Persius/hicric huggingface dataset:
Cure
A cure is a substance or procedure that makes a sick or diseased person well. A cure can be a medication, a surgical operation, a change in lifestyle, or even a philosophical mindset that helps a person heal.

# Difference between preventions, treatments, and cures
A prevention or preventive measure is a way to avoid an injury, sickness, or disease in the first place, and generally it will not help someone who is already ill (though there are exceptions).  For instance, many American babies are given a polio vaccination soon after they are born, which prevents them from contracting polio. But the vaccination does not work on patients who already have polio. A treatment or cure is applied after a medical problem has already started.
A treatment treats a problem, and may lead to its cure, but treatments more often ameliorate a problem only for as long as the treatment is continued.  For example, there is no cure for AIDS, but treatments are available to slow down the harm done by HIV and delay the fatality of the disease.  Treatments don't always work.  For example, chemotherapy is a treatment for cancer which may cure the disease sometimes - it does not have a 100% cure rate.  Therefore, chemotherapy isn't considered a bona fide cure for cancer.

# Examples of Cures
There are a few examples of complete cures. In 1999, the CDC and the World Health Organization established a goal to cure 85% of tuberculosis patients in Russia. They reached an 80% success rate, with 75% of the diseased cured, and 5% that had successfully finished treatment.
GJA5
Gap junction alpha-5 protein (GJA5), also known as connexin 40 (Cx40)  is a protein that in humans is encoded by the GJA5 gene.

# Function
This gene is a member of the connexin gene family. The encoded protein is a component of gap junctions, which are composed of arrays of intercellular channels that provide a route for the diffusion of low molecular weight materials from cell to cell. Mutations in this gene may be associated with atrial fibrillation. Alternatively spliced transcript variants encoding the same isoform have been described.
GJA5 has been identified as the gene that is responsible for the phenotypes observed with congenital heart diseases on the 1q21.1 location. In case of a duplication of GJA5 tetralogy of Fallot is more common. In case of a deletion other congenital heart diseases than tetralogy of Fallot are more common.

# Related gene problems
- 1q21.1 deletion syndrome
- 1q21.1 duplication syndrome
Cyst

# Overview
A cyst is a closed sac having a distinct membrane and division on the nearby tissue. It may contain air, fluid, or semi-solid material. A collection of pus is called an abscess, not a cyst. Once formed, the cyst will remain in the tissue but can be removed by surgery or resolve by taking medications.
A cyst may also be a sack that encloses an organism during a dormant period, such as in the case of certain parasites. This type of cyst may, for instance, protect a parasite from the churning acid of the stomach so it may pass through to the intestines unharmed where it can then break out. 
Cystic fibrosis is an example of a genetic disorder whereby cysts and fibrosis develop in the lungs.

# Locations
- Arachnoid cyst (between the surface of the brain and the cranial base or on the arachnoid membrane)
- Chalazion cyst (eyelid)
- Cysticercal cyst (the larval stage of Taenia sp.)
- Dentigerous Cyst (associated with the crowns of non-erupted teeth)
- Epididymal Cyst (found in the vessels attached to the testes)
- Ganglion cyst (hand/foot joints and tendons)
- Glial Cyst (in the brain)
- Gartner's duct cyst (vaginal or vulvar cyst of embryological origin)
- Keratocyst (in the jaws, these can appear solitary or associated with the Gorlin-Goltz or Nevoid basal cell carcinoma syndrome. The latest World Health Organization classification considers Keratocysts as tumors rather than cysts)
- Meibomian cyst (eyelid)
- Nabothian cyst (cervix)
- Ovarian cyst (ovaries, functional and pathological)
- Paratubal cyst (fallopian tube)
- Pilonidal cyst (skin infection near tailbone)
- Renal cyst (kidneys)
- Radicular cyst (associated with the roots of non-vital teeth)
- Sebaceous cyst (sac below skin)
- Tarlov cyst (spine)
- Vocal fold cyst
- Dermoid cyst (Skull and ovaries)
- Breast cyst

# Related structures
A pseudocyst is collection without a distinct membrane.
A syrinx in the spinal cord or brainstem is sometimes inaccurately referred to as a cyst.

