Persius/hicric huggingface dataset:
Allyl

# Overview
An allyl group is an alkene hydrocarbon group with the formula H2C=CH-CH2-.  It is made up of a vinyl group, CH2=CH-, attached to a methylene -CH2.  For example allyl alcohol has the structure H2C=CH-CH2OH .  Compounds containing the allyl group are often referred to as being allylic.
Allylic carbons are sp3 hybridized, vinylic carbons are sp2 hybridized.
The site of the saturated carbon atom, where the vinyl group attaches (e.g. next to the OH in allyl alcohol) is called the allylic position or allylic site.  A group, such as -OH, attached at an allylic site is sometimes described as allylic. Two examples of simple allyl compounds are allyl chloride and allyl alcohol.
Substituted versions of the above, such as the trans-but-2-en-1-yl or crotyl group (CH3CH=CH-CH2-) may be also referred to as allylic groups.
Allylic methylene groups show special reactivity such as demonstrated in allylic oxidations, ene reactions and the Trost asymmetric allylic alkylation.
Anise

# Overview
Anise or Aniseed, less commonly anis (stressed on the second syllable) (Pimpinella anisum), is a flowering plant in the family Apiaceae, native to the eastern Mediterranean region and southwest Asia. It is a herbaceous annual plant growing to 1m tall. The leaves at the base of the plant are simple, 2-5 cm long and shallowly lobed, while leaves higher on the stems are feathery pinnate, divided into numerous leaflets. The flowers are white, 3 mm diameter, produced in dense umbels. The fruit is an oblong dry schizocarp, 3-5 mm long.
Pimpinella species are used as food plants by the larvae of some Lepidoptera species, including the lime-speck pug and wormwood pug.

# Uses

## Culinary
- Sweet and very aromatic. Anise contains liquorice-like components. 
- Aniseed is used to make the British confectionery Aniseed balls and the old fashioned New Zealand confectionery, Aniseed wheels.
- Aniseed is also used to make the Mexican drink atole called champurrado(similar to hot chocolate).
- Anise oil is used to make Italian cookies called pizzelles, and used in the frosting of yellow Italian cake-like cookies called "Drops" or "Anise Drops."
- Anise flavouring is used in the Norwegian candy pills "Knott", produced by Nidar.
- Anise toast is a dry bread popular in Italy.
- Anise (Saunf,Badi-Sheb) is used in India as a digestive after meals.

## Medicinal uses
- Anise leaves are used to treat digestive problems, to relieve toothache, and its essential oil is used to treat lice and scabies.
- In aromatherapy, aniseed essential oil is used to treat colds and flu. It is being researched for the treatment of bird flu as well.
- In India, aniseed (Saunf in Hindi) is also used as mouth freshener. It is also used for flavouring some foods.
- According to Pliny the Elder, anise was used as a cure for sleeplessness, chewed with alexanders and a little honey in the morning to freshen the breath, and when mixed with wine as a remedy for scorpion stings (N.H. 20.72).
- In the Middle East, aniseed is used in producing alcoholic beverages, such as Arak (Morocco) and Ouzo (Greece).
- In Thailand it is used to flavor tea.

