Persius/hicric huggingface dataset:
BCL2L2
Bcl-2-like protein 2 is a protein that in humans is encoded by the BCL2L2 gene. It was originally discovered by Leonie Gibson, Suzanne Cory and colleagues at the Walter and Eliza Hall Institute of Medical Research, who called it Bcl-w.

# Function
This gene encodes a pro-survival (anti-apoptotic) member of the bcl-2 protein family. The proteins of this family form hetero- or homodimers and act as anti- and pro-apoptotic regulators. Expression of this gene in cells has been shown to contribute to reduced cell apoptosis under cytotoxic conditions. Studies of the related gene in mice indicated a role in the survival of NGF- and BDNF-dependent neurons. Mutation and knockout studies of the mouse gene demonstrated an essential role in adult spermatogenesis.
Relative to its Bcl-2 counterparts there is considerably less data on this particular protein. Located on chromosome 14q11 it appears to be redundant in most tissues apart from specific examples.

# Interactions
BCL2L2 has been shown to interact with:
- BCL2L11
- BAD, and
- PPP1CA.
BLOSUM
BLOSUM (BLOcks of Amino Acid SUbstitution Matrix) is a substitution matrix used for sequence alignment of proteins. BLOSUM matrices are used to score alignments between evolutionarily divergent protein sequences.  Blosum  is based on local alignments. Blosum was first introduced in a paper by Henikoff and Henikoff (1992; PNAS 89:10915-10919). They scanned the BLOCKS database for very conserved regions of protein families (that do not have gaps in the sequence alignment) and then counted the relative frequencies of amino acids and their substitution probabilities. Then, they calculated a log-odds score for each of the 210 possible substitutions of the 20 standard amino acids.  All Blosum matrices are based on observed alignments; they are not extrapolated from comparisons or closely related proteins.
Blosum matrices with high numbers are designed for comparing closely related sequences, while Blosum matrices with low numbers are designed for comparing distant related sequences.  For example, Blosum80 is used for less divergent alignments, and Blosum45 is used for more divergent alignments. Scores within a Blosum matix are log-odds scores that measure the logarithm for the ratio of the likelihood of two amino acids appearing by chance. 
The matrices are based on the minimum percentage identity of the aligned protein sequence used in calculating them.   Every possible identity or substitution is assigned a score based on its observed frequences in the alignment of related proteins.  A positive score is given to the more likely substitutions while a negative score is given to the less likely substitutions.
BLOSUM62 is the matrix calculated by using the observed substitutions between proteins which have 62% or more sequence identity. BLOSUM has proved better at scoring distantly related sequences than the once-widely-used Point Accepted Mutation (PAM) matrices. To calculate a matrix for Blosum62, the following equation is used: B= (1/)log {(P i,j)/(i,j)}
BMPR1A
The bone morphogenetic protein receptor, type IA also known as BMPR1A is a protein which in humans is encoded by the BMPR1A gene. BMPR1A has also been designated as CD292 (cluster of differentiation 292).

# Function
The bone morphogenetic protein (BMP) receptors are a family of transmembrane serine/threonine kinases that include the type I receptors BMPR1A (this protein) and BMPR1B and the type II receptor BMPR2. These receptors are also closely related to the activin receptors, ACVR1 and ACVR2. The ligands of these receptors are members of the TGF beta superfamily. TGF-betas and activins transduce their signals through the formation of heteromeric complexes with 2 different types of serine (threonine) kinase receptors: type I receptors of about 50-55 kD and type II receptors of about 70-80 kD. Type II receptors bind ligands in the absence of type I receptors, but they require their respective type I receptors for signaling, whereas type I receptors require their respective type II receptors for ligand binding.
BMP's repress WNT signaling to maintain stable stem cell populations. BMPR1A null mice died at embryonic day 8.0 without mesoderm specification, demonstrating its vital role in gastrulation. It has been demonstrated in experiments using dominant negative BMPR1A chick embryos that BMPR1A plays a role in apoptosis and adipocyte development. Using constitutively active forms of BMR1A it has been shown that it plays a role in cell differentiation. Signals tranduced by the BMPR1A receptor are not essential for osteoblast formation or proliferation; however, BMPR1A is necessary for the extracellular matrix deposition by osteoblasts. In the chick embryo, BMPR1A receptors are found in low levels in limb bud mesenchyme, a differing location to BMPR1B, supporting the differing roles they play in osteogenesis.

