Persius/hicric huggingface dataset:
Molecular engineering
Molecular engineering is any means of manufacturing molecules. It may be used to create, on an extremely small scale, most typically one at a time, new molecules which may not exist in nature, or be stable beyond a very narrow range of conditions.
Today this is an extremely difficult process, requiring manual manipulation of molecules using such devices as a scanning tunneling microscope.  Eventually it is expected to exploit life-like self-replicating 'helper molecules' that are themselves engineered.  Thus the field can be seen as a precision form of chemical engineering that includes protein engineering, the creation of protein molecules, a process that occurs naturally in biochemistry, e.g., prion reproduction. However, it provides far more control than genetic modification of an existing genome, which must rely strictly on existing biochemistry to express genes as proteins, and has little power to produce any non-proteins.
Molecular engineering is an important part of pharmaceutical research and materials science.
Emergence of scanning tunneling microscopes and picosecond-burst lasers in the 1990s, plus discovery of new carbon nanotube applications to motivate mass production of these custom molecules, drove the field forward to commercial reality in the 2000s.
As it matures, it is seeming to converge with mechanical engineering, since the molecules being designed often resemble small machines. A general theory of molecular mechanosynthesis to parallel that of photosynthesis and chemosynthesis (both used by living things) is the ultimate goal of the field.  This may lead to a molecular assembler, according to some, such as K. Eric Drexler, Ralph Merkle, and Robert Freitas, and of the potential for integrating vast numbers of assemblers into a kg-scale nanofactory.
Molecular engineering is sometimes called generically "nanotechnology", in reference to the nanometre scale at which its basic processes must operate.  That term is considered to be vague, however, due to misappropriation of the word in association with other techniques, such as X-ray lithography, that are not used to create new free-floating ions or molecules.
Future developments in molecular engineering hold out the promise of great benefits, as well as great risks.  See the nanotechnology article for an extensive discussion of the more speculative aspects of the technology.  Of these, the one that sparks the most controversy is that of the molecular assembler.
Molecular recognition
The term molecular recognition refers to the specific interaction between two or more molecules through noncovalent bonding such as including hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, pi-pi interactions, and/or electrostatic effects. The host and guest involved in molecular recognition exhibit molecular complementarity.

# Biological systems
Molecular recognition plays an important role in biological systems and is observed in between receptor-ligand, antigen-antibody, DNA-protein, sugar-lectin, RNA-ribosome, etc.  An important example of molecular recognition is the antibiotic vancomycin that selectively binds with the peptides with terminal D-alanyl-D-alanine in bacterial cells through five hydrogen bonds.  The vancomycin is lethal to the bacteria since once it has bound to these particular peptides they are unable to be used to construct the bacterias cell wall.

# Supramolecular systems
Chemists have demonstrated that artificial supramolecular systems can be designed that exhibit molecular recognition.  One of the earliest examples of such a system are crown ethers which are capable of selectively binding specific cations.  However a number of artificial systems have since been established.

# Static vs. dynamic
Molecular recognition can be subdivided into static molecular recognition and dynamic molecular recognition.  Static molecular recognition is likened to the interaction between a key and a keyhole; it is a 1:1 type complexation reaction between a host molecule and a guest molecule to form a host-guest complex. To achieve advanced static molecular recognition, it is necessary to make recognition sites that are specific for guest molecules.
In the case of dynamic molecular recognition the binding of the first guest to a the first binding site of a host affects the association constant of a second guest with a second binding site.  In the case of positive allosteric systems the binding of the first guest increases the association constant of the second guest.  While for negative allosteric systems the binding of the first guest decreases the association constant with the second.  The dynamic nature of this type of molecular recognition is particularly important since it provides a mechanism to regulate binding in biological systems.  Dynamic molecular recognition is also being studied for application in highly functional chemical sensors and molecular devices.
Mononuclidic elements
Mononuclidic elements are chemical elements which either have only one stable isotope, or for which there is only one very long-lived isotope that dominates the element's  natural isotopic abundance.  There are nineteen elements in the first category, and three ( Bi,  Th and  Pa) in the second.  Elements such as Rb, In, and La, that have a single stable isotope and a significant fraction of a very long-lived isotope in their natural abundance, are not considered mononuclidic.

