Persius/hicric huggingface dataset:
Cookie-cutter shark
The cookie-cutter shark, Isistius brasiliensis, also known as the cigar shark or luminous shark, is a small rarely-seen dogfish shark.

# Anatomy and morphology
Cookie-cutter sharks often glow green and grow up to 50 cm (20 in) long. The underside of the shark is bioluminescent, glowing a pale blue-green that matches the background light from the ocean's surface that serves as camouflage to creatures beneath it. However, a small non-luminescent patch appears black, deceiving the shark's prey, smaller predatory fish (like tuna), into thinking the shark is an even smaller fish. When the predatory fish tries to strike at the shark, the shark strikes back, scoring itself another meal . This is the only known instance whereby a bioluminescent lure is created by the absence of luminescence (contrast with anglerfish).

# Distribution
Worldwide in deep water. The cookie-cutter shark has been found at depths of about 1,000 m (3,300 ft).

# Ecology and life history

## Feeding ecology
It derived its name from its habit of removing small circular chunks of flesh from whales and large fish.  It is hypothesized that the shark seizes its much larger prey with its jaws, then rotates its body to achieve a highly symmetrical cut. They are considered parasites.

## Life history
Cookie-cutter sharks reproduce through aplacental viviparity in the same way as great white sharks. Little else is known about their reproduction.

# Etymology and taxonomic history
Its name comes from its feeding style which often creates perfect "cookie-cutter" shaped plugs in the skin of large marine mammals and other large sharks (as well as the rubber coating of submarines).

# Interaction with humans
There has been little interaction between humans and the cookie-cutter shark. However, there was an incident in which a cookie-cutter shark took a bite out of the rubber sonar dome of a US Navy submarine, causing damage to the housing, and forcing the submarine out of service until the rubber could be replaced.
Coordination number
In chemistry, coordination number (c.n.), as defined originally in 1893 by Alfred Werner, is the total number of neighbors of a central atom in a chemical compound.  In methane the coordination number for the carbon atom is 4. In inorganic chemistry the number of sigma bonds between ligand and the central atom count but not the number of pi bonds.
In materials science, the bulk coordination number is the number of atoms touching any other atom in a crystal lattice.
Examples of high coordination number compounds are uranium and thorium bidentate nitrate-coordinated cluster compounds U(NO3)62- and Th(NO3)62-. When the surrounding ligands get smaller even higher coordination numbers are possible. One in silico study found a particularly stable PbHe152+ ion comprised of a central lead ion coordinated with no less than 15 helium atoms..
Coriaria myrtifolia
Coriaria myrtifolia is a shrub to 2-3 m tall. The leaves are single and opposite, thornless, 6-10 cm long and 1-3 cm broad (like myrtle). The small greenish flowers, with five petals, appear from April to June in racemes. The fruit is a fleshy black berry achene very similar to a blackberry but toxic. It is especially dangerous for children who may eat it if they confuse it with edible berries.
The Spanish name emborrachacabras ("goats-drunk") refers to the leaves' effect on goats that eat them. The French(redoul) and Catalan name(roldor) derive from latin rhus tyrius (Sirian-Tyr sumac), referring to the leaves' use in the traditional tannery industry
Grows in some parts of the Mediterranean basin (South France, Spain, east Mediterranean areas etc.) Is locally very common but absent in other nearby areas (in the Balearic islands it only appears in Ibiza)
Corneal perforation

# Overview
Corneal Perforation is an anomaly in the cornea resulting from damage to the corneal surface.  A corneal perforation means that the cornea has been penetrated, thus leaving the cornea damaged.
The cornea is a clear part of the eye which controls and focuses the entry of light into the eye.  Damage to the cornea due to corneal perforation can cause decreased visual acuity.

# Causes
- Diseases that cause progressive corneal thinning.
- Accidents during eye surgery, that results in scraping or injury of the cornea.
- Infection of the cornea post eye surgery.

# Indications
- Difficulty in seeing.
- Discoloration of the cornea.
- Persistent eye pain.

# Diagnosis
Corneal perforation can be diagnosed by using the Seidel test.  Any aqueous leakage is revealed during the Seidel test confirms corneal perforation.  A fluorescence strip is wiped over the wound.   If the clear aqueous humor from the eye runs through the yellow stain, the patient tests positive for corneal perforation.

