Persius/hicric huggingface dataset:
Mycobacterium gilvum
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Mycobacterium gilvum
Etymology: gilvum, Latin for pale yellow.

# Description
Pleomorphic gram-positive, nonmotile and acid-fast rods.
Colony characteristics
- Pale yellow, Scotochromogenic, and smooth pleomorphic colonies.
Physiology
- Rapid growth on Lowenstein-Jensen medium at 25C and 37C, but not at 45C, within 7 days.
- Resistant to isoniazid, rifampicin, and sodium aminosalicylate.
Differential characteristics
- 5 species-specific antigens, demonstrable in immunodiffusion tests.

# Pathogenesis
- Not assumed to be pathogenic
- Biosafety level 1

# Type Strain
First isolated from sputum and pleura fluid (London).
Strain ATCC 43909 = CCUG 37676 = CIP 106743 = DSM 44503 = JCM 6395 = NCTC 10742.
Mycobacterium goodii
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Mycobacterium goodii

# Description
Gram-positive, nonmotile and acid-fast rods.
Colony characteristics
- Smooth to mucoid, off-white to cream coloured colonies. Yellow to orange pigment produced in 78% of all strains, after 10-14 days incubation.
Physiology
- Rapid growth on Middlebrook 7H10 and trypticase soy agar at 30C, 35C and 45C within 2-4 days.
- Susceptible to amikacin, ethambutol, sulfamethoxazole.
- Intermediate susceptible to ciprofloxacin, doxycycline and tobramycin.
- Variable susceptible to cefmetazole, cefoxitin and clarithromycin.
- Resistant to isoniazid and rifampicin.
Differential characteristics
- Comparable clinical settings to M. smegmatis and members of the M. fortuitum complex.

# Pathogenesis
- Production of post-traumatic wound infections especially those following open fractures and with associated osteomyelitis and chronic lipoid pneumonia.

# Type Strain
First isolated from a patient with a post-traumatic osteomyelitis of the heel(USA).
Strain MO69 = ATCC 700504 = CIP 106349 = DSM 44492 = JCM 12689.
Mycobacterium goodii was previously known as Mycobacterium smegmatis group 2.
Mycobacterium terrae

# Overview
Mycobacterium terrae is a slow-growing species of Mycobacterium. It is an ungrouped member of the third Runyon (nonchromatogenic mycobacteria). It is known to cause serious skin infections, which are "relatively resistant to antibiotic therapy".

# Discovery
Richmond and Cummings were the first to isolate Mycobacterium terrae, which they described as "an acidfast saprophyte". It is sometimes called the radish bacillus", because it was isolated from radish water.

# Pathology
This bacterium was originally injected into guinea pigs, and did not cause apparent illness, leading to the misconception that this strain was nonpathogenic. In reality, however, infection by this organism can cause disease of the joints, tendons, lungs, gastrointestinal tract, and genitourinary tract. In humans, symptoms of infection include swelling, lesions, and inflammation, and may mimic the symptoms of osteoarthritis.

# Uses
This bacterium is used to study effectiveness of disinfection processes for reusable medical instruments.
Mycobacterium terrae is used during validations of reprocessing procedures of surgical instruments, more specifically as a test organism in determining disinfection efficiency. In order to establish a microbial count the extraction media is filtered and the filters are then placed onto agar plates for an incubation of up to 15 days at 37 2 C. At the end of the incubation period the number of colony forming units are counted. This count is used to calculate the log reduction to determine disinfection efficiency. The Association For The Advancement of Medical Instrumentation (AAMI) Technical Information Report TIR30 lists acceptance criteria for this test.

