Persius/hicric huggingface dataset:
ARHGDIB
Rho GDP-dissociation inhibitor 2 is a protein that in humans is encoded by the ARHGDIB gene. Aliases of this gene include RhoGDI2, GDID4, Rho GDI 2, and others.

# Interactions
ARHGDIB has been shown to interact with VAV1 and Src.

# Gene family
RhoGDI2 (ARHGDIB) is part of a family of three members: RhoGDI1, RhoGDI2 (also known as RhoGDIB, D4-GDI or Ly-GDI) and RhoGDI3.  RhoGDI1 is expressed in many organs and is the best studied member of the family. RhoGDI2 was initially believed to be expressed specifically in blood forming cells, but has subsequently been found to be highly expressed in a variety of other cell types as well. RhoGDI3 is predominantly expressed in brain, lung, kidney, testis and pancreas, and is targeted to specific parts of the cell such as the Golgi where it may play a role in transport or proteins in cells.

# Disease involvement
Despite a high degree of sequence similarity, RhoGDI1 and RhoGDI2 are very different in their binding affinities for specific GTPases, and more importantly, in their roles in tumor formation and spread of tumor to other organs (the process of metastasis).  For example, RhoGDI2 functions as a suppressor of metastasis but not a tumor suppressor in bladder cancer cells, while RhoGDI1 is a ubiquitous suppressor of tumor growth in all sites so far examined in bladder cancer models), suggesting that their cellular functions must diverge to cause these differential effects.
While there are clear links between the alteration of RhoGDI2 protein levels and disease progression and/or metastasis in several types of cancer, the mechanistic underpinnings of the mode of RhoGDI2 action under carcinogenic cellular conditions are only now beginning to be understood.  Evidence demonstrates that RhoGDI2 inhibits the endothelin axis and crosstalk with macrophages within the micrometastatic microenvironment to inhibit metastatic outgrowth. As such, RhoGDI2 could prove important in the regulation of tumor dormancy. Targeting this axis with orally available endothelin receptor antagonists may prove efficacious in mimicking the inhibitory role of RhoGDI2 by preventing macrophage infiltration into the micrometastatic niche. Recent work has also determined that genetic and pharmacologic targeting of chemokine (C-C motif) ligand 2 (CCL2) also known as monocyte chemotactic protein-1 (MCP-1) or small inducible cytokine A2, its receptor CCR2 and pharmacologic ablation of macrophages can also phenocopy the effect of RhoGDI2 expression to prevent metastatic colonization of the lung67 and that RhoGDI2 is suppressor of versican, a protein that has been shown to promote cell migration and metastasis in several tumor models.
In contrast to its role as a metastasis suppressor in bladder cancer, in breast, RhoGDI2 expression has been reported to be upregulated in cancer and to promote invasion of breast cancer cells, while another report found a biphasic expression pattern of RhoGDI2 in breast cancer with decreased expression correlating with lymph node metastasis.
ARHGEF4
Rho guanine nucleotide exchange factor 4 is a protein that in humans is encoded by the ARHGEF4 gene.

# Function
Rho GTPases play a fundamental role in numerous cellular processes that are initiated by extracellular stimuli that work through G protein-coupled receptors. The encoded protein may form complex with G proteins and stimulate Rho-dependent signals. This protein is similar to rat collybistin protein. Alternative splicing of this gene generates two transcript variants that encode different isoforms. Also, there is possibility for the usage of multiple polyadenylation sites for this gene.

# Model organisms
Model organisms have been used in the study of ARHGEF4 function. A conditional knockout mouse line, called Arhgef4tm1a(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.
Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Twenty two tests were carried out on homozygous mutant mice and one significant abnormality was observed: males has atypical peripheral blood lymphocyte parameters, including a decreased B cell number and an increased granulocyte number.

# Interactions
ARHGEF4 has been shown to interact with APC.
ARL6IP4
ADP-ribosylation-like factor 6 interacting protein 4 (ARL6IP4), also called SRp25 is the gene product of the ARL6IP4 gene located on chromosome 12q24.31.It is 360 amino acids in length.It is expressed ubiquitously but only in G1/S phase of the cell cycle. The human and mouse mRNA of this protein have 77% homology.