# Resources
- Template:FPnotebook
- "Cyst Symptoms and Causes" by Melissa Conrad Stoppler, MD and William C. Shiel, Jr., MD, FACP, FACR.
cs:Cysta (lekarstvi)
de:Zyste
io:Kisto
it:Cisti (medicina)
he:
hu:Ciszta
nl:Cyste
no:Cyste
fi:Kysta
sv:Cysta
DAPI
DAPI or 4',6-diamidino-2-phenylindole is a fluorescent stain that binds strongly to DNA.  It is used extensively in fluorescence microscopy.  Since DAPI will pass through an intact cell membrane, it may be used to stain both live and fixed cells.
For fluorescence microscopy, DAPI is excited with ultraviolet light.  When bound to double-stranded DNA its absorption maximum is at 358 nm and its emission maximum is at 461 nm.  (This emission is fairly broad, and appears blue/cyan.)  DAPI will also bind to RNA, though it is not as strongly fluorescent.  Its emission shifts to around 500 nm when bound to RNA.
DAPI's blue emission is convenient for microscopists who wish to use multiple fluorescent stains in a single sample.  There is fluorescence overlap between DAPI and green-fluorescent molecules like fluorescein and green fluorescent protein (GFP), or red-fluorescent stains like Texas Red, but using spectral unmixing or taking images sequentially can get around this.
Apart from labelling cell nuclei, the most popular application of DAPI is in detection of mycoplasma or virus DNA in cell cultures.
Because DAPI readily enters live cells and binds tightly to DNA, it is toxic and mutagenic.  Care should be taken in its handling and disposal.
The Hoechst stains are similar to DAPI in that they are also blue-fluorescent DNA stains which are compatible with both live- and fixed-cell applications.
de:DAPI
DASB
DASB is a compound that binds to the serotonin transporter.
Labeled with carbon-11  a radioactive isotope  it has been used as a radioligand in neuroimaging with positron emission tomography (PET) since around year 2000.
In this context it is regarded as one of the superior radioligands for PET study of the serotonin transporter in the brain,
since it has high selectivity for the serotonin transporter.
The DASB image from a human PET scan shows high binding in the midbrain, thalamus and striatum, moderate binding in the medial temporal lobe and anterior cingulate, and low binding in neocortex.
The cerebellum is often regarded as a region with no specific serotonin transporter binding and the brain region is used as a reference in some studies.
Since the serotonin transporter is the target of SSRIs used in the treatment of major depression it has been natural to examine DASB binding in depressed patients.
Several such research studies have been performed.
There are a number of alternative PET radioligands for imaging the serotonin transporter: ADAM, AFM, DAPA,  McN5652, and -NS 4194.
A related molecule to DASB, that can be labeled with fluorine-18, has also been suggested as a PET radioligand. 
With single-photon emission computed tomography (SPECT) using the radioisotope iodine-123 there are further radioligands available: ODAM, IDAM, ADAM, and -CIT.
A few studies have examined the difference in binding between the radioligands in nonhuman primates, 
as well as in pigs.
Other compounds that can be labeled to work as PET radioligands for the study of the serotonin system are, e.g., altanserin and WAY-100635.

# Methodological issues
The binding potential of DASB can be estimated with kinetic modeling on a series of brain scans.
A test-retest reproducibility PET study indicates that DASB can be used to measure the serotonin transporter parameters with high reliability  in receptor-rich brain regions.
When the DASB neuroimages are analyzed the kinetic models suggested by Ichise and coworkers can be employed to estimate the binding potential.
A test-retest reproducibility experiment has been performed to evaluate this approach.

# Studies
Besides the studies listed below a few occupancy studies have been reported.
DAX1
DAX1 (dosage-sensitive sex reversal, adrenal hypoplasia critical region, on chromosome X, gene 1) is a nuclear receptor protein that in humans is encoded by the NR0B1 gene (nuclear receptor subfamily 0, group B, member 1). The NR0B1 gene is located on the short (p) arm of the X chromosome between positions 21.3 and 21.2, from base pair 30,082,120 to base pair 30,087,136.