# Treatment

## Antimicrobial regimen
- Mycobacterium terrae 
- 1. In vitro susceptibility
- All six of the isolates from a single center and 90% or more of an additional 22 isolates of M. terrae complex were susceptible to Ciprofloxacin and Sulfonamides. Recently, 11 isolates of M. terrae complex were also shown to be susceptible to Linezolid
- 2. Antimicrobial therapy
- Based on in vitro susceptibility results
N-Nitrosonornicotine

# Overview
N-Nitrosonornicotine (abbreviated NNN) is a nitrosamine found in tobacco that has been classified by the IARC as a Group 2B carcinogen.
Although no adequate studies of the relationship between exposure to NNN and human cancer have been reported, there is sufficient evidence that NNN causes cancer in experimental animals.
NNN is found in a variety of tobacco products including chewing tobacco, snuff, cigarettes, and cigars. It is present in smoke from cigars and cigarettes, in the saliva of people who chew betel quid with tobacco, and in the saliva of oral-snuff users. NNN is produced by the nitrosation of nicotine during the curing, ageing, processing, and smoking of tobacco. Roughly half of the NNN originates in the unburnt tobacco, with the remainder being formed during burning.
Some of the NNN present in the saliva of tobacco users is produced endogenously from nitrite in saliva and tobacco alkaloids including nicotine.
Neomycin description

# Description
NEO-FRADIN Oral Solution for oral administration contains neomycin which is an antibiotic obtained from the metabolic products of the actinomycete Streptomyces fradiae. The pH range is 5.0 to 7.5. NEO-FRADIN Oral Solution is a clear orange solution with a cherry flavor. Each 5 mL of NEO-FRADIN Oral Solution contains 125 mg of neomycin sulfate (equivalent to 87.5 mg of neomycin).
Inactive ingredients: benzoic acid, FD&C yellow no. 6, cherry flavor, glycerin, methylparaben, proplyparaben, sodium phosphate dibasic heptahydrate, sulfuric acid, and purified water.
Sodium phosphate dibasic heptahydrate and sulfuric acid are used as pH adjusters.
The chemical name for Neomycin is: 0-2, 6-diamino-2, 6-dideoxy--D-lucopyranosyl-(13)- 0-D-ribofuranosyl-(15)0--2-deoxy-D-streptamine.
Neomycin B is identical except that the --D-glucopyranosyl residue in the neobiosamine moiety is -L-idopyranosly.
The molecular weight of Neomycin is 614.67. The structural formula is represented below:
Neurological fatigue
Thought to be unique to sufferers of multiple sclerosis, neurological fatigue is a feeling of overwhelming lassitude or tiredness that can occur at any time of the day, for any duration and does not necessarily recur in a recognisable pattern for any given patient. Neurological fatigue has been described as an overwhelming feeling of weakness not associated with increased physical effort. There is near universal support that the fatigue experienced by people with MS goes beyond that of people without the disease. Many multiple Sclerosis patients report sleeping more than 12 hours a night on successive nights and still being too tired to complete their daily duties despite feeling physically rested. This fatigue is also highly variable and there are some with MS who do not experience neurological fatigue as a primary symptom.
As this fatigue is an invisible symptom, and because of the difficulty of explaining the 'tired brain' feeling of neurological fatigue, others can misinterpret the behavior of persons with MS as lack of effort, but it is important for those dealing with MS patients to realize that this may not be the case.

# Suspected Causes
The specific causes of neurological fatigue in Multiple Sclerosis sufferers is not fully understood. The leading theory includes 'tired neurons,' whereby the patient experiences marked mental fatigue due to the overworking of demyelinated neurons within the brain and central nervous system. This is thought to be compounded by depression, which is very common in Multiple Sclerosis and many other degenerating diseases.

# Treatment
Treatment with modafinil has been shown to significantly improve fatigue and sleepiness and is well tolerated by patients with MS. Unlike the higher dose regimen required in narcolepsy, a low-dose regimen of modafinil  is effective in MS.
Other treatments include elevated doses of caffiene, cold body suits, and regular exercise.

# External Information
Modafinil in treatment of fatigue in multiple sclerosis
Fatigue and Multiple Sclerosis (MS)
Neurotensin receptor
The neurotensin receptors are transmembrane receptors that bind the  neurotransmitter neurotensin. Two of the receptors encoded by the NTSR1 and NTSR2 genes contain seven transmembrane helices and are G protein coupled.  The third receptor has a single transmembrane domain and is encoded by the SORT1 gene.