# Structure
Two types of amino acid clusters have been observed, a serine cluster and a basic cluster.

# Function
The function of this protein is unknown.However, due to sequence homology of the protein with SR splicing factors it is widely believed that the protein is nuclear and may have a role in splicing regulation. The protein is also believed to be a mediator in the RAC1 signalling pathway.

# RNA editing
The pre-mRNA of the ARL6IP4 gene product is subject to RNA Editing.

## Type
A to I RNA editing is catalyzed by a family of adenosine deaminases acting on RNA (ADARs) that specifically recognize adenosines within double-stranded regions of pre-mRNAs and deaminate them to inosine.Inosines are recognised as guanosine by the cells translational machinery.There are three members of the ADAR family ADARs 1-3 with ADAR 1 and ADAR 2 being the only enzymatically active members.ADAR3 is thought to have a regulatory role in the brain.ADAR1 and ADAR 2 are widely expressed in tissues while ADAR 3 is restricted to the brain.The double stranded regions of RNA are formed by base-pairing between residues in the region close to  the editing site with residues usually in a neighboring intron but can be an exonic sequence.The region that base pairs with the editing region is known as an Editing Complementary Sequence(ECS)

## Location
Editing occurs at a K/R editing site within  amino acid position 225 of the final protein.Using RT-PCR and sequencing of 100 individual clones, 7% of isoform 3 of the protein  showed a G instead of an A at this position during sequencing. Other minor editing sites may be potentially present including some in the same exon as the major editing site.Like in the case of IGFBP7 pre-mRNA,editing is unusual as the RNA fold back structure is made up off exonic sequence only.

## Effects on protein structure
Editing at this site results in a codon changed from a Lysine to an Arginine.This occurs in a highly basic region of the protein.

## Effects on protein function
The function of the unedited protein is largely uncharacterised.Therefore, the effect of editing on the pre-mRNA on the proteins function is also unknown.The amino acid change is conservative and is unlikely to massively alter protein function. However,the editing site maybe important since  the amino acid being altered is a Lysine, which may be involved in the  regulation of protein expression. Lysines can be sites of post-translational modification and the conversion of Lysine to an Arginine could affect post translational modification.
ATG16L1
Autophagy-related protein 16-1 is a protein that in humans is encoded by the ATG16L1 gene.

# Function
Autophagy is the major intracellular degradation system delivering cytoplasmic components to lysosomes, and it accounts for degradation of most long-lived proteins and some organelles. Cytoplasmic constituents, including organelles, are sequestered into double-membraned autophagosomes, which subsequently fuse with lysosomes. ATG16L1 is a component of a large protein complex essential for autophagy.

# Clinical significance
Mutations in the ATG16L1 gene may be linked to Crohn's disease.
ATP6AP2
The renin receptor also known as ATPase H(+)-transporting lysosomal accessory protein 2, or the prorenin receptor, is a protein that in humans is encoded by the ATP6AP2 gene.