# Treatment
The treatment of corneal perforation depends on the location, severity and the cause of damage
- Tissue adhesive can be used to seal small perforation, but this method cannot be used to treat perforations larger than 1 mm.
- Non infected corneal perforation generally heals when a pressure bandage is used.
- For certain types of corneal perforations, lamellar keratoplasty is used as treatment.
Costocervical trunk
The costocervical trunk arises from the upper and back part of the subclavian artery, behind the scalenus anterior on the right side, and medial to that muscle on the left side.
Passing backward, it splits into the deep cervical artery and the supreme intercostal artery (or the Highest intercostal artery), which descends behind the pleura in front of the necks of the first and second ribs, and anastomoses with the first aortic intercostal (3rd posterior intercostal artery).
As it crosses the neck of the first rib it lies medial to the anterior division of the first thoracic nerve, and lateral to the first thoracic ganglion of the sympathetic trunk.
In the first intercostal space, it gives off a branch which is distributed in a manner similar to the distribution of the aortic intercostals.
The branch for the second intercostal space usually joins with one from the highest aortic intercostal artery.
This branch is not constant, but is more commonly found on the right side; when absent, its place is supplied by an intercostal branch from the aorta.
Each intercostal gives off a posterior branch which goes to the posterior vertebral muscles, and sends a small spinal branch through the corresponding intervertebral foramen to the medulla spinalis and its membranes.

# Branches
- Deep cervical artery
- Supreme intercostal artery
Countertransference
In psychotherapy, countertransference is a condition where the therapist, as a result of the therapy sessions, begins to transfer the therapist's own unconscious feelings to the patient.  For example, a therapist might have a strong desire for a client to get all 'A's' in university because the client reminds her of her children at that stage in life, and the anxieties that the therapist experienced during that time.
Countertransference is also sometimes defined as the entire body of feelings that the therapist has toward the patient, and also includes cases where the therapist literally takes on the suffering of his/her patient . In the most extreme of cases, it can result in the therapist taking on the neurosis or psychosis of the patient, such as bouts of paranoia or psychotic intervals, illustrated by Jung in the case of schizophrenia.
Countertransference is defined in opposition to transference, where a person in therapy begins to transfer feelings (whether positive or negative) to the therapist.  For example, the person in therapy may begin to look at the therapist as if the therapist were the patient's mother, transferring their feelings for the real mother to the therapist.  This is considered a positive sign in psychoanalytic therapy, showing that the patient is making progress.
In On Becoming a Counselor, Eugene Kennedy states that countertransference  has the potential to be present in any counseling relationship . He states that it is often one of the biggest challenges for a new counselor to overcome, and while there is no way to totally overcome the problem of counter-transference (since as humans we all form opinions of others) learning to not let countertransference affect a counseling relationship is key. The mantra "only connect" is often associated with this effect.
Countertransference can also be seen as a useful phenomenon for the therapist because it can allow them to gain insight into the kinds of emotions and reactions the client often tends to induce in others. In this way, the countertransference is a welcomed phenomenon which can prove invaluable to the clinical relationship. In this way, countertransference is related to the psychoanalytic concept of projective identification, a defense mechanism in which the client projects  onto and induces their own inner experience within the clinician.
In Mental Space, Robert Young (1994, ch.4) offers a history of the concept of countertransference and argues that it is a species of projective identification.
A related concept is counterresistance, which includes therapist behaviours that influence the therapeutic process through such "blockings" as (hostile) silence, attempting to change the subject, or otherwise preventing unwanted ideas or feelings from rising to the fore.  Counterresistance can result from a therapist's colluding with the patient's resistance to explore or work through unpleasant issues but can also originate exclusively from the therapist.  An example would be an overweight therapist consistently steering an equally overweight client away from discussions about weight loss.
Covariance function
For a random field or Stochastic process Z(x) on a domain D, a covariance function C(x, y) gives the covariance of the values of the random field at the two locations x and y:
The same C(x, y) is called autocovariance in two instances: in time series (to denote exactly the same concept, where x is time), and in multivariate random fields (to refer to the covariance of a variable with itself, as opposed to the cross covariance between two different variables at different locations, Cov(Z(x1), Y(x2))).

# Admissibilty
For locations x1, x2, ..., xN  D the variance of every linear combination
can be computed as
A function is a valid covariance function if and only if this variance is non-negative for all possible choices of N and weights w1, ..., wN. A function with this property is called positive definite.