# Ligands

## Agonists
- Beta-lactotensin (NTS2)
- JMV-449
- Neurotensin
- Neuromedin N (NTS1 selective)
- PD-149,163 (NTS1 selective, reduced amide bond 8-13 fragment of neurotensin)
- Partial agonists derived from SR-48692

## Antagonists
- Levocabastine (NTS2 selective, also H1 histamine antagonist)
- SR-48692 (NTS1 selective)
- SR-142,948 (unselective, CAS# 184162-64-9)

# Biophysical Investigation
Unusually for GPCRs, NTS1 can be expressed in an active form in the bacteria E. coli.  It can be purified and analysed in vitro and has been analysed by a number of biophysical techniques such as surface plasmon resonance, FRET and cryo-electron microscopy.
New drug application
The New Drug Application (NDA) is the vehicle in the United States through which drug sponsors formally propose that the FDA approve a new pharmaceutical for sale and marketing. The goals of the NDA are to provide enough information to permit FDA reviewers to establish the following:
- Is the drug safe and effective in its proposed use(s), and do the benefits of the drug outweigh the risks?
- Is the drugs proposed labeling (package insert) appropriate, and what should contain?
- Are the methods used in manufacturing (Good Manufacturing Practice, GMP) the drug and the controls used to maintain the drugs quality adequate to preserve the drugs identity, strength, quality, and purity?
To legally gather this data on safety and effectiveness in the U.S., the maker must first obtain an Investigational New Drug (IND) designation from FDA.
The documentation required in an NDA is supposed to tell the drugs whole story, including what happened during the clinical tests, what the ingredients of the drug formulation are, the results of the animal studies, how the drug behaves in the body, and how it is manufactured, processed and packaged. Once approval of an NDA is obtained, the new drug can be legally marketed starting that day in the U.S.
Biologics, such as vaccines and many recombinant proteins used in medical treatments are approved by FDA via a Biologic License Application (BLA), rather than an NDA. Manufacture of biologics is considered to differ fundamentally from that of less complex chemicals, requiring a somewhat different approval process.
Generic drugs that have already been approved via an NDA submitted by another maker are approved via an Abbreviated New Drug Application (ANDA), which does not require all of the clinical trials normally required for a new drug in an NDA. Biological drugs, including most recombinant proteins are considered ineligible for an ANDA under current US law.

# Reference
-  FDA, CBER The Biologics License Application Process: An Overview
-  FDA, CDER Office of Generic Drugs
-  Rouhi, A.M. Beyond Hatch-Waxman: Legislative action seeks to close loopholes in U.S. law that delay entry of generics into the market Chem & Eng News 80(38):53-59
Nictitating membrane
The Nictitating membrane is a transparent or translucent third eyelid present in some animals that can be drawn across the eye for protection and to moisten the eye while also keeping visibility.  Various reptiles, birds and sharks have a full nictitating membrane while in many mammals there is a small vestigial remnant of the membrane present in the corner of the eye.  Some mammals such as polar bears, seals and ardvarks also have a full nictitating membrane. It is often called a third eyelid or haw and may be referred to as the plica semilunaris or palpebra tertia in more advanced applications.
Nictitating membranes are found in birds, reptiles, amphibians, fishes, but is less common in mammals, mainly being present in monotremes and marsupials. In humans, the nictitating membrane is the pink lump in the inner corner of the eyes; it is permanently folded into that corner and no longer functions, apparently rendered redundant by evolution some time in the past. Its associated muscles are also vestigial (see human vestigiality). Those of Africans and Australian Aborigines have been said to have slightly larger  than other peoples. Only one species of primate -- the Calabar angwantibo -- is known to have a functioning nictitating membrane.
Unlike human eyelids, the nictitating membrane moves horizontally across the eyeball.  It is normally translucent.  In some diving animals, for example beavers and manatees, it moves across the eye to protect it while under water, and in these species it is transparent; in other diving animals including sea lions, it is activated on land, to remove sand and other debris.  This is its function in most animals.  In birds of prey, it also serves to protect the parents' eyes from their chicks while they are feeding them.  In polar bears it protects the eyes from snow blindness.  In sharks it protects the eye while the shark strikes at its prey. Woodpeckers tighten their nictitating membrane a millisecond prior to their beak impacting the trunk of a tree in order to prevent their eyes from leaving their sockets.
In cats and dogs, the nictitating membrane is not usually visible, and its being chronically visible should be taken as a sign of poor condition or ill health. It can, however, be seen clearly when gently opening the eye of the healthy animal when it is asleep. In some breeds of dogs, the nictitating membrane can be prone to prolapse, resulting in a condition called Cherry eye.
In many species, any stimulus to the eyeball (such as a puff of air) will result in reflex nictitating membrane response.  This reflex is widely used as the basis for experiments on classical conditioning in rabbits.
Nocardiosis overview