# Function
The renin receptor binds renin and prorenin. Binding of renin to this receptor induces the conversion of angiotensinogen to angiotensin I.
This protein is associated with adenosine triphosphatases (ATPases). Proton-translocating ATPases have fundamental roles in energy conservation, secondary active transport, acidification of intracellular compartments, and cellular pH homeostasis. There are three classes of ATPases- F, P, and V. The vacuolar (V-type) ATPases have a transmembrane proton-conducting sector and an extramembrane catalytic sector. This protein has been found associated with the transmembrane sector of the V-type ATPases.
ATP6V0B
V-type proton ATPase 21 kDa proteolipid subunit is an enzyme that in humans is encoded by the ATP6V0B gene.
This gene encodes a component of vacuolar ATPase (V-ATPase), a multisubunit enzyme that mediates acidification of eukaryotic intracellular organelles. V-ATPase dependent organelle acidification is necessary for such intracellular processes as protein sorting, zymogen activation, receptor-mediated endocytosis, and synaptic vesicle proton gradient generation. V-ATPase is composed of a cytosolic V1 domain and a transmembrane V0 domain. The V1 domain consists of three A and three B subunits, two G subunits, plus the C, D, E, F, and H subunits. The V1 domain contains the ATP catalytic site. The V0 domain consists of five different subunits: a, c, c', c'', and d.
Additional isoforms of many of the V1 and V0 subunit proteins are encoded by multiple genes, or alternatively spliced transcript variants. This encoded protein is part of the transmembrane V0 domain, and is the human counterpart of yeast VMA16. Two alternatively spliced transcript variants that encode different proteins have been found for this gene.
ATP6V1F
V-type proton ATPase subunit F is an enzyme that in humans is encoded by the ATP6V1F gene.
This gene encodes a component of vacuolar ATPase (V-ATPase), a multisubunit enzyme that mediates acidification of eukaryotic intracellular organelles. V-ATPase dependent organelle acidification is necessary for such intracellular processes as protein sorting, zymogen activation, receptor-mediated endocytosis, and synaptic vesicle proton gradient generation. V-ATPase is composed of a cytosolic V1 domain and a transmembrane V0 domain. The V1 domain consists of three A and three B subunits, two G subunits plus the C, D, E, F, and H subunits. The V1 domain contains the ATP catalytic site. The V0 domain consists of five different subunits: a, c, c', c", and d. Additional isoforms of many of the V1 and V0 subunit proteins are encoded by multiple genes or alternatively spliced transcript variants. This encoded protein is the V1 domain F subunit protein.
Subunit F is a 16 kDa protein that is required for the assembly and activity of V-ATPase, and has a potential role in the differential targeting and regulation of the enzyme for specific organelles. This subunit is not necessary for the rotation of the ATPase V1 rotor, but it does promote catalysis.
AVICINE

# Overview
AVICINE was developed by AVI BioPharma Inc. It is a cancer vaccine which was created to cause
an immune reaction to the tumor associated antigen, human chorionic gonadotropin (hCG).
This vaccine will be designed to work by actively stimulating immunization amongst tumor cells, or tumor associated antigens. These can be the keys to unlocking the cancer cells, making way for the therapeutic values of AVICINE.

# Research behind the drug
This particular vaccine is a synthesized formulation of peptides developed to create an unstable environment for the hCG-producing cancer cells. By joining them together with diphtheria toxoids, the AVICINE peptide formulation is able to cause a specific immune response to hCG which wont interfere with related glycoprotein hormones.

# Common elements between pregnancy and cancer
During pregnancy, women naturally generate the hCG hormone, leading scientists to believe it stimulates growth and protects the developing fetus from auto-immune attack, therefore making the pregnancy successful.  Cancer cells are believed to produce hCG for the same reasons.  In both Cancer and Pregnancy hCG :
- encourages rapid cell division
- musters development/reaction and tissue invasion
- promotes formation of blood vessels
- Allows tumor or fetus to cancel rejection by suppressing the immune system
An anti-hCG vaccine would result in an immune attack on tumor cells, as well as prevent them from benefiting from hCG production.

# Clinical Studies
AVICINE has been shown to be effective in blocking fertility, suggesting that it should also work in fighting cancer. These studies also note that the drug will help in patient survival.
AZD2171

# Overview
AZD2171 (tentative trade name Recentin) is a potent inhibitor of vascular endothelial growth factor (VEGF) receptor tyrosine kinases. It is being developed by AstraZeneca as a possible chemotherapeutic agent for oral administration.
As of 2007, it is undergoing Phase I clinical trials for the treatment of non-small cell lung cancer and colorectal cancer in adults, as well as tumors of the central nervous system in children.