# Ligands
- Agonists: BMP2, BMP4, BMP6, BMP7, GDF6
- Antagonists: Noggin, Chordin

# Diseases
BMPR1A, SMAD4 and PTEN are responsible for juvenile polyposis syndrome, juvenile intestinal polyposis and Cowden's disease.

# Interactions
BMPR1A has been shown to interact with:
- BMP2,
- SF3B4,  and
- ZMYND11.
BMPR1B
Bone morphogenetic protein receptor type-1B also known as CDw293 (cluster of differentiation w293) is a protein that in humans is encoded by the BMPR1B gene.

# Function
BMPR1B is a member of the bone morphogenetic protein (BMP) receptor family of transmembrane serine/threonine kinases. The ligands of this receptor are BMPs, which are members of the TGF-beta superfamily. BMPs are involved in endochondral bone formation and embryogenesis. These proteins transduce their signals through the formation of heteromeric complexes of 2 different types of serine (threonine) kinase receptors: type I receptors of about 50-55 kD and type II receptors of about 70-80 kD. Type II receptors bind ligands in the absence of type I receptors, but they require their respective type I receptors for signaling, whereas type I receptors require their respective type II receptors for ligand binding.
The BMPR1B receptor plays a role in the formation of middle and proximal phalanges.

# Clinical significance
Mutations in this gene have been associated with primary pulmonary hypertension.
In the chick embryo, it has been shown that BMPR1B is found in precartilaginous condensations. BMPR1B is the major transducer of signals in these condensations as demonstrated in experiments using constitutively active BMPR1B receptors. BMPR1B is a more effective transducer of GDF5 than BMPR1A. Unlike BMPR1A null mice, which die at an early embryonic stage, BMPR1B null mice are viable.
BPIFB1
BPI fold containing family B, member 1 is a protein that in humans is encoded by the BPIFB1 gene.

# Function
The protein encoded by this gene may be involved in the innate immune response to bacterial exposure in the mouth, nasal cavities, and lungs. The encoded protein is secreted and is a member of the BPI/LBP/PLUNC protein superfamily. This gene is found with other members of the superfamily in a cluster on chromosome 20. .

# Model organisms
Model organisms have been used in the study of BPIFB1 function. A conditional knockout mouse line called Bpifb1tm1e(KOMP)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
Baryte
Baryte (BaSO4) is a mineral consisting of barium sulfate. It is generally white or colorless, and is the main source of barium. Barite is the unofficial American spelling. The mineral is also called heavy spar or tiff.  The radiating form, sometimes referred to as Bologna Stone, attained some notoriety among alchemists for the phosphorescent specimens found in the 1600s near Bologna by Vincenzo Cascariolo. Its Mohs hardness is 3, the refractive index is 1.63 and it has a specific gravity of 4.3-5. Its crystal structure is orthorhombic.
Baryte commonly occurs in lead-zinc veins in limestones, in hot spring deposits, and with hematite ore. It is often associated with the minerals anglesite and celestine.
The name baryte is derived from the Greek word  (heavy). In commerce, the mineral is sometimes referred to as "barytes."  When the International Mineralogical Association formed in 1959 the American spelling "barite" was chosen as the official over the older "baryte".  This decision  was reversed in 1978.  The term "primary baryte" refers to the first marketable product, which includes crude baryte (run of mine) and the products of simple beneficiation methods, such as washing, jigging, heavy media separation, tabling, flotation, and magnetic separation.  Most crude baryte requires some upgrading to minimum purity or density.  Baryte that is used as an aggregate in a "heavy" cement is crushed and screened to a uniform size.  Most baryte is ground to a small, uniform size before it is used as a filler or extender, an addition to industrial products, or a weighting agent in petroleum well drilling mud.
Some 77% worldwide is used as a weighting agent for drilling fluids in oil and gas exploration. Other uses are in added-value applications which include the car, electronics, TV screen, rubber, and glass ceramics and paint industry, radiation shielding and medical applications (barium meals). Baryte is supplied in a variety of forms and the price depends on the amount of processing; filler applications commanding higher prices following intense physical processing by grinding and micronising, and there are further premiums for whiteness and brightness and colour.
Baryte is used in the manufacture of paints and paper.  Although baryte contains a "heavy" metal (barium), it is not considered to be a toxic chemical by most governments because of its extreme insolubility.
Benzyl