## Other uses
Anise can be made into a liquid scent and is used for both hunting and fishing. Anise smells similar to liquorice and is put on fishing lures to attract fish. Anethole, the principal component of anise oil is a precursor that can eventually produce 2,5-dimethoxybenzaldehyde which is used in the clandestine synthesis of psychedelic drugs such as 2C-B, 2C-I and DOB. 
Anise is also the main flavor of Absinthe as well as being used as a flavoring for pastis, ouzo, pernod, sambuca, Raki, Becherovka, anice tutone, Chartreuse and other liqueurs. Anise has a particular effect on some dogs that parallels the effect of catnip on house cats. Some cats as well seem attracted to anise. Anise is perfectly safe for cats and dogs alike to ingest. However, like anything, not in excess.
Apiol
Apiol is an organic chemical compound, also known as parsley apiol, apiole or parsley camphor. It is found in parsley seeds and the essential oil of parsley. Heinrich Christoph Link, an apothecary in Leipzig, discovered the substance in 1715 as greenish crystals reduced by steam from oil of parsley.  In 1855 Joret and Homolle discovered that apiol was an effective treatment of amenorrea or lack of menstruation.
In medicine it has been used, as essential oil or in purified form, for the treatment of menstruation disorders. It is an irritant and in high doses it is toxic and can cause liver and kidney damage.
Hippocrates wrote about parsley as a herb to cause an abortion. This effect was caused by the apiol.
Apiol was used by women in the Middle Ages to terminate pregnancies. Its use was widespread in the USA, often as ergoapiol or apergol, until a highly toxic adulterated product containing apiol and tri-orthocresyl phosphate (also famous as the adulterant added to Jamaican ginger) was introduced on the American market.
The toxic effects of pure crystalline apiol are disputed. It causes a "relatively safe abortion" in pregnant women if taken in small quantities. It also restores the cycle of menstruation. A larger dose does not cause an abortion, it causes nausea and damages the liver and kidneys.
Now that other methods of abortion are available apiol is almost forgotten in the West, but it is still produced and is used in the Middle East.
The name apiol is also used for other closely related compounds, found in dill (dillapiole, 1-allyl-2,3-dimethoxy-4,5-methylenedioxybenzene) and in fennel roots.
Atmit
Atmit is a nutritional supplement used to fight famine in impoverished countries.  The creamy, nutritious food is indigenous to Ethiopia and is now used to feed the severely malnourished and weakened adults and children.  The word atmit originated in Ethiopia and means "thin, nourishing porridge."
Atmit is made from rolled oats, powdered milk, powdered sugar, vitamins, and minerals.  It is easily digestible, high in protein and calorie content.  Since severely malnourished people cannot eat solid food, atmit is an ideal way to get them essential nutrients.
Marta Gabre-Tsadick, the first woman Senator from Ethiopia and the co-founder of Project Mercy, Inc., a Christian relief organization, adapted the recipe for production in the USA for shipment to Ethiopia and other African countries.  During 1985 and 1986, Project Mercy sent 930 tons of atmit to Ethiopia, where World Vision relief workers used it to prepare millions of hot, nutritious meals which helped strengthen many people weakened from the famine.
Charity and relief organizations have created various formulas for this porridge.  The Church of Jesus Christ of Latter-day Saints formula of atmit, which was sent in 2005 to Niger was made of the following:
- 50% Fine oatmeal flour
- 25% Nonfat milk
- 20% Sugar
- 5% Vitamins and minerals
Recently, atmit has been distributed to Uganda, Sudan, South Africa, Haiti, Gaza, Bangladesh, Indonesia, Sri Lanka and Niger.

# Reference
- "Atmit to the Rescue". Ensign: The Church of Jesus Christ of Latter-day Saints. January 2006. pp. 7475..mw-parser-output cite.citation{font-style:inherit}.mw-parser-output q{quotes:"\"""\"""'""'"}.mw-parser-output code.cs1-code{color:inherit;background:inherit;border:inherit;padding:inherit}.mw-parser-output .cs1-lock-free a{background:url("")no-repeat;background-position:right .1em center}.mw-parser-output .cs1-lock-limited a,.mw-parser-output .cs1-lock-registration a{background:url("")no-repeat;background-position:right .1em center}.mw-parser-output .cs1-lock-subscription a{background:url("")no-repeat;background-position:right .1em center}.mw-parser-output .cs1-subscription,.mw-parser-output .cs1-registration{color:#555}.mw-parser-output .cs1-subscription span,.mw-parser-output .cs1-registration span{border-bottom:1px dotted;cursor:help}.mw-parser-output .cs1-hidden-error{display:none;font-size:100%}.mw-parser-output .cs1-visible-error{display:none;font-size:100%}.mw-parser-output .cs1-subscription,.mw-parser-output .cs1-registration,.mw-parser-output .cs1-format{font-size:95%}.mw-parser-output .cs1-kern-left,.mw-parser-output .cs1-kern-wl-left{padding-left:0.2em}.mw-parser-output .cs1-kern-right,.mw-parser-output .cs1-kern-wl-right{padding-right:0.2em}
Atopy