# Function
This gene encodes a protein that lacks the normal DNA-binding domain contained in other nuclear receptors. The encoded protein acts as a dominant-negative regulator of transcription of other nuclear receptors including steroidogenic factor 1. This protein also functions as an anti-testis gene by acting antagonistically to SRY. Mutations in this gene result in both X-linked congenital adrenal hypoplasia and hypogonadotropic hypogonadism.
DAX1 plays an important role in the normal development of several hormone-producing tissues. These tissues include the adrenal glands above each kidney, the pituitary gland and hypothalamus, which are located in the brain, and the reproductive structures (the testes and ovaries). DAX1 controls the activity of certain genes in the cells that form these tissues during embryonic development. Proteins that control the activity of other genes are known as transcription factors. DAX1 also plays a role in regulating hormone production in these tissues after they have been formed.

# Role in disease
X-linked adrenal hypoplasia congenita is caused by mutations in the NR0B1 gene. More than 90 NR0B1 mutations that cause X-linked adrenal hypoplasia congenita have been identified. Many of these mutations delete all or part of the NR0B1 gene, preventing the production of DAX1 protein. Some mutations cause the production of an abnormally short protein. Other mutations cause a change in one of the building blocks (amino acids) of DAX1. These mutations are thought to result in a misshapen, nonfunctional protein. Loss of DAX1 function leads to adrenal insufficiency and hypogonadotropic hypogonadism, which are the main characteristics of this disorder.
Duplication of genetic material on the X chromosome in the region that contains the NR0B1 gene can cause a condition called dosage-sensitive sex reversal. The extra copy of the NR0B1 gene prevents the formation of male reproductive tissues. People who have this duplication usually appear to be female, but are genetically male with both an X and a Y chromosome.
In some cases, genetic material is deleted from the X chromosome in a region that contains several genes, including NR0B1. This deletion results in a condition called adrenal hypoplasia congenita with complex glycerol kinase deficiency. In addition to the signs and symptoms of adrenal hypoplasia congenita, individuals with this condition may have elevated levels of lipids in their blood and urine and may have problems regulating blood sugar levels. In rare cases, the amount of genetic material deleted is even more extensive and affected individuals also have Duchenne muscular dystrophy.

# Interactions
DAX1 has been shown to interact with:
- COPS2,
- NRIP1,
- Steroidogenic factor 1, and
- SREBF1.
DAZ1
Deleted in azoospermia 1, also known as DAZ1, is a protein which in humans is encoded by the DAZ1 gene.

# Function
This gene is a member of the DAZ gene family and is a candidate for the human Y-chromosomal azoospermia factor (AZF). Its expression is restricted to pre-meiotic germ cells, particularly in spermatogonia. It encodes an RNA-binding protein that is important for spermatogenesis. Four copies of this gene are found on chromosome Y within palindromic duplications; one pair of genes is part of the P2 palindrome and the second pair is part of the P1 palindrome. Each gene contains a 2.4 kb repeat including a 72-bp exon, called the DAZ repeat; the number of DAZ repeats is variable and there are several variations in the sequence of the DAZ repeat. Each copy of the gene also contains a 10.8 kb region that may be amplified; this region includes five exons that encode an RNA recognition motif (RRM) domain. This gene contains three copies of the 10.8 kb repeat. However, no transcripts containing three copies of the RRM domain have been described; thus the RefSeq for this gene contains only two RRM domains.

# Interactions
DAZ1 has been shown to interact with DAZAP2, DAZL and DAZ associated protein 1.
DBC1
Deleted in bladder cancer protein 1 is a protein that in humans is encoded by the DBC1 gene.
This gene is located within chromosome 9 (9q32-33), a chromosomal region that frequently shows loss of heterozygosity in transitional cell carcinoma of the bladder.  It contains a 5' CpG island that may be a frequent target of hypermethylation, and it may undergo hypermethylation-based silencing in some bladder cancers.
The functions of this gene are unknown, and it has not yet been placed in a protein family or functional pathway. Nonetheless, it is suspected to act as a tumor suppressor gene.
DBN1
Drebrin is a protein that in humans is encoded by the DBN1 gene.
The protein encoded by this gene is a cytoplasmic actin-binding protein thought to play a role in the process of neuronal growth. It is a member of the drebrin family of proteins that are developmentally regulated in the brain. A decrease in the amount of this protein in the brain has been implicated as a possible contributing factor in the pathogenesis of memory disturbance in Alzheimer's disease. At least two alternative splice variants encoding different protein isoforms have been described for this gene.

# Model organisms
Model organisms have been used in the study of DBN1 function. A conditional knockout mouse line called Dbn1tm1b(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
DCC1
Sister chromatid cohesion protein DCC1 is a protein that in humans is encoded by the DSCC1 gene.