# Overview
In organic chemistry, benzyl is the  term for the radical, ion or functional group C6H5CH2, which can be obtained formally by removing a hydrogen atom from toluene's methyl group. The benzyl functional group is sometimes abbreviated "Bn", not to be confused with "Bz", which is short for the benzoyl group.  For example, benzyl alcohol can be abbreviated to BnOH.
In substituent nomenclature, benzyl and phenyl are commonly confused.  Benzyl can be seen as a phenyl attached to a CH2 before attaching to the parent compound.

# Benzyl protective groups
Benzyl groups are frequently used in organic synthesis as protective group for alcohols and carboxylic acids.
Two common methods for benzyl ether protection:
- reaction of alcohol with benzyl bromide and a strong base such as sodium hydride as in a Williamson ether synthesis
- reaction of alcohol with benzyl trichloroacetimidate (C6H5CH2OC(CCl3)=NH) promoted by trifluoromethanesulfonic acid
The benzyl group can be removed by hydrogenation.
One study  employs a benzyl pyridinium salt as a benzyl donor for alcohols.
The solvent is trifluoromethylbenzene and magnesium oxide is an acid scavenger. The reaction type for this conversion is believed to be SN1 based on the detection of trace amounts of Friedel-Crafts reaction sideproducts with toluene as a solvent.
Biceps
A biceps is a muscle from either of two muscle pairs (right and left) in the body.  Biceps is  the Latin adjective meaning two-headed. These muscles are so-called because each  has two insertions at its upper end.
- In general usage, the biceps is the biceps brachii, the prominent muscle on the inside of each upper arm, popularly associated with bodily strength because it can be flexed very visibly.
- Less commonly, the biceps is the biceps femoris, one of the hamstring muscles of the underside of each thigh.

# Usage note
Biceps is the singular. The muscle is often mistakenly called a bicep.
de:Bizeps
nl:Musculus biceps
Hallux

# Overview
The hallux pl. halluces, also known as the big toe or "thumb toe" is the innermost toe of the foot, counted as digit I.
In humans, the hallux is longer than the second or pointer toe for a majority of people. This is an inherited trait in humans, where the dominant gene causes the normal length hallux while the  homozygous recessive geneotype presents with a longer second toe. (Commonly known as "mitten foot").

# Diseases
People with the rare genetic disease fibrodysplasia ossificans progressiva characteristically have short big toes.
The big toe is the most common focus of gout and Ingrown nail attacks.
Biopsy
Synonyms and keywords: Bone biopsy, Soft tissue biopsy, Biopsy in musculoskeletal system, Biopsy of organs

# Overview
Biopsy is the gold standard test for the diagnosis of tumors. The tumor is then staged into benign and malignant tumors.

## Biopsy
- Biopsy is the gold standard test for the diagnosis of tumors.
Prerequisites for a Biopsy
- CBC, platelets and coagulation studies should be done.
- Cross-sectional imaging to evaluate local anatomy such CT scan and MRI.
- Treatment center carrying out biopsy must be capable of proper diagnosis and treatment.
- The surgeon who performs biopsy should preferably be the one who is later going to do the final excision.
Technique
- Open
- Closed

## Open Technique
- The tumor is surgically exposed and biopsy of the tumor is taken.

## Types

## Incisional biopsy
- A small surgical incision carefully placed to access tumor without contamination of critical structures.