# Use in metrology
Mononuclidic elements are of scientific importance because their atomic weights can be measured to high accuracy, since there is minimal uncertainty associated with the isotopic abundances present in a given sample.

# Contamination by unstable trace isotopes
Trace concentrations of unstable isotopes of some mononuclidic elements are found in natural samples.  For example,  10Be, with a half-life of 1.5 million years, is produced by cosmic rays in the Earth's upper atmosphere;  129I, with a half-life of 15.7 million years, is produced by various cosmogenic and nuclear mechanisms;  137Cs, with a half-life of 30 years, is generated by nuclear fission.  Such isotopes are used in a variety of analytical and forensic applications.

# Complete list
Data from Atomic Weights and Isotopic Compositions ed. J. S. Coursey, D. J. Schwab and R. A. Dragoset, National Institute of Standards and Technology (2005).
Moraxella catarrhalis

# Overview
Moraxella catarrhalis is a gram-negative, aerobic, oxidase-positive diplococcus which may both colonise and cause respiratory tract-associated infection in humans.

# Organism
Moraxella catarrhalis is a gram-negative, aerobic, oxidase-positive diplococcus which may both colonise and cause respiratory tract-associated infection in humans.
M. catarrhalis was previously placed in a separate genus named Branhamella.  The rationale for this was that other members of the genus Moraxella are rod-shaped and rarely caused infections in humans.  However results from DNA hybridization studies and 16S rRNA sequence comparisons were used to justify inclusion of the species catarrhalis in the genus Moraxella.  Consequently, the name Moraxella catarrhalis is currently preferred for these bacteria.  Nevertheless, some in the medical field continue to call these bacteria Branhamella catarrhalis.
Clinically, these bacteria are known to cause bronchitis, sinusitis, laryngitis and otitis media. Elderly patients and long-term heavy smokers with chronic pulmonary disease should be aware that M. catarrhalis is associated with bronchopneumonia, as well as exacerbations of existing chronic obstructive pulmonary disease (COPD).
Treatment options include antibiotic therapy or a so-called "watchful waiting" approach. The great majority of clinical isolates of this organism produce beta-lactamases and are resistant to penicillin, with some suggestion of trimethoprim resistance in certain regions of the world. It is susceptible to trimethoprim-sulfamethoxazole (TMP-SMZ), fluoroquinolones, and most second and third generation cephalosporins.  In addition, M. catarrhalis infection may be treated with erythromycin and amoxicillin-clavulanate (Augmentin).
The peak rate of colonisation by M. catarrhalis appears to occur at approximately 2 years of age, with a striking difference in colonisation rates between children and adults (very high to very low).
Current research priorities involve trying to find a suitable vaccine for this genotypically diverse organism, as well as determining factors involved with virulence e.g. complement resistance.

# Treatment

## Antimicrobial regimen
- Moraxella catarrhalis treatment 
- Preferred regimen(1): TMP-SMX 1DS PO bid
- Preferred regimen(2): Erythromycin 500 mg PO qid
- Preferred regimen(3): Clarithromycin 500 mg PO bid or XL 1 g PO qd
- Preferred regimen(4): Azithromycin 500 mg PO single dose THEN 250 mg PO qd
- Preferred regimen(5): Doxycycline 100 mg PO/IV bid/q12h
- Preferred regimen(6): Cefprozil 200-500 mg PO bid
- Preferred regimen(7): Cefpodoxime 200-400 mg PO bid
- Preferred regimen(8): Cefuroxime 250-500 mg PO bid
- Preferred regimen(9): Cefdinir 300 mg PO bid
- Preferred regimen(10): Moxifloxacin 400 mg IV/PO qd
- Preferred regimen(11): Levofloxacin 500 mg IV/PO qd
- Preferred regimen(12): Amoxicillin clavulanate 875/125 mg PO bid or XL 2000/125 PO bid
Mowat-Wilson syndrome
Mowat Wilson syndrome is a rare genetic disorder that was clinically delineated by Dr. D. R. Mowat and Dr. M. J. Wilson in 1998.