# Overview
Nocardiosis is an infectious disease affecting either the lungs (pulmonary nocardiosis) or the whole body (systemic nocardiosis). It is due to infection by bacterium of the genus Nocardia, most commonly Nocardia asteroides or Nocardia brasiliensis.
It is most common in men, especially those with a compromised immune system. In patients with brain infection, mortality exceeds 80%; in other forms, mortality is 50%, even with appropriate therapy. It is one of several conditions that have been called the great imitator.Cutaneous nocardiosis commonly occurs in immunocompetent hosts.

# Diagnosis

## Laboratory Findings
Diagnosis may be difficult.Nocardiae are weakly acid-fast organisms and can be visualized by  modified Ziehl Neelsen stains like Fite-Faraco method. In the clinical laboratory, routine cultures may be held for insufficient time to grow nocardiae, and referral to a reference laboratory may be needed for species identification.

## X Ray
Infiltration and pleural effusion are usually seen via x-ray.
Normalizing constant
The concept of a normalizing constant arises in probability theory and a variety of other areas of mathematics.

# Definition and examples
In probability theory, a normalizing constant is a constant by which an everywhere nonnegative function must be multiplied in order that the area under its graph is 1, i.e., to make it a probability density function or a probability mass function.  For example, we have
so that
is a probability density function.  This is the density of the standard normal distribution.  (Standard, in this case, means the expected value is 0 and the variance is 1.)
Similarly,
and consequently
is a probability mass function on the set of all nonnegative integers.  This is the probability mass function of the Poisson distribution with expected value .
Note that if the probability density function is a function of various parameters, so too will be its normalizing constant.  The parametrised normalizing constant for the Boltzmann distribution plays a central role in statistical mechanics. In that context, the normalizing constant is called the partition function.

# Bayes' theorem
Bayes' theorem says that the posterior probability measure is proportional to the product of the prior probability measure and the likelihood function .  Proportional to implies that one must multiply or divide by a normalizing constant in order to assign measure 1 to the whole space, i.e., to get a probability measure.  In a simple discrete case we have
where P(H0) is the prior probability that the hypothesis is true; P(D|H0) is the conditional probability of the data given that the hypothesis is true, but given that the data are known it is the likelihood of the hypothesis (or its parameters) given the data; P(H0|D) is the posterior probability that the hypothesis is true given the data. P(D) should be the probability of producing the data, but on its own is difficult to calculate, so an alternative way to describe this relationship is as one of proportionality:
Since P(H|D) is a probability, the sum over all possible (mutually exclusive) hypotheses should be 1, leading to the conclusion that
In this case, the reciprocal of the value
is the normalizing constant.  It can be extended from countably many hypotheses to uncountably many by replacing the sum by an integral.

# Non-probabilistic uses
The Legendre polynomials are characterized by orthogonality with respect to the uniform measure on the interval  and the fact that they are normalized so that their value at 1 is 1.  The constant by which one multiplies a polynomial in order that its value at 1 will be 1 is a normalizing constant.
Orthonormal functions are normalized such that
with respect to some inner product .
The constant 1/2 is used to establish the hyperbolic functions cosh and sinh from the lengths of the adjacent and opposite sides of a hyperbolic triangle.