## Excisional biopsy
- It is done for small, superficial soft tissue masses.
Incision
- Longitudinal incision in the extremities is taken.
- It should allow for extension of the incision for definitive management.
Approach
- Never expose neurovascular structures during the procedure.
- During the biopsy, all tissue exposed is considered contaminated with tumor.
- Meticulous hemostasis must be carried out.
- Post-surgery hematomas are considered contaminated with tumor.
- Always deflate the tourniquet prior to wound closure.
Biopsy
- Perform through the involved compartment of the tumor.
- For bone lesions with a soft tissue mass, perform the biopsy using the soft tissue mass.
Closure
- If drain is kept, remove the drain out of the skin in line with surgical incision.
- This helps in excising the drain site with definitive surgical extensive incision.

## Closed Technique

## Types

## Fine Needle Aspiration (FNA)
- It provides cytologic specimen.
- It is the most commonly used for carcinoma.
- It is usually not preferred for sarcoma.

## Core biopsy (Tru-cut Biopsy)
- It allows for tumor structural examination.
- It allows evaluation of both the cytologic and stromal elements of the tumor.
- It is frequently used for sarcomas.
- The various investigations must be performed in the following order:
- X-ray
MRI
- X-ray
- MRI
- Biopsy
Cnicus
Cnicus benedictus (Blessed Thistle), the sole species in the genus Cnicus, is a thistle-like plant in the family Asteraceae, native to the Mediterranean region, from Portugal north to southern France and east to Turkey. It is also sometimes called Cursed Thistle.
It is an annual plant growing to 60 cm tall, with leathery, hairy leaves up to 30 cm long and 8 cm broad, with small spines on the margins. The flowers are yellow, produced in a dense flowerhead (capitulum) 3-4 cm diameter, surrounded by numerous spiny basal bracts.
The related genus Notobasis is included in Cnicus by some botanists; it differs in slender, much spinier leaves, and purple flowers.

# Medical uses
It has sometimes been used as a herb to promote lactation. The crude drug contains about 0.2% cnicin.
It is a compontent in Bitters formulas which used to treat digestive issues.

# Edibility
These thistles are not considered edible, unlike Cirsium, Arctium and Onocordum species; the leaves are considered unpalatable if not bitter.
Osteon

# Overview
Osteons (also called Haversian system in honor of Clopton Havers) are predominant structures found in some lamellar or compact bone. Osteons are  found in many of the bones of many mammals, birds, reptiles, and amphibians running in a meandering way but generally parallel to the long axis of bones. It is this section of compact bone that is called matrix.
In the center of the osteon is a central canal, called the Haversian canal.
The central canal is surrounded by concentric layers of matrix called lamellae.  These lamellae are laid down one after the other over time, each successive one inside the preceding one. Collagen fibers in a lamella run parallel to each other but the orientation of collagen fibers across separate lamellae is oblique. The fiber density is also lower at the border between adjacent lamellae, which accounts for the distinctive appearance of an osteon.
Osteocytes are found between concentric lamellae and connected to each other and the central canal by cytoplasmic processes through the canals called canaliculi. This network permits the exchange of nutrients and metabolic waste.
Osteons are separated from each other by cement lines. Collagen fibers and canaliculi do not cross cement lines.
The space between separate osteons is occupied by interstitial lamellae, which were formed by pre-existing osteons that have since been reabsorbed.
Osteons are connected to each other and the periosteum by oblique channels called Volkmann's canals.