# Overview
Atopy (Greek  - placelessness) or atopic syndrome is an allergic hypersensitivity affecting parts of the body not in direct contact with the allergen. It may involve eczema (atopic dermatitis), allergic conjunctivitis, allergic rhinitis and asthma. There appears to be a strong hereditary component. One study concludes that "the general risk of developing atopic dermatitis (3%) and atopy (7%) increases by a factor of two with each first-degree family member already suffering from atopy"
The hereditary component is presumably due to certain genes coding proteins involved in the normal immune response mechanism, i.e., human leukocyte antigen, although environmental factors have also been implicated. Atopic syndrome can be fatal for those who experience serious allergic reactions such as anaphylaxis, brought on by reactions to food or environment.
The individual components are all caused at least in part by allergy (type I hypersensitivity reactions). These responses appear after the body is exposed to various allergens, for example specific kinds of food, pollen, dander or insect venoms. Although atopy has various definitions, most consistently it is defined by the presence of elevated levels of total and allergen-specific IgE in the serum of patient, leading to positive skin-prick tests to common allergens.
The multicenter PARSIFAL study in 2006, involving 6630 children age 5 to 13 in 5 European countries, suggested that restrictive use of antibiotics and antipyretics, are associated with a reduced risk of allergic disease in children.
Some symptoms, from an atopy questionnaire:
- Cracks in the skin under the earlobe
- Eczema
In elbow flexures and/or hollow of the knees
Nipple eczema
Neurodermatitis
Subtype Dyshidrosis
- In elbow flexures and/or hollow of the knees
- Nipple eczema
- Neurodermatitis
- Subtype Dyshidrosis
- Keratosis pilaris
- Perleche
- Conjunctivitis
- Chronic or seasonal rhinitis

# Atopic diseases of childhood
The atopic diseases of childhood consist of atopic dermatitis, allergic rhinitis, and asthma.
BACE1
-Secretase  also called BACE1 (-site of APP cleaving enzyme) or memapsin-2  is an aspartic-acid protease important in the pathogenesis of Alzheimer's disease, and in the formation of myelin sheaths in peripheral nerve cells. The transmembrane protein, contains two active site aspartate residues in its extracellular protein domain and may function as a dimer.

# Function in Alzheimer's
Generation of the 40 or 42 amino acid-long amyloid- peptides that aggregate in the brain of Alzheimer's patients requires two sequential cleavages of the amyloid precursor protein (APP). Extracellular cleavage of APP by BACE releases a soluble extracellular fragment and is followed by APP cleavage within its transmembrane domain by -secretase.  The second cleavage releases the intracellular domain of APP and amyloid-.  Since -secretase cleaves APP closer to the cell membrane than BACE does, it removes a fragment of the amyloid- peptide. Initial cleavage of APP by -secretase rather than BACE prevents eventual generation of amyloid-.
Unlike APP and the presenilin proteins important in -secretase, no known mutations in the gene encoding BACE cause the early-onset, familial Alzheimer's disease.  However, levels of this enzyme have been shown to be elevated in Alzheimer's. The physiological purpose of BACE's cleavage of APP and other transmembrane proteins is unknown.  BACE2 is a close homolog of BACE1.

# BACE inhibitors
Drugs to block this enzyme (BACE inhibitors) in theory would prevent the build up of beta-amyloid and may help slow or stop the disease. Several companies are in the early stages of development and testing of this new potential class of treatment.
BACH2
Transcription regulator protein BACH2 (broad complex-tramtrack-bric a brac and Cap'n'collar homology 2) is a protein that in humans is encoded by the BACH2 gene. It contains a BTB/POZ domain at its N-terminus which forms a disulphide-linked dimer  and a bZip_Maf domain at the C-terminus.

# Disease associations
Single nucleotide variants in BACH2 have been linked to a number of autoimmune diseases in humans. Mendelian BACH2-related immunodeficiency and autoimmunity (BRIDA) syndrome in humans is caused by haploinsufficiency of this transcription factor resulting from germline mutations.

# Model organisms
Model organisms have been used in the study of BACH2 function. A conditional knockout mouse line called Bach2tm1a(EUCOMM)Wtsi was generated at the Wellcome Trust Sanger Institute. Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Additional screens performed:  - In-depth immunological phenotyping - in-depth bone and cartilage phenotyping
BAZ1A
Bromodomain adjacent to zinc finger domain protein 1A is a protein that in humans is encoded by the BAZ1A gene.

# Structure
The protein encoded by this gene belongs to a family of proteins which includes BAZ1B, BAZ2A, and BAZ2B. All family members contain the following domains and structural motifs:
- N-terminus  PHD finger (C4HC3 zinc finger)
- WAKZ motif
- LH (leucine-rich helical domain) motif
- C-terminus  bromodomain

# Function
BAZ1A along with SMARCA5, POLE3, and CHRAC1 comprise the WCRF/CHRAC ATP-dependent chromatin-remodeling complex.
The purified CHRAC complex can mobilize nucleosomes into a regularly spaced nucleosomal array, and the spacing activity is ATP-dependent. Furthermore, the BAZ1A-SMARCA5 complex  enables DNA replication through highly condensed regions of chromatin.

# Interactions
BAZ1A has been shown to interact with SMARCA5 and SATB1.
BAZ1B
Tyrosine-protein kinase BAZ1B is an enzyme that in humans is encoded by the BAZ1B gene.