# Simplifications with Stationarity
In case of a weakly stationary random field, where
for any lag h, the covariance function can represented by a one parameter function
which is called a covariogram and also a covariance function. Implicitly the C(xi, xj) can be computed from Cs(h) by:
The positive definiteness of this single argument version of the covariance function can be checked by Bochner's theorem.
Crabtree's catalyst
Crabtree's catalyst is the name given to a complex of iridium with 1,5-cyclooctadiene, tris-cyclohexylphosphine, and pyridine. It is a homogeneous catalyst for hydrogenation reactions, developed by Robert H. Crabtree, a professor at Yale University. The iridium atom in the complex has a square planar molecular geometry, as expected for a d8 complex.
Crabtree and graduate student George Morris discovered this catalyst in the 1970s while working on iridium analogues of Wilkinson's rhodium-based catalyst at the Institut de Chimie des Substances Naturelles at Gif-sur-Yvette, near Paris. One advantage of Crabtree's catalyst is that it is about 100 times more active than Wilkinson's and can hydrogenate even tri- and tetrasubstituted alkenes.
Crabtree's catalyst has also been used as the basis for the development of newer catalysts; by modifying the ligands, one can modulate the properties of the catalyst. For example, use of chiral ligands has led to the development of enantioselective catalysts.
In the hydrogenation of a certain terpen-4-ol the comparison with traditional catalysts works out as follows.
With palladium on carbon in ethanol the product distribution is 20:80 in favor of the  the cis isomer (2B in scheme 1). The polar side (with the hydroxyl group) interacts with the solvent leaving the apolar to the catalyst surface. In cyclohexane as solvent the distribution changes to 53:47 where the polar side now has a slight preference for the catalyst. The distribution changes completely in favor of the cis isomer 2A when Crabtree's catalyst is used in dichloromethane. This directing effect is due to a bonding interaction of the hydroxyl group with the iridium center.  Carbonyl groups are also known to direct the hydrogenation by the Crabtree catalyst.
Crabtree catalyst in hydrogenation
Deactivating groups
In organic chemistry, a deactivating group is a functional group attached to a benzene molecule that removes electron density from the benzene ring, making electrophilic aromatic substitution reactions slower and more complex relative to benzene. Depending on their relative strengths, deactivating groups also determine the positions (relative to themselves) on the benzene ring where substitutions must take place; this property is therefore important in processes of organic synthesis.

# Categories
Deactivating groups are generally sorted into three categories. Weakly deactivating groups direct electrophiles to attack the benzene molecule at the ortho- and para- positions, while strongly and moderately deactivating groups direct attacks to the meta- position. This is not a case of favouring the meta- position like para- and ortho- directing functional groups, but rather disfavouring the para- and ortho- positions more than they disfavour the meta- position.

## Strongly Deactivating Groups
-NO2, nitro groups
-NR3+ Quaternary amine /Quaternary ammonium base
-CF3, CCl3 trihalides

## Moderately Deactivating Groups
-CN cyano groups
-SO3H sulfonates
-CO2H, -CO2R carboxylic acids
-CHO, -COR Aldehydes and Ketones

## Weakly Deactivating Groups
-F
-Cl
-Br
-I

# Mechanism
While steric effects are a consideration not to be ignored the major contribution of deactivating groups is achieved by utilizing the nature of conjugated systems (specifically the ease through which mesomeric effects travel through such systems) to create regions of positive charge within the resonance contributors.
Take for example a benzene with a nitro group substituent, the mechanistic explanation of the resulting deactivation is best explained diagrammatically:
The resulting resonance hybrid, now possessing + charges in the ortho- and para- positions repels approaching electrophiles increasing the relative success of attack in the meta position.
The selectivities observed with activating groups and deactivating groups were first described in 1892 and have been known as the Crum Brown-Gibson Rule
Cryptic splice site
There are four sequence elements within introns of mammalian pre-mRNAs which are required for efficient splicing. These are the conserved sequence at the 5' splice junction, the invariant AG dinucleotide at the 3' splice junction, a weakly conserved sequence at the site of lariat formation etc..
Cryptic splice sites are also such kind of motif that are present in many regions throughout pre-mRNAs and yet are not recognized under normal conditions,whereas in transcripts bearing point mutations or deletions within natural elements,such sites can be activated.

# Reference
-  Selection of Splice Sites in Pre-mRNAs with Short Internal Exons.MOLECULAR AND CELLULAR BIOLOGY, Dec. 1991, p. 6075-6083
D-block contraction
d-block contraction (sometimes called scandide contraction) is a term used in chemistry to describe the effect of having  full d orbitals on the  period 4 elements. The elements in question are the  Ga, Ge, As, Se and Br. Their electronic configurations include completely filled d orbitals (d10). d-block contraction is best illustrated by comparing some properties of the group 13 elements to highlight the effect on gallium.
Gallium can be seen to be anomalous. The most obvious effect is that the sum of the first three ionization potentials of gallium is higher than that of aluminium, whereas the trend in the group would be for it to be lower. The second table below shows the trend in the sum of the first three ionization potentials for the elements B, Al, Sc, Y, La. Sc, Y, La are group 3 elements and have three valence electrons above a noble gas electron core.  In contrast to the group 13 elements  this sequence shows a smooth reduction.
Other effects of the d-block contraction are that the Ga3+ ion is smaller than expected, being closer in size to Al3+. Care must be taken in interpreting the ionisation potentials for indium and thallium, other effects e.g. the inert pair effect become increasingly important for the heavier members of the group.
The cause of the d-block contraction is the poor  shielding of the nuclear charge by the  electrons in the d orbitals. The  outer valence electrons are more strongly attracted by the nucleus causing the observed increase in ionization potentials. The d-block contraction can  be compared to the lanthanide contraction which is caused by inadequate shielding of nuclear charge by electrons occupying f orbitals.
DNA polymerase beta
DNA polymerase, beta, also known as POLB, is an enzyme present in eukaryotes. In humans, it is encoded by the  POLB gene.