# Presentation
The disorder is characterized by a number of health defects including Hirschsprung's disease,  mental retardation, seizure disorder, delayed growth and motor development, congenital heart disease, genitourinary anomalies and absence of the corpus callosum.  Distinctive physical features include microcephaly, narrow chin, cupped ears with protruding lobes, deep and widely set eyes, open mouth, wide nasal bridge and a shortened philtrum.

# Causes
The disorder is an autosomal dominant disorder resulting from new mutations or deletions of the ZFHX1B (SMADIP1) gene on chromosome 2q22.  However, some of those affected by the disease do not have abnormalities of this gene that are currently detectable.

# Prognosis
There is no cure for this syndrome.  Treatment is supportive and symptomatic.
Mucociliary clearance

# Overview
Mucociliary clearance, also referred to as mucociliary apparatus or mucociliar clearance (MCC), derived from mucus, cilia  (cilia of the tracheal surface epithelium in the respiratory tract) and clearance describes the self-clearing mechanism of the bronchi.
The passage of airway in the respiratory tract that conducts air into the lungs main bronchi down to the final branchings of the respiratory tree (which act as the primary gas exchange units of the lung) alveoli are lined with a moist lining of the airway respiratory epithelium. On that, cilium is present, bearing hair-shaped structures on its surface (cilia). The cilia are surrounded by a thin fluid film of mucus. On top of that is a second viscous film of mucus, in which foreign particles and microorganisms get stuck. Within the thin fluid film of mucus the cilia act out movements coordinated in direction towards the pharynx. Thereby the viscous film of mucus including its freight is transported off in direction towards the mouth, where it is either swallowed or expelled via coughing.
Important for good mucociliary clearance are the number of cilia, their structure, activity, and coordinated movement. Optimum functionality of mucociliary clearance presupposes a temperature of 37 C and an absolute humidity of 44 mg/dm3 corresponding to a relative humidity of 100%. Under the condition of insufficient temperature and humidity, after a short time the ciliary cells suspend their transport function. Under such circumstances, bacterial germinal colonization is facilitated. Pulmonary infections and damaging of the pulmonic tissues may be the consequence.
High humidity enhances the functionality of the mucociliary clearance. Two methods of supporting mucociliary clearance are the active and the passive respiratory gas humidification, which in particular are applied in mechanical ventilation.
Mucogingival junction

# Overview
The mucogingival junction is the interface between the more apically located alveolar mucosa and the more coronally located attached gingiva of the gingiva.
There exists a mucogingival junction on all three gingival surfaces on which there exists freely moveable alveolar mucosa: the facial gingiva of the maxilla and both the facial and lingual gingiva of the mandible.  The palatal gingiva of the maxilla is continuous with the tissue of the palate, which is bound down to the palatal bones.  Because the palate is devoid of freely moveable alveolar mucosa, there is no mucogingival junction.

# Clinical importance
The clinical importance of the mucogingival junction is in measuring the width of attached gingiva.  Attached gingiva is important because it is bound very tightly to the underlying alveolar bone and provides protection to the mucosa during functional use of the structures of the oral cavity during function, such as chewing.  Without attached gingiva, the freely moveable alveolar mucosa, being more fragile, would suffer injury during eating and cleansing activities, such as brushing of the teeth.
The width of attached tissue is critical, because the more there is available provides a greater sense of protection against the aforementioned insults to the tissue.  Using the mucogingival junction as the boundary demarcating the apical border of the attached gingiva, a periodontal probe in inserted into the gingival sulcus to measure how much of the keratinized gingiva coronal to the mucogingival junction is in fact attached to the underlying bone. The depth of the gingival sulcus, determined by the depth to which the probe enters the sulcus, is not attached to the underlying bone, and is subtracted from the total height of the keratinized tissue.
Thus, if the entire height of the keratinized gingiva, from the free gingival margin to the mucogingival junction is 8 mm, and the probing depth on the tooth at that location is 2 mm, the effective width of attached gingiva is 6 mm.
If the probe enters the sulcus and can descend up to or beyond the mucogingival junction, that area is said to represent a mucogingival defect.
Mucolipidosis type IV

# Overview
Mucolipidosis type IV (ML IV), like other types of mucolipidosis is an inherited neurodegenerative lysosomal storage disorder. Patients with this autosomal recessive disorder have symptoms including delayed psychomotor development and various ocular aberrations. This type of mucolipidosis is caused by mutation of a non-selective cation channel, TRPML1. These mutations disrupt lysosomal storage and lead to neurodegeneration through an unknown mechanism.