# Function
This gene encodes a member of the bromodomain protein family. The bromodomain is a structural motif characteristic of proteins involved in chromatin-dependent regulation of transcription. This gene is deleted in Williams-Beuren syndrome, a developmental disorder caused by deletion of multiple genes at 7q11.23.

# Animal models
Model organisms have been used in the study of BAZ1B function. A conditional knockout mouse line, called Baz1btm2a(KOMP)Wtsi, was generated as part of the International Knockout Mouse Consortium program  a high-throughput mutagenesis project to generate and distribute animal models of disease to interested scientists  at the Wellcome Trust Sanger Institute.
Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion.
Six significant phenotypes were reported:
- Fewer homozygous mutant mice survived to weaning than expected.
- Mutant mice had decreased body weights compared to wildtype control mice.
- Mutant mice showed increased activity, VO2 and energy expenditure, determined by indirect calorimetry.
- Radiography found teeth abnormalities.
- Dual-energy X-ray absorptiometry (DEXA) showed mutant female mice had a decrease in bone mineral density and content.
- Male heterozygous mice had higher bacterial counts after Salmonella infection.

# Interactions
BAZ1B has been shown to interact with:
- CHAF1A,
- SMARCB1,
- SMARCC1,
- SMARCC2,
- SUPT16H
- TOP2B, and
- VDR.
BCCIP
BRCA2 and CDKN1A-interacting protein is a protein that in humans is encoded by the BCCIP gene.
This gene product was isolated on the basis of its interaction with BRCA2 and p21 proteins. It is an evolutionarily conserved nuclear protein with multiple interacting domains. The N-terminal half shares moderate homology with regions of calmodulin and M-calpain, suggesting that it may also bind calcium. Functional studies indicate that this protein may be an important cofactor for BRCA2 in tumor suppression, and a modulator of CDK2 kinase activity via p21. Several transcript variants encoding different isoforms have been described for this gene.

# Interactions
BCCIP has been shown to interact with BRCA2, P21, and PTPmu (PTPRM)
BECN1
Beclin-1 is a protein that in humans is encoded by the BECN1 gene. Beclin-1 is a mammalian  ortholog of the yeast autophagy-related gene 6 (Atg6)  and BEC-1 in the C. elegans nematode. This protein interacts with either BCL-2 or PI3k class III, playing a critical role in the regulation of both autophagy and cell death.

# Role in disease
Beclin-1 plays an important role in tumorigenesis, and neurodegeneration, being implicated in the autophagic programmed cell death. Ovarian cancer with upregulated autophagy has a less aggressive behavior and is more responsive to chemotherapy.
Schizophrenia is associated with low levels of Beclin-1 in the hippocampus of the affected which causes diminished autophagy which in turn results in increased neuronal cell death.

# Interactions
BECN1 has been shown to interact with:
- Bcl-2
- BCL2L2
- GOPC
- MAP1LC3A

# Modulators
BIMU8
BIMU-8 is a novel compound which acts on an area of the brain stem known as the pre-Botzinger complex.

# Explanation
The pre-Botzinger complex has been found to drive respiration.  BIMU-8 stimulates this area of the brain, causing an increase in the rate of respiration. BIMU-8 acts as a selective 5HT4 agonist and is one of the first compounds to be developed that was selective for this serotonin receptor subtype.

# Practical use of BIMU-8
The most obvious practical use of BIMU-8 is to combine it with opiates in order to counteract the dangerous respiratory depressing properties of the latter. BIMU-8 does not affect the painkilling properties of opiates, which means that if combined with BIMU-8, large therapeutic doses of opiates could theoretically be given to humans without risking a decrease in breathing rate.  Studies have shown BIMU-8 to be effective in rats at counteracting the respiratory depression caused by the potent opioid fentanyl, which has caused many accidental deaths in humans. However no human trials of BIMU-8 have yet been carried out.
Other studies have suggested a role for 5HT4 agonists in learning and memory, BIMU-8 was found to increase conditioned responses in mice, and so this drug might also be useful for improving memory in humans. Interestingly other selective 5HT4 agonists such as mosapride (the only 
5HT4 agonist currently available for use in humans) have been found not to reduce respiratory depression, suggesting that BIMU-8 may affect 5HT4 receptors in a different way to other 5HT4 agonists, or alternatively that the anti-respiratory depressant effect of BIMU-8 is instead mediated through a different mechanism of action which has not yet been elucidated.
BIRC6
Baculoviral IAP repeat-containing protein 6 is a protein that in humans is encoded by the BIRC6 gene.