# Function
In eukaryotic cells, DNA polymerase beta (POLB) performs base excision repair (BER) required for DNA maintenance, replication, recombination, and drug resistance.
The mitochondrial DNA of mammalian cells is constantly under attack from oxygen radicals released during ATP production.  Mammalian cell mitochondria contain an efficient base excision repair system employing POLB that removes some frequent oxidative DNA damages.  POLB thus has a key role in maintaining the stability of the mitochondrial genome.
An analysis of the fidelity of DNA replication by polymerase beta in the neurons from young and very aged mice indicated that aging has no significant effect on the fidelity of DNA synthesis by polymerase beta.  This finding was considered to provide evidence against the error catastrophe theory of aging.

# Regulation of expression
DNA polymerase beta maintains genome integrity by participating in base excision repair. Overexpression of POLB mRNA has been correlated with a number of cancer types, whereas deficiencies in POLB results in hypersensitivity to alkylating agents, induced apoptosis, and chromosomal breaking . Therefore, it is essential that POLB expression is tightly regulated.
POLB gene is upregulated by CREB1 transcription factor's binding to the cAMP response element(CRE) present in the promoter of the POLB gene in response to exposure to alkylating agents. POLB gene expression is also regulated at the post transcriptional level as the 3UTR of the POLB mRNA has been shown to contain three stem-loop structures that influence gene expression. These three-stem loop structures are known as M1, M2, and M3, where M2 and M3 have a key role in gene regulation. M3 contributes to gene expression, as it contains the polyadenylation signal followed by the cleavage and polyadenylation site, thereby contributing to pre-mRNA processing. M2 has been shown to be evolutionary conserved, and, through mutagenesis, it was shown that this stem loop structure acts as a RNA destabilizing element.
In addition to these cis-regulatory elements present within the 3UTR a trans-acting protein, HAX1 is thought to contribute to the regulation of gene expression. Yeast three-hybrid assays have shown that this protein binds to the stem loops within the 3UTR of the POLB mRNA, however the exact mechanism in how this protein regulates gene expression is still to be determined.

# Interactions
DNA polymerase beta has been shown to interact with PNKP and XRCC1.
Deoxyribonuclease I
Deoxyribonuclease I (usually called DNase I), is an endonuclease coded by the human gene DNASE1.
DNase I is a nuclease that cleaves DNA preferentially at phosphodiester linkages adjacent to a pyrimidine nucleotide, yielding 5'-phosphate-terminated polynucleotides with a free hydroxyl group on position 3', on average producing tetranucleotides. It acts on single-stranded DNA, double-stranded DNA, and chromatin. In addition to its role as a waste-management endonuclease, it has been suggested to be one of the deoxyribonucleases responsible for DNA fragmentation during apoptosis.
DNase I binds to the cytoskeletal protein actin. It binds actin monomers with very high (sub-nanomolar) affinity and actin polymers with lower affinity. The function of this interaction is unclear. However, since actin-bound DNase I is enzymatically inactive, the DNase-actin complex might be a storage form of DNase I that prevents damage of the genetic information.
This gene encodes a member of the DNase family. This protein is stored in the zymogen granules of the nuclear envelope and functions by cleaving DNA in an endonucleolytic manner. At least six autosomal codominant alleles have been characterized, DNASE1*1 through DNASE1*6, and the sequence of DNASE1*2 represented in this record. Mutations in this gene, as well as factor inactivating its enzyme product, have been associated with systemic lupus erythematosus (SLE), an autoimmune disease. A recombinant form of this protein is used to treat one of the symptoms of cystic fibrosis by hydrolyzing the extracellular DNA in sputum and reducing its viscosity. Alternate transcriptional splice variants of this gene have been observed but have not been thoroughly characterized.

# In genomics
In genomics, DNase I hypersensitive sites are thought to be characterized by open, accessible chromatin; therefore, a DNase I sensitivity assay is a widely used methodology in genomics for identifying which regions of the genome are likely to contain active genes 

# DNase I Sequence Specificity
It has been recently reported that DNase I shows some levels of sequence specificity that may depend on experimental conditions. In contrast to other enzymes which have high substrate specificity, DNase I certainly does not cleave with an absolute sequence specificity. However, cleavage at sites that contain C or G at their 3' end is less efficient.