# Historical Perspective

# Classification

# Pathophysiology
ML IV is caused by mutations in the cation channel TRPML1 (Mucolipin-1). TRPML1 is localized in endosomes and may function as either a proton leak channel and/or aid in the regulation of calcium levels. An important property of TRPML1 is that decreasing pH (acidification) results in deactivation of the protein, likely through an assembly defect. There are 10 mutations in TRPML1, located throughout the channel. Three of these mutations (Q79X, R102X and R172X) result in early truncation of the channels and the loss of functional protein. The other seven mutations result in either amino acid substitution or deletion. Of these, V446I and F408 are known to be functional as channels. In these mutants, however, there is no acidification induced defect in assembly. These alterations result in the blockage of endocytic transport and prevention of lysosome formation. Over-acidification of these organelles may result in decreased lipase activity. This decreased lipase activity might then result in the increased levels of lipids and membraneous materials seen in patients. Alternatively, build-up of intra-compartmental calcium may prevent the fusion processes in these organelles.

# Causes

# Differentiating Mucolipidosis type IV from Other Diseases

# Epidemiology and Demographics
Ashkenazi Jews have a high carrier frequency of 1:90 to 1:100.

# Risk Factors

# Screening

# Natural History, Complications, and Prognosis

# Diagnosis

## Diagnostic Criteria

## History and Symptoms
Most patients with ML IV show psychomotor retardation (i.e., delayed development of movement and coordination), corneal opacity, retinal degeneration and other ophthalmological abnormalities. Other symptoms include agenesis of the corpus callosum, iron deficiency, and improper stomache pH (achlorohydria). Achlorhydria in these patients results in an increase in blood gastrin levels. These symptoms typically manifest early in life (within the first year) and progress slowly.

## Physical Examination

## Laboratory Findings

## Imaging Findings

## Other Diagnostic Studies

# Treatment
See the equivalent section in the  main mucolipidosis article.

## Medical Therapy

## Surgery

## Prevention
Multivariate analysis

# Overview
Multivariate analysis (MVA) is based on the statistical principle of multivariate statistics, which involves observation and analysis of more than one statistical variable at a time. In design and analysis, the technique is used to perform trade studies across multiple dimensions while taking into account the effects of all variables on the responses of interest.
Uses for multivariate analysis includes:
- Design for capability (also known as capability-based design)
- Inverse design, where any variable can be treated as an independent variable
- Analysis of alternatives, the selection of concepts to fulfill a customer need
- Analysis of concepts with respect to changing scenarios
- Identification of critical design drivers and correlations across hierarchical levels
Multivariate analysis can be complicated by the desire to include physics-based analysis to calculate the effects of variables for a hierarchical "system-of-systems." Often, studies that wish to use multivariate analysis are stalled by the dimensionality of the problem. These concerns are often eased through the use of surrogate models, highly accurate approximations of the physics-based code. Since surrogate models take the form of an equation, they can be evaluated very quickly. This becomes an enabler for large-scale MVA studies: while a Monte Carlo simulation across the design space is difficult with physics-based codes, it becomes trivial when evaluating surrogate models, which often take the form of response surface equations.
Mupirocin description