# Notes
-  Continuous Distributions at University of Alabama.
-  Feller, 1968, p. 22.
-  Feller, 1968, p. 174.
-  Feller, 1968, p. 156.
-  Feller, 1968, p. 124.
Nucleoside analogues
Nucleoside analogues are a range of antiviral products used to prevent viral replication in infected cells. The most commonly used is Aciclovir.  They work as antimetabolites by being similar enough to nucleosides to be incorporated into growing DNA strands, but different enough ensure that the resultant DNA is non-functional.  They also affect normal cell growth, such as bone marrow cells, so there can be significant toxic effects.
There is a large family of nucleoside analogue reverse transcriptase inhibitors, because DNA production by reverse transcriptase is very different from normal human DNA replication, so it is possible to design nucleoside analogues that are preferentially incorporated by the former.
Less selective nucleoside analogues are used as chemotherapy agents to treat cancer.
Related drugs are nucleobase analogues such as Aciclovir and nucleotide analogues.
Nucleoside analogue drugs include:
- deoxyadenosine analogues
Didanosine
Vidarabine (chemotherapy)
- Didanosine
- Vidarabine (chemotherapy)
- deoxycytidine analogues
Cytarabine (chemotherapy)
Emtricitabine
Lamivudine
Zalcitabine
- Cytarabine (chemotherapy)
- Emtricitabine
- Lamivudine
- Zalcitabine
- deoxyguanosine analogues
Abacavir
- Abacavir
- (deoxy-)thymidine analogues
Stavudine
Zidovudine (Azidothymidine, or AZT)
- Stavudine
- Zidovudine (Azidothymidine, or AZT)
- deoxyuridine analogues
Idoxuridine
Trifluridine
- Idoxuridine
- Trifluridine
nl:Nucleoside-analoog
Nystatin description

# Description
Nystatin is an antimycotic polyene antibiotic obtained from Streptomyces noursei. Its structural formula:
Nystatin tablets are provided for oral administration as coated tablets containing 500,000 units nystatin.
Inactive ingredients: anhydrous lactose, carnauba wax, corn starch, FD&C Blue No. 2 Aluminum Lake, FD&C Red No. 40 Aluminum Lake, hydroxypropyl cellulose, hypromellose, magnesium stearate, microcrystalline cellulose, polyethylene glycol, povidone, sodium starch glycolate, stearic acid, and titanium dioxide.
Ocular larva migrans
Ocular larva migrans is the ocular form of the larva migrans syndrome that occurs when toxocara canis larvae invade the eye. They may be associated with visceral larva migrans. Unilateral visual disturbances, strabismus, and eye pain are the most common presenting symptoms.

# Exam findings
The disease presents with an eosinophilic granulomatous mass, most commonly in the posterior pole of the retina. The granulmatous mass develops around the entrapped larva, in an attempt to contain the spread of the larva.

# Differential diagnosis
The retinal lesion can mimic retinoblastoma in appearance, and mistaken diagnosis of the latter condition can lead to unnecessary enucleation.

# Complications
The eye involvement can cause the following inflammatory disorders:
- endophthalmitis
- uveitis
- chorioretinitis

# Epidemiology
In contrast to visceral larva migrans, ocular toxocariasis usually develops in older children or young adults with no history of pica. These patients seldom have eosinophilia or visceral manifestations.
Olfactory epithelium

# Overview
The olfactory epithelium is a specialized epithelial tissue inside the nasal cavity that is involved in smell.  In humans, it measures about 1 inch wide by 2 inches long (about 2 cm by 5 cm) and lies on the roof of the nasal cavity about 3 inches (about 7 cm) above and behind the nostrils. The olfactory epithelium is the part of the olfactory system directly responsible for detecting odors.
Olfactory epithelium consists of three distinct types of cells: Olfactory cells, supporting cells, and basal cells
The olfactory cells of the epithelium are bipolar neurons which congregate to form the olfactory nerve (cranial nerve I).  The apical poles of these neurons are ciliated and coated with a serous secretion from Bowman's glands located in the lamina propria.
Analogous to neural glial cells, the supporting cells of the olfactory epithelium function as metabolic and physical support for the olfactory cells.  Histologically, the supporting cells are tall columnar cells featuring microvilli and a prominent terminal web.  The nuclei of supporting cells are more apically located than those of the other olfactory epithelial cells.
Resting on the basal lamina of the olfactory epithelium, basal cells are stem cells capable of division and differentiation into either supporting or olfactory cells.  The constant divisions of the basal cells leads to the olfactory epithelium being replaced every 2-4 weeks.
The olfactory epithelium can be damaged by inhalation of toxic fumes, physical injury to the interior of the nose, and possibly by the use of some nasal sprays.  Because of its regenerative capacity, damage to the olfactory epithelium can be temporary but in extreme cases, injury can be permanent, leading to anosmia.