# Further reading
- Wedge S, Kendrew J, Hennequin L;  et al. (2005). "AZD2171: a highly potent, orally bioavailable, vascular endothelial growth factor receptor-2 tyrosine kinase inhibitor for the treatment of cancer". Cancer Res. 65 (10): 4389400. PMID 15899831.CS1 maint: Explicit use of et al. (link) CS1 maint: Multiple names: authors list (link) .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}
Abscess

# Overview
Abscess is defined as collection of pus in a specific part of body. Abscess can form in any tissues secondary to initial inflammation or trauma. Skin is the most common site for abscess formation. Abscess may be classified based on pathogen. Pathogen is varied depending on abscess' location however, Staphylococcus aureus is the leading cause of abscesses. Secondary to local inflammation and cytokine release, polymorphonuclear cells (PMNs) are the first and the most important responding cells in abscess formation. Neutrophils, are responsible for phagocytosis. Once the pathogen is opsonized by complement system, it will be recognized by neutrophils and the phagocytosis process will begin. After phagocytosis the bactricidal process will begin by producing superoxide radicals and other reactive oxygen species (ROS). Conditions that may result in immunosuppresion, such as chronic steroid therapy, chemotherapy, diabetes, cancer, and AIDS are predisposing factors for abscess formation. Diagnosis is based on clinical features, laboratory, and imaging findings. Treatment depends on location and etiology and it is mostly drainage and antibiotics.

# Causes
Abscesses are caused by many different pathogens based on their anatomical location. The following table summarizes pathogenic causes of abscesses.

# Classification
Abscesses may be classified based on their location. These are listed below.

# Differential diagnosis
The following table summarizes differential diagnosis list for different abscesses.
Abdomen

# Overview
The abdomen is the part of the body that lies between the chest and the thigh and encloses the ureters, intestines, liver, anus, bladder, gallbladder, and reproductive system outside the breast. It is also called  the belly or venter. In humans, and in many other vertebrates, it is the region between the thorax and the pelvis (Separating the thoracic cavity and the abdominal cavity is the thoracic diaphragm). In fully developed insects, the abdomen is the third (or posterior) segment, after the head and thorax.

# Vertebrates
In vertebrates, the abdomen contains several organs:
- Part of the digestive system (gallbladder, liver, anus, appendix, rectum, and intestines),
- Part of the urinary system (ureters, bladder, urethra).
- The internal reproductive organs (ovaries, fallopian tubes, uterus, vulva, and vagina in women, testes, vas deferens, seminal vesicles, prostate, penis and urethra in men)
The abdomen also contains some of the largest and most easily accessible blood vessels in many animals, and is often used in medicine  experimentation for catheterisation.
For various reasons, the abdomen is often coloured differently from the rest of the body.  In animals with furry or hairy bodies, the abdomen is frequently hairless, or nearly so.
The abdomen is oval in shape and is the largest cavity in the body.  It can be broken down into the lower and upper extremity.  The lower extremity covers the inner surface of the bony pelvis.  The Levator ani and Coccygeus are located on either side
The diaphragm forms the upper extremity and acts as a dome over the abdomen extending to the upper border of the fifth rib. It is an element in the anterior chain.

# Invertebrates
The invertebrate abdomen is built up of a series of concave upper plates known as tergites and convex lower plates known as sternites, the whole being held together by a tough yet stretchable membrane.
The abdomen contains the insect's digestive tract and reproductive organs, it consists of eleven segments in most orders of insects though the eleventh segment is absent in the adult of most higher orders. The number of these segments does vary from species to species with the number of segments visible reduced to only seven in the common honeybee. In the Collembola (Springtails) the abdomen has only six segments.
Unlike other Arthropods, insects possess no legs on the abdomen in adult form, though the Protura do have rudimentary leg-like appendages on the first three abdominal segments, and Archaeognatha possess small, articulated "styli" which are sometimes considered to be rudimentary appendages. Many larval insects including the Lepidoptera and the Symphyta (Sawflies) have fleshy appendages called prolegs on their abdominal segments (as well as their more familiar thoracic legs), which allow them to grip onto the edges of plant leaves as they walk around.
Aboulia

# Overview
Aboulia or Abulia (from the Greek "", meaning "non-will"), in neurology, refers to a lack of will or initiative.  The patient is unable to act or make decisions independently. It may range in severity from subtle to overwhelming.