# Model organisms
Model organisms have been used in the study of DSCC1 function. A conditional knockout mouse line, called Dscc1tm1a(KOMP)Wtsi was generated at the Wellcome Trust Sanger Institute 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.
Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Twenty four tests were carried out on mutant mice and four significant abnormalities were observed. Few homozygous mutant embryos were identified during gestation, and some displayed oedema, therefore less than expected survived until weaning. Those that did survive had increased chromosomal instability in a micronucleus test and numerous skeletal abnormalities by radiography.

# Interactions
DCC1 has been shown to interact with CHTF18.
DDB1
DNA damage-binding protein 1 is a protein that in humans is encoded by the DDB1 gene.

# Gene
The gene's position is on chromosome 11q12-q13.

# Protein
The DDB1 gene encodes the large subunit of DNA damage-binding protein, a heterodimer composed of a large and a small (DDB2) subunit. DDB1 contains 1140 amino acids, amounting to a mass of 127 kDa.

# Function
As its name suggests, DDB1 was initially implicated in the process of a specific type of DNA repair known as nucleotide excision repair. Since then, researchers have found that DDB1 primarily functions as a core component of the CUL4A- and CUL4B-based E3 ubiquitin ligase complexes. DDB1 serves as a bridge or adaptor protein which interacts with dozens of proteins known as DDB1 and CUL4-associated factors (DCAFs). These DCAFs are often ubiquitin ligase substrates and regulate numerous essential processes in the cell including DNA repair (DDB2), DNA replication, chromatin remodeling (Cdt2) and more.

# Interactions
DDB1 has been shown to interact with Transcription initiation protein SPT3 homolog, GCN5L2, DDB2, CUL4A, CUL4B and P21.
DFFA
DNA fragmentation factor subunit alpha (DFFA), also known as Inhibitor of caspase-activated DNase (ICAD), is a protein that in humans is encoded by the DFFA gene.
Apoptosis is a cell death process that removes toxic and/or useless cells during mammalian development. The apoptotic process is accompanied by shrinkage and fragmentation of the cells and nuclei and degradation of the chromosomal DNA into nucleosomal units. DNA fragmentation factor (DFF) is a heterodimeric protein of 40-kD (DFFB) and 45-kD (DFFA) subunits. DFFA is the substrate for caspase-3 and triggers DNA fragmentation during apoptosis. DFF becomes activated when DFFA is cleaved by caspase-3. The cleaved fragments of DFFA dissociate from DFFB, the active component of DFF. DFFB has been found to trigger both DNA fragmentation and chromatin condensation during apoptosis. Two alternatively spliced transcript variants encoding distinct isoforms have been found for this gene.
The C-terminal domain of DFFA (DFF-C) consists of four alpha-helices, which are folded in a helix-packing arrangement, with alpha-2 and alpha-3 packing against a long C-terminal helix (alpha-4). The main function of this domain is the inhibition of DFFB by binding to its C-terminal catalytic domain through ionic interactions, thereby inhibiting the fragmentation of DNA in the apoptotic process. In addition to blocking the DNase activity of DFFB, the C-terminal region of DFFA is also important for the DFFB-specific folding chaperone activity, as demonstrated by the ability of DFFA to refold DFFB.

# Interactions
DFFA has been shown to interact with DFFB.
DKK1
Dickkopf-related protein 1 is a protein that in humans is encoded by the DKK1 gene.

# Function
This gene encodes a protein that is a member of the dickkopf family. It is a secreted protein with two cysteine rich regions and is involved in embryonic development through its inhibition of the Wnt signaling pathway.  Dickkopf WNT signaling pathway inhibitor 1 (Dkk1) is a protein-coding gene that acts from the anterior visceral endoderm.  The dickkopf protein encoded by DKK1 is an antagonist of the Wnt/-catenin signalling pathway that acts by isolating the LRP6 co-receptor so that it cannot aid in activating the WNT signaling pathway. DKK1 was also demonstrated to antagonize the Wnt/-catenin pathway via a reduction in -catenin and an increase in OCT4 expression.
This inhibition plays a key role in heart, head and forelimb development during anterior morphogenesis of the embryo.