# Use in archaeology and forensics
Osteons carry their history so that given the right conditions they can be used to "read" the sex, age, health history, motor history and apparently something of the diet of an individual's bone. Osteons and their arrangement also vary according to  taxon, so that genus and sometimes species can be differentiated using a bone fragment not otherwise identifiable.  This is of use in archaeology, paleontology and forensics.
Borage
Borage (Borago officinalis L.), also known as "starflower" (  in Persian) is an annual herb originating in Syria, but naturalized throughout the Mediterranean region, as well as most of Europe, North Africa, and Iran. It grows to a height of 60-100 cm (2-3 feet), and is bristly-hairy all over the stems and leaves; the leaves are alternate, simple, and 5-15 cm (2-6 in) long. The flowers are small, blue or pink, with five narrow, triangular-pointed petals. It has an indeterminate growth habit allowing it to produce many seeds which may lead to it spreading prolifically beyond where it is first sown or planted. In milder climates, borage will bloom continuously for most of the year.
The leaves have been found to contain small amounts (10 ppm of dried herb) of the liver-toxic pyrrolizidine alkaloids: intermedine, lycopsamine, amabiline and supinine. They taste like fresh cucumber and are used in salads and soups especially in Germany. One of the better known recipes with borage is the Green Sauce made in Frankfurt. Frankfurter Grune Sauce, as it is called in Germany, is made from seven herbs: parsley, chervil, chives, cress, sorrel, burnet and borage. Borage is also an ingredient in the traditional recipe for a Pimm's Cup. In the Spanish regions of Aragon and Navarra, it's also commonly eaten.  One of the simplest recipes uses winter grown borage (because these have grown slowly and taste better) and before flowers appear (although not mandatory) usually cooking it in boiling water with a pair of potatoes. Once plated, the vegetables are seasoned with a little olive oil and salt, before being enjoyed.
The flower, which contains the non-toxic pyrrolizidine alkaloid thesinine, has a sweet honey-like taste and is often used to decorate desserts and dishes.
Tea made from the dried flowers is a traditional calming drink in Iran. It has a rich purple color that  turns bright pink by adding a few drops of lemon juice.
Interest in borage remains high because it is the highest known plant based source of gamma-linolenic acid (18:3, cis 6,9,12-octadecatrienoic acid).  The seed oil is often marketed as "starflower oil" or "borage oil."
Borage is also rich in oleic and palmitic acid, conferring a hypocholesterolemic effect.  This oil, which has recently been commercialised, may regulate metabolism and the hormonal system, and is considered by many naturopathic practitioners to be a good remedy for PMS and menopause symptoms such as the hot flash.  Borage is also sometimes indicated to alleviate and heal colds, bronchitis, and respiratory infections in general for its anti-inflammatory and balsamic properties. The flowers can be prepared in infusion to take advantage of its medicinal properties.

# As a companion plant
Borage is not only a pretty, flowering, edible herb, but it also improves the flavor of tomato vines when grown within a few feet of them.
Borate
Borates  in chemistry are chemical compounds containing boron bonded to three oxygen atoms written as B(OR)3. In B(OR)4 anions, this number increases to four.
The borate ion is BO33. it forms salts with metallic elements. Boron found in nature is commonly as a borate mineral. Boron is also found combined with silicate to form complex borosilicate minerals such as the tourmalines.
Borate exists in many forms. In acid and near-neutral conditions, it is boric acid, commonly written as H3BO3 but more correctly B(OH)3. The pKa of boric acid is 9.14 at 25C. Boric acid does not dissociate in aqueous solution, but is acidic due to its interaction with water molecules, forming tetrahydroxyborate:
Polyborate anions are formed at pH 710 if the boron concentration is higher than about 0.025 mol/L. The best known of these is the tetraborate ion, found in the mineral borax:
Even though boric acid adds hydroxide to form B(OH)4, you may find for pKa values and other calculations, the fictitious ions are easier to use. Thus for a typical polyprotic acid, the deprotonation series dihydrogen borate  , hydrogen borate  and borate  may be written as pH increases.
Boric acid can be used to form many polymeric ions. The tetraborate ion, B4O72, is very common;  the hydrogen tetraborate ion, HB4O7, as well as triborate and pentaborate, are also seen. The various metaborate ions have an empirical formula of BO2, and form metaborate compounds. Formation of these complicated, potentially infinite network structures is extensive, perhaps surpassed only by the silicates.
Common borate salts include sodium metaborate, NaBO2, and sodium tetraborate, Na2B4O7. The latter also occurs naturally as the hydrous mineral borax, Na2B4O710H2O. Boron, California contains large borax deposits and is used extensively for borate mining. The Atacama Desert in Chile also contains mineable borate concentrations.
Various forms of borate are used as wood preservatives or fungicides such as disodium octaborate tetrahydrate.

# Borate esters
Borate esters are organic compounds of the type B(OR)3 where R is an organic residue (for example alkyl or aryl). Borate esters include trimethyl borate, B(OCH3)3, which is used as a precursor to boronic esters for Suzuki couplings.