and is particularly abundant in neurons, the placenta, and the kidney. Loss of NTE activity results in abnormally elevated levels of phosphatidylcholine in brain and impairment of the constitutive secretory pathway in neurons.
In kidney, the expression of neuropathy target esterase is regulated by TonEBP as part of osmolyte production when a concentrated urine is produced.

# Clinical significance
Mutations in this gene result in autosomal recessive spastic paraplegia, and the protein is the target for neurodegeneration induced by organophosphorus compounds and chemical warfare agents.
Recessively-inherited mutations in NTE that substantially reduce its catalytic activity cause a rare form of hereditary spastic paraplegia (SPG39), in which distal parts of long spinal axons degenerate leading to limb weakness and paralysis. Organophosphate-induced delayed neuropathy a paralysing syndrome with distal degeneration of long axons results from poisoning with neuropathic organophosphorus compounds that irreversibly inhibit NTE.
Nitrofurantoin description

# Description
Nitrofurantoin is an antibacterial agent specific for urinary tract infections. The Macrobid brand of nitrofurantoin is a hard gelatin capsule shell containing the equivalent of 100 mg of nitrofurantoin in the form of 25 mg of nitrofurantoin macrocrystals and 75 mg of nitrofurantoin monohydrate.
The chemical name of nitrofurantoin macrocrystals is 1-methylene]amino]-2,4-imidazolidinedione. The chemical structure is the following:
Molecular Weight: 238.16
The chemical name of nitrofurantoin monohydrate is 1-methylene]amino]-2,4- imidazolidinedione monohydrate. The chemical structure is the following:
Nystatin adverse reactions

# Adverse Reactions
Nystatin is well tolerated even with prolonged therapy. Oral irritation and sensitization have been reported.

## Gastrointestinal
Diarrhea (including one case of bloody diarrhea), nausea, vomiting, gastrointestinal upset/disturbances.

### Dermatologic
Rash, including urticaria has been reported rarely. Stevens-Johnson syndrome has been reported very rarely.
Oculodentodigital syndrome
Oculodentodigital syndrome (ODD syndrome) is an extremely rare genetic condition that typically results in small eyes, underdeveloped teeth, and problems with the fourth and fifth fingers.  It has also been called oculo-dento-digital syndrome, oculodentodigital dysplasia (ODDD), and oculodentoosseous dysplasia (ODOD).

# Presentation
People with ODD syndrome often have a characteristic appearance.  Visible features of the condition include:
- small teeth that are prone to caries because of underdeveloped tooth enamel;
- a long, thin nose;
- unusually small eyes; and
- type III syndactyly of the fourth and fifth fingers.
Iris atrophy and glaucoma are more common than average. The size of the eyes often interferes with learning to read; special eyeglasses may be required.  Hair may be fine, thin, dry, or fragile; in some families, it is curly.
Neurologic abnormalities may be seen in adults.  The neurologic changes may appear earlier in each subsequent generation and can include abnormal white matter, conductive deafness, and various kinds of paresis, including ataxia, spastic paraplegia, difficulty controlling the eyes, and bladder and bowel disturbances.

# Genetics
ODD is commonly an autosomal dominant condition, but can be inherited as a recessive trait.  16816024  It is generally believed to be caused by a mutation in the gene GJA1, which codes for the gap junction protein connexin 43.  Slightly different mutations in this gene may explain the different way the condition manifests in different families.  Most people inherit this condition from their mothers or fathers, but new cases arise through mutation, particularly in older fathers.  The mutation has high penetrance and variable expression, which means that nearly all people with the gene show signs of the condition, but these signs can range from very mild to very obvious.

# Epidemiology
The actual incidence of this disease is not known, but only 243 cases have been reported in the scientific literature, suggesting an incidence of on the order of one affected person in ten million people.
Tumor induced osteomalacia

# Overview
Tumor induced osteomalacia (also known as oncogenic hypophosphatemic osteomalacia or oncogenic osteomalacia) is an uncommon disorder resulting in increased renal phosphate excretion, hypophosphatemia and osteomalacia.

# Signs and symptoms
Adult patients have worsening myalgias, bone pains and fatigue which are followed by recurrent fractures. Children present with difficulty in walking, stunted growth and deformities of the skeleton (features of rickets).

# Diagnosis
Biochemical studies reveal hypophosphatemia, elevated alkaline phosphatase and low serum calcitriol (1, 25 dihydroxyvitamin D) levels. Routine laboratory tests do not include serum phosphate levels and this can result in considerable delay in diagnosis.

# Pathogenesis
FGF-23 (fibroblast growth factor-23) inhibits phosphate transport in the renal tubule and reduces calcitriol production by the kidney. Tumor production of FGF-23, frizzled-related protein 4 and matrix extracellular phosphoglycoprotein (MEPE) have all been identified as possible causative agents for the hypophosphatemia.

# Causative tumors
Tumor induced osteomalacia is usually referred to as a paraneoplastic phenomenon, however, the tumors are usually benign and the symptomatology is due to osteomalacia or rickets. Seen most often are benign mesenchymal or mixed connective tissue tumors (commonly hemangiopericytomas). Association with malignant tumors has also been reported. 
Locating the tumor can prove to be difficult and may require whole body magnetic resonance imaging (MRI). Some of the tumors express somatostatin receptors and may be located by octreotide scanning.