# Pathophysiology
Abulia may result from a variety of brain injuries which cause personality change, such as dementing illnesses, trauma, or intracerebral hemorrhage (stroke), especially stroke causing diffuse injury to the right hemisphere. Abulia has also been associated with amphetamine withdrawal.It may complicate rehabilitation when a stroke patient is uninterested in performing tasks like walking despite being capable of doing so. It should be differentiated from apraxia, when a brain injured patient has impairment in comprehending the movements necessary to perform a motor task despite not having any paralysis that prevents performing the task; that condition can also result in lack of initiation of activity.
Especially in patients with progressive dementia, it may affect feeding. Patients may continue to chew or hold food in their mouths for hours without swallowing it. The behavior may be most evident after these patients have eaten part of their meals and no longer have strong appetites. Caregivers can use sweet or salty flavored foods later in meals to provide interest and increase oral intake, but must always clear the mouth of food after each meal.

# Causes

## Common Causes
- Amphetamine withdrawal
- Dementia
- Intracerebral hemorrhage
- Traumatic brain injury

## Causes by Organ System

## Causes in Alphabetical Order
- Acute caudate vascular lesions
- Alzheimer's disease
- Amphetamine withdrawal
- Anterior cingulate circuit damage
- Capsular genu infarction
- CNS lupus
- Damage to the basal ganglia
- Dementia
- Depression
- Huntington's disease
- Hydrocephalus
- Intracerebral hemorrhage
- Multiple sclerosis
- Parkinson's disease
- Progressive supranuclear palsy
- Schizophrenia
- Traumatic brain injury
Aphonia

# Overview
Aphonia is the medical term for the inability to speak. It is considered more severe than dysphonia. A primary cause of aphonia is bilateral disruption of the recurrent laryngeal nerve, which supplies nearly all the muscles in the larynx. Damage to the nerve may be the result of surgery (e.g., thyroidectomy) or a tumor.
Aphonia means "no voice." In other words, a person with this disorder has "lost" his/her voice.

# Differentiating Aphonia from other Disorders
Functional (or psychogenic) aphonia is often seen in patients with underlying psychological problems. Laryngeal examination will show usually bowed vocal folds that fail to adduct to the midline during phonation. However, the vocal folds will adduct when the patient is asked to cough. Treatment should involve consultation and counseling with a speech pathologist and, if necessary, a psychologist.
In this case, the patient's history and the observed unilateral immobility rules out functional aphonia.

# Causes
There are many reasons why this may happen. Injuries seem to be the cause of aphonia rather frequently - minor injuries which affect the second and third dorsal area in such a manner that the lymph patches concerned with coordination become either atrophic or relatively nonfunctioning.
Basically, any injury or condition that prevents the vocal cords, the paired bands of muscle tissue positioned over the trachea, from coming together and vibrating will have the potential to make a person unable to speak. When a person prepares to speak, the vocal folds come together over the trachea and vibrate due to the airflow from the lungs. This mechanism produces the sound of the voice. If the vocal folds cannot meet together to vibrate, sound will not be produced.
Poor eliminations can bring about disturbances and sometimes are the primary cause of aphonia; this build-up of wastes within the bloodstream becomes a toxic force and makes it necessary for the body to achieve its own balance after a lapse of time. When this comes about, the throat and larynx area might be disassociated in function from the rest of the body, and the forces there bring about local inflammation in an effort to achieve balance. Fear also is often a concomitant and a contributor.

## Causes by Organ System

## Causes in Alphabetical Order

# Treatment of Aphonia
Therapy should first be aimed at correcting those conditions which might produce a disturbance in the centers of coordination between the three nervous systems. Then the overtaxed nerve forces of the body as a whole should be relieved, the incoordination which has been a factor in the disease process should be eliminated, and the forces of the body should be coordinated. The diet should be corrected and sufficient stimulus of a medicinal nature should be added to keep the body in a normal force. Some cases that are psychological - where the body is amenable to suggestion - would benefit by suggestive therapy. Attention should be paid to attitudes of mind and to ideals.

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