# Function
This gene encodes a protein with a BIR (baculoviral inhibition of apoptosis protein repeat) domain and a UBCc (ubiquitin-conjugating enzyme E2, catalytic) domain. This protein inhibits apoptosis by facilitating the degradation of apoptotic proteins by ubiquitination.

# Interactions
BIRC6 has been shown to interact with KIF23.

# Diseases
BIRC6 is implicated in leukemia, melanoma, breast cancer, lung cancer, colorectal cancer, and other cancers (see the Atlas of Genetics and Cytogenetics in Oncology and Haematology).
BIRC7
Baculoviral IAP repeat-containing protein 7 is a protein that in humans is encoded by the BIRC7 gene.
The protein encoded by this gene is a member of the family of inhibitor of apoptosis proteins (IAP) and contains a single copy of a baculovirus IAP repeat (BIR) as well as a RING-type zinc finger domain. The BIR domain is essential for inhibitory activity and interacts with caspases, while the RING finger domain sometimes enhances antiapoptotic activity but does not inhibit apoptosis alone. Two transcript variants encoding different isoforms have been found for this gene. The two isoforms have different antiapoptotic properties, with isoform alpha protecting cells from apoptosis induced by staurosporine and isoform b protecting cells from apoptosis induced by etoposide.
In melanoma, BIRC7 gene expression is regulated by the Microphthalmia-associated transcription factor.
BNIP3
BCL2/adenovirus E1B 19 kDa protein-interacting protein 3 is a protein that in humans is encoded by the BNIP3 gene.
BNIP3 is a member of the apoptotic Bcl-2 protein family that is involved an atypical programmed cell death pathway resembling both necrosis and apoptosis. Many Bcl-2 family proteins modulate the permeability state of the outer mitochondrial membrane by forming homo- and hetero-oligomers. However, sequence similarity with Bcl-2 family members was not detected. Humans and other animals (Drosophila, Caenorhabditis), as well as lower eukaryotes (Dictyostelium, Trypanosoma, Cryptosporidium, Paramecium) encode several BNIP3 paralogues including the human NIP3L, which induces apoptosis by interacting with viral and cellular anti-apoptosis proteins.

# Structure
The right-handed parallel helix-helix structure of the domain with a hydrogen bond-rich His-Ser node in the middle of the membrane, accessibility of the node for water, and continuous hydrophilic track across the membrane suggest that the domain can provide an ion-conducting pathway through the membrane. Incorporation of the BNIP3 transmembrane domain into an artificial lipid bilayer resulted in a pH-dependent conductivity increase. Necrosis-like cell death induced by BNIP3 may be related to this activity.

# Function
BNIP3 interacts with the E1B 19 kDa protein which is responsible for the protection of virally induced cell death, as well as E1B 19 kDa-like sequences of BCL2, also an apoptotic protector. This gene contains a BH3 domain and a transmembrane domain, which have been associated with pro-apoptotic function.  The dimeric mitochondrial protein encoded by this gene is known to induce apoptosis, even in the presence of BCL2. Change of BNIP3 expression along other members of the Bcl-2 family measured by qPCR captures important characteristics of malignant transformation, and are defined as markers of resistance toward cell death, a key Cancer Hallmark.

## Transport reaction
The reaction catalyzed by BNIP3 is:

# Interactions
BNIP3 has been shown to interact with CD47, BCL2-like 1 and Bcl-2.
BRCC3
Lys-63-specific deubiquitinase BRCC36 is an enzyme that in humans is encoded by the BRCC3 gene.

# Function
This gene encodes a subunit of the BRCA1-BRCA2-containing complex (BRCC), which is an E3 ubiquitin ligase. This protein is also thought to be involved in the cellular response to ionizing radiation and progression through the G2/M checkpoint. Alternative splicing results in multiple transcript variants.

# Interactions
BRCC3 has been shown to interact with BRE, BRCA2, RAD51, BRCA1, P53 and BARD1.
BRIP1
Fanconi anemia group J protein is a protein that in humans is encoded by the BRCA1-interacting protein 1 (BRIP1) gene.

# Function
The protein encoded by this gene is a member of the RecQ DEAH helicase family and interacts with the BRCT repeats of breast cancer, type 1 (BRCA1). The bound complex is important in the normal double-strand break repair function of breast cancer, type 1 (BRCA1). This gene may be a target of germline cancer-inducing mutations.
This protein also appears to be important in ovarian cancer where it seems to act as a tumor suppressor. Mutations in BRIP1 are associated with a 10-15% risk of ovarian cancer.

# Interactions
BRIP1 has been shown to interact with BRCA1.