# Interactions
DKK1 has been shown to interact with LRP6 and is a high affinity ligand of Kremen proteins.

# Clinical significance
Elevated levels of DKK1 in bone marrow, plasma and peripheral blood is associated with the presence of osteolytic bone lesions in patients with multiple myeloma.

# Animal studies
Scientists have created a DKK1 knockout model in mice that revealed the effects of this gene.  All mice that were homozygous for the DKK1 knockout were dead at birth due to defects in the cranium and structures formed by the neural crest, such as failed development of eyes, olfactory placodes, frontonasal mass and mandibular processes, as well as incomplete development of the forebrain and midbrain and fusion of the digits of the forelimb. This evidence supports the idea that inhibition of the Wnt signaling pathway by DKK1 is crucial to proper cranial development.

# In vitro studies
DKK1 is one of the most upregulated genes in androgen-potentiated balding, with DKK-1 messenger RNA upregulated a few hours after DHT treatment of hair follicles at the dermal papilla in vitro. Neutralizing antibody against DKK-1 reversed DHT effects on outer root sheath keratinocytes. DKK-1 expression is attenuated by L-threonate in vitro, with the latter a metabolite of ascorbate.
DLCO

# Overview
DLCO stands for the Diffusing capacity of the Lung for Carbon Monoxide, the test used to determine this parameter. DLCO is the extent to which oxygen passes from the air sacs of the lungs into the blood. It was introduced in 1909.

# Mechanism of test
The DLCO Test
This test involves measuring the partial pressure difference between inspired and expired carbon monoxide. It relies on the strong affinity and large absorption capacity of erythrocytes for carbon monoxide and thus demonstrates gas uptake by the capillaries that is less dependent on cardiac output.

# Factors reducing DLCO
DLCO can be reduced by the following:
- Hindrance in the alveolar wall. e.g. fibrosis, alveolitis, vasculitis
- Decrease of total lung area, e.g. emphysema.
- Uneven spread of air in lungs, e.g. emphysema.
- Cardiac insufficiency
- Hemoglobin decrease in blood
- Pulmonary hypertension
Factors increasing dlco include polycythaemia and increased pulmonary blood volume as occurs in exercise.
DLG1
Discs large homolog 1 (DLG1), also known as synapse-associated protein 97 or SAP97, is a scaffold protein that in humans is encoded by the SAP97 gene.
SAP97 is a mammalian MAGUK-family member protein that is similar to the Drosophila protein Dlg1 (the protein is alternatively referred to as hDlg1, and the human gene is DLG1).  SAP97 is expressed throughout the body in epithelial cells.  In the brain it is involved in the trafficking of ionotropic receptors from the endoplasmic reticulum to the plasma membrane, and may be involved in the trafficking AMPAR during synaptic plasticity.

# Function
SAP97 is expressed throughout the body in epithelial cells, including the kidney and brain.  There is some evidence that SAP97 regulates cell-to-cell adhesion during cell death, and may interact with HPV.  In the brain, SAP97's function is involved in the trafficking of transmembrane receptors from the ER to the plasma membrane.
SAP97's function has been investigated by reducing its expression by knockout or increasing its expression heterologously.  Mice in which the SAP97 gene has been knocked out die perinatally, have a cleft palate, and deficiencies in renal function.  Overexpression of SAP97 in mammalian neurons leads to increased synaptic strength.

# Clinical significance
Mutations in DLG1 are associated to                 Crohn's Disease            .

# Structure
SAP97's protein structure consists of an alternatively-spliced n-terminal domain, three PDZ domains, an SH3 domain, hook domain, I3 domain, and finally an inactive guanylate kinase (GK) domain.  Each of these domains has specific interacting partners that help define SAP97's unique function.
The n-terminal of SAP97 can be alternatively spliced to contain a double-cysteine/palmitoylation site (-isoform), or an L27 domain (-isoform.  The L27 domain is involved in SAP97 oligomerization with other SAP97 molecules, CASK, and other L27-domain-containing proteins.  There is also a myosin VI binding site near n-terminal which may be involved in the internalization of AMPAR.
Each of SAP97's PDZ domains have different binding partners, including the AMPAR subunit GluR1 for the first PDZ domain, and neuroligin for the last.  SAP97's I3 domain is unique to SAP97 among the MAGUK family, and is known to regulate the post-synaptic localization of SAP97 and to bind the protein 4.1N.  The GK domain allows SAP97 to bind to GKAP/SAPAP-family proteins.