# Differential diagnosis
Serum chemistries are identical in tumor induced osteomalacia, X-linked hypophosphatemic rickets (XHR) and autosomal dominant hypophosphatemic rickets (ADHR). A negative family history can be useful in distinguishing tumor induced osteomalacia from XHR and ADHR. If necessary, genetic testing for PHEX (phosphate regulating gene with homologies to endopepetidase on the X-chromosome) can be used to conclusively diagnose XHR and testing for the FGF-23 gene will identify patients with ADHR.

# Treatment
Resection of the tumor is the ideal treatment and results in correction of hypophosphatemia (and low calcitriol levels) within hours of resection. Resolution of skeletal abnormalities may take many months.
If the tumor cannot be located, treatment with calcitriol (1-3 g/day) and phosphorus (1-4 g/day in divided doses) is instituted. Tumors which secrete somatostatin receptors may respond to treatment with octreotide
Ornithine aminotransferase
Ornithine aminotransferase (OAT) is an enzyme which is encoded in human by the OAT gene located on chromosome 10.
The OAT involved in the ultimate formation of the non-essential amino acid proline from the amino acid ornithine. Ornithine aminotransferase forms the initial intermediate in this process. It catalyzes the reverse reaction as well, and is therefore essential in creating ornithine from the starting substrate proline.

# Structure
The OAT gene encodes for a protein that is approximately 46 kDa in size. The OAT protein is expressed primarily in the liver and the kidney but also in the brain and the retina. The OAT protein is localized to the mitochondrion within the cells where it is expressed.
The structure of the OAT protein has been resolved usign X-ray cyrstallography and shows similarity to other subgroup 2 aminotransferases such as dialkyglucine decarboxylatse. The OAT protein functions as a dimer and each monomer consists of a large domain, which contributes most to subunit interface, and a C-terminal small domain, and an N-terminal region containing a helix, loop, and three-sranded beta-meander. In the central large domain is a seven-stranded beta-sheet covered by eight helices. The co-factor of the OAT protein (pyridoxal-5'-phosphate) binds to OAT through a Schiff base at the lysine 292 position situated between two of the seven-stranded beta-sheet. Three amino acids (R 180, E 235, and R413) are thought to be involved in substrate binding at the active site.

# Function
Ornithine aminotransferase catalyzes the transfer of the delta-amino group from L-ornithine
- L-ornithine + a 2-oxo acid = L-glutamate 5-semialdehyde + an L-amino acid
The reaction requires pyridoxal 5'-phosphate as a co-factor and forms part of the subpathway that synthesizes L-glutamate 5-semialdehyde from L-ornithine.

# Clinical significance
Mutations in the OAT gene can lead to malfunctioning proteins, including both point mutations that abolish catalytic activities, large frame-shift mutations, as well as mutated proteins that are not properly targeted to the mitochondrion where its normal functionality occurs. In the latter, abnormality of mitochondrial import causes ectopic accumulation of the OAT protein in the cytosol followed by rapid degradation by proteolysis. Deficiency of OAT activities causes ornithine aminotransferase deficiency, also known as  gyrate atrophy of choroid and retina.
The mechanism of gyrate atrophy of choroid and retina is thought to involve the toxicity of glyoxylate.
Periodic acid-Schiff stain

# Overview
Periodic acid-Schiff (PAS) is a staining method used in histology and pathology. This method is primarily used to identify glycogen in tissues. The reaction of periodic acid selectively oxidizes the glucose residues, creates aldehydes that react with the Schiff reagent and creates a purple-magenta color. A suitable basic stain is often used as a counterstain.
PAS staining is mainly used for staining structures containing high proportion of carbohydrate macromolecules (glycogen, glycoprotein, proteoglycans), typically found in eg. connective tissues, mucus, and basal laminae.
PAS staining can be used to distinguish between different types of glycogen storage diseases.
Platelet function analyzer
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# Overview
The Platelet Function Analyzer-100(PFA-100, Siemens Healthcare Diagnostics, Inc., Deerfield, IL) is a test based on the principle of shear-induced aggregation. Although it is not a COX-1specific assay, it allows monitoring of aspirin effects by providing a quantitative measure of platelet-related hemostasis in anticoagulated whole blood.
The system comprises a microprocessor-controlled tool and a disposable test cartridge containing a biologically active nitrocellulose membrane. To perform the test, 0.8 ml of citrated whole blood is transferred into the reservoir of the cartridge within 4 h of blood sampling. After warming the anticoagulated blood to 37 C, the instrument aspirates a blood sample under vacuum from the reservoir through a 200 m diameter stainless steel capillary and a 150 m aperture cut into the membrane, which is coated with collagen and epinephrine (CEPI) or collagen and ADP (CADP).
The presence of these biochemical stimuli, and the high shear rates of 50006000 s1 generated under the standardized flow conditions, result in platelet aggregate forms that block the aperture of the membrane. The time required to obtain full occlusion of the aperture is reported as the closure time (CT).
Prolonged CT with only the CEPI cartridge is observed with mild inherited platelet function disorders and with aspirin ingestion, while prolonged CTs with both CEPI and CADP cartridges are associated with more severe inherited platelet dysfunctions. 
An advantage of the PFA-100 application as a platelet function assay is that it is a rapid, accurate, simple, and reproducible test that requires only a small volume of blood. It cannot be considered as a point of care as minimal pipetting is required to use this test. One of its major disadvantages is that it is poorly sensitive in detecting effects of thienopyridines and therefore should not be used for this purpose. Newer generation assays are currently under development to assess thienopyridine effects.
Protoporphyrinogen oxidase
Protoporphyrinogen oxidase is an enzyme that in humans is encoded by the PPOX gene.
Protoporphyrinogen oxidase is responsible for the seventh step in biosynthesis of protoporphyrin IX. This porphyrin is the precursor to hemoglobin, the oxygen carrier in animals, and chlorophyll, the dye in plants. The enzyme catalyzes the dehydrogenation (removal of hydrogen atoms) of protoporphyrinogen IX (the product of the sixth step in the production of heme) to form protoporphyrin IX. One additional enzyme must modify protoporphyrin IX before it becomes heme.  Inhibition of this enzyme is a strategy used in certain herbicides.