# Description
BACTROBAN CREAM (mupirocin calcium cream, 2%) contains the dihydrate crystalline calcium hemi-salt of the antibiotic mupirocin. Chemically, it is (E,2S,3R,4R,5S)-5-tetrahydro-3,4-dihydroxy--methyl-2H-pyran-2-crotonic acid, ester with 9-hydroxynonanoic acid, calcium salt (2:1), dihydrate.
The molecular formula of mupirocin calcium is (C26H43O9)2Ca2H2O, and the molecular weight is 1075.3. The molecular weight of mupirocin free acid is 500.6. The structural formula of mupirocin calcium is:
BACTROBAN CREAM is a white cream that contains 2.15% w/w mupirocin calcium (equivalent to 2.0% mupirocin free acid) in an oil and water-based emulsion. The inactive ingredients are benzyl alcohol, cetomacrogol 1000, cetyl alcohol, mineral oil, phenoxyethanol, purified water, stearyl alcohol, and xanthan gum.
Musculophrenic artery
The Musculophrenic Artery arises from the internal thoracic artery, directed obliquely downward and lateralward, behind the cartilages of the false ribs; it perforates the diaphragm at the eighth or ninth costal cartilage, and ends, considerably reduced in size, opposite the last intercostal space.
It gives off intercostal branches to the seventh, eighth, and ninth intercostal spaces; these diminish in size as the spaces decrease in length, and are distributed in a manner precisely similar to the intercostal arteries from the internal thoracic artery.
The musculophrenic also gives branches to the lower part of the pericardium, and others which run backward to the diaphragm, and downward to the abdominal muscles.
Mycobacterium celatum

# Overview
Mycobacterium celatum is a species of the phylum actinobacteria (Gram-positive bacteria with high guanine and cytosine content, one of the dominant phyla of all bacteria), belonging to the genus mycobacterium.
Type strain: strain ATCC 51131 = CCUG 39185 = CDC 90-0899 = CIP 106109 = DSM 44243 = JCM 12373.

# Characteristics
Mycobacterium celatum is a species of mycobacterium described as a slow growing nonphotochromogenic mycobacterium whose cells are acid-fast, slender and predominantly rod-shaped. It does not form cords or branches. Colonies are predominantly small, smooth, dome- shaped and unpigmented.

# Health risks
Mycobacterium celatum, a slowly growing potentially pathogenic mycobacterium, was first described in humans in 1993. Mycobacterium celatum has been shown to cause fatal disease in both immunocompetent and immunocompromised patients. Clinical symptoms include cough, malaise, and weight loss associated with cavitary lesions and pulmonary infiltrates, whereas the initial laboratory testing includes positive acid-fast stain.

# Treatment

## Antimicrobial regimen
- Mycobacterium celatum 
- Preferred regimen: Clarithromycin AND Ethambutol AND Ciprofloxacin  Rifabutin
Mycobacterium doricum
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Mycobacterium doricum

# Type Strain
Strain FI-13295 = CCUG 46352 = CIP 106867 = DSM 44339 = JCM 12405.
Mycobacterium duvalii
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Mycobacterium duvalii

# Description
Gram-positive, nonmotile and pleomorphic acid-fast rods.
Colony characteristics
- Bright yellow pigmented, scotochromogenic and rough or smooth colonies on Lowenstein-Jensen medium.
Physiology
- Fast growth on [Lowenstein-Jensen medium at 25C and 37C within 7 days. No growth at 45C.
- Resistant to isoniazid, rifampicin, and sodium aminosalicylate.
Differential characteristics
- Characterised by the possession of 6 species-specific antigens demonstrable in immunodiffusion tests.
Pathogenicity.

# Pathogenesis
Not pathogenic, but evidence insufficient.  Biosafety level 1.

# Type Strain
First isolated from cases of human leprosy by C. W. Duval.
Strain ATCC 43910 = CCUG 41352 = CIP 104539 = DSM 44244 = JCM 6396 = NCTC 358.
Mycobacterium hodleri
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Mycobacterium hodleri

# Description
Gram-positive, nonmotile and acid-fast rods (1m x 1.8-2.3m).
Colony characteristics
- Scotochromogenic colonies, production of a saffron yellow pigment on Middlebrook 7H10 agar and a chrome yellow pigment on Trypticase soy agar.
Physiology
- Fast growth on Middlebrook 7H10 and on Trypticase soy agar at temperatures between 18C and 28C.
- Capable of cooxidizing fluoranthene with polycyclic aromatic hydrocarbons, including pyrene and anthracene.

# Pathogenesis
- Pathogenicity is not known.
- Biosafety level 1

# Type Strain
- First isolated from a fluoranthene-contaminated site near Julich, Germany.
Strain EMI2 = CIP 104909 = DSM 44183 = JCM 12141 = LMG 19253