# Gene
The PPOX gene is located on the long (q) arm of chromosome 1 at position 22, from base pair 157,949,266 to base pair 157,954,082.

# Function
This gene encodes the penultimate enzyme of heme biosynthesis, which catalyzes the 6-electron oxidation of protoporphyrinogen IX to form protoporphyrin IX. This protein is a flavoprotein associated with the outer surface of the inner mitochondrial membrane.

# Heme biosynthetic pathway
The following genes encode enzymes that catalyze the various steps in the heme biosynthetic pathway:
- ALAD: aminolevulinate, delta-, dehydratase
- ALAS1: aminolevulinate, delta-, synthase 1
- ALAS2: aminolevulinate, delta-, synthase 2 (sideroblastic/hypochromic anemia)
- CPOX: coproporphyrinogen oxidase
- FECH: ferrochelatase (protoporphyria)
- HMBS: hydroxymethylbilane synthase
- PPOX: protoporphyrinogen oxidase
- UROD: uroporphyrinogen decarboxylase
- UROS: uroporphyrinogen III synthase (congenital erythropoietic porphyria)

# Clinical significance
Variegate porphyria is caused by mutations in the PPOX gene. More than 100 mutations that can cause variegate porphyria have been identified in the PPOX gene. One mutation, a substitution of the amino acid tryptophan for arginine at position 59 (also written as Arg59Trp or R59W), is found in about 95 percent of South African families with variegate porphyria. Mutations in the PPOX gene reduce the activity of the enzyme made by the gene, allowing byproducts of heme production to build up in the body. This buildup, in combination with nongenetic factors (such as certain drugs, alcohol and dieting), causes this type of porphyria.
Pallister-Killian syndrome
Pallister-Killian syndrome (also tetrasomy 12p mosaicism or Pallister mosaic aneuploidy syndrome) is an extremely rare genetic disorder occurring in humans.  Pallister-Killian occurs due to tetrasomy of the twelfth chromosome. This leads to the development of isochromosome 12p, made up of the two short legs of the chromosome.  Because not all cells have the extra isochromosome, Pallister-Killian is mosaic.
It was first described by Philip Pallister in 1977 and further researched by Maria Teschler-Nicola and W. Killian in 1981.

# Symptoms
Symptoms include varying degrees of mental retardation, epilepsy, hypotonia, and both hypopigmentation and hyperpigmentation.  Patients also exhibit a distinctive facial structure, characterized by high foreheads, sparse hair on the temple, a wide space between the eyes, a fold of skin over the inner corner of the eyes, and a flat nose.  Visual impairments and deafness may occur. Patients may also exhibit congenital heart defects, gastroesophageal reflux, cataracts, and supernumerary nipples.  Diaphragm problems seen in newborns can lead to death shortly after birth.
As patients pass into adolescence, the syndrome is characterized by a coarse and flat face, macroglossia prognathia, inverted lower lip, and psychomotor retardation with muscular hypertonia and contractures.

# Causes
Pallister-Killian does not appear to be hereditary. Some research has suggested that the presence of the extra chromosome may be linked to premeiotic mitotic errors, both maternally and paternally. Several theories regarding to mechanism of this formation have been introduced.

# Diagnosis
The isochromosome can be primarily detected in samples of skin fibroblasts, as well as in chorionic villus and amniotic fluid cell samples. Very rarely, it can also be detected in blood lymphocytes. It is also possible to detect the isochromosome in circulating lymphocytes, as well as other amniotic and placental samples. There is no strict limit as to where the isochromosome can be found. However, it is often unlikely that these samples will be tested when the blood karyotype is normal.
Using an ultrasound, Pallister-Killian may be diagnosed through observation of hypertelorism, broad neck, shorts limbs, abnormal hands or feet, diaphragmatic hernia, and hydramnios. Once born, a child may be diagnosed by observation of the syndrome's distinct facial features.