Persius/hicric huggingface dataset:
ADAMTS13
ADAMTS13 (a disintegrin and metalloproteinase with a thrombospondin type 1 motif, member 13)also known as von Willebrand factor-cleaving protease (VWFCP)is a zinc-containing metalloprotease enzyme that cleaves von Willebrand factor (vWf), a large protein involved in blood clotting. It is secreted in blood and degrades large vWf multimers, decreasing their activity.

# Genetics
The ADAMTS13 gene maps to the ninth chromosome (9q34).

# Discovery
Since 1982 it had been known that thrombotic thrombocytopenic purpura (TTP), one of the microangiopathic hemolytic anemias (see below), was characterized in its familial form by the presence in plasma of unusually large von Willebrand factor multimers (ULVWF).
In 1994, vWF was shown to be cleaved between a tyrosine at position 1605 and a methionine at 1606 by a plasma metalloprotease enzyme when it was exposed to high levels of shear stress. In 1996, two research groups independently further characterized this enzyme. In the next two years, the same two groups showed that the congenital deficiency of a vWF-cleaving protease was associated with formation of platelet microthrombi in the small blood vessels. In addition, they reported that IgG antibodies directed against this same enzyme caused TTP in a majority of non-familial cases.

# Proteomics
Genomically, ADAMTS13 shares many properties with the 19 member ADAMTS family, all of which are characterised by a protease domain (the part that performs the protein hydrolysis), an adjacent disintegrin domain and one or more thrombospondin domains. ADAMTS13 in fact has eight thrombospondin domains. It has no hydrophobic transmembrane domain, and hence it is not anchored in the cell membrane.

# Role in disease
Deficiency of ADAMTS13 was originally discovered in Upshaw Schulman Syndrome, the recurring familial form of thrombotic thrombocytopenic purpura. By that time it was already suspected that TTP occurred in the autoimmune form as well, owing to its response to plasmapheresis and characterisation of IgG inhibitors. Since the discovery of ADAMTS13, specific epitopes on its surface have been shown to be the target of inhibitory antibodies.
Low levels of ADAMTS13 are also associated with an increased risk of arterial thrombosis, including myocardial infarction and cerebrovascular disease.
Finally, since the link between aortic valve stenosis and angiodysplasia was proven to be due to high shear stress (Heyde's syndrome), it has been accepted that increased exposure of vWf to ADAMTS13 due to various reasons would predispose to bleeding by causing increased degradation of vWf. This phenomenon is characterised by a form of von Willebrand disease (type 2a).
ADAMTS17
ADAM metallopeptidase with thrombospondin type 1 motif, 17 is a protein that in humans is encoded by the ADAMTS17 gene.

# Function
This gene encodes a member of the ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) protein family. ADAMTS family members share several distinct protein modules, including a propeptide region, a metalloproteinase domain, a disintegrin-like domain, and a thrombospondin type 1 (TS) motif. Individual members of this family differ in the number of C-terminal TS motifs, and some have unique C-terminal domains. The protein encoded by this gene has a high sequence similarity to the protein encoded by ADAMTS19, another family member. The function of this protein has not been determined. .

# Clinical significance
Mutations in ADAMTS17 are associated with                 Weill-Marchesani syndrome            .
APOBEC3C
DNA dC->dU-editing enzyme APOBEC-3C is a protein that in humans is encoded by the APOBEC3C gene.
A3C belong to the A3 family of cytidine deaminases that act as restriction factors against diverse retroviruses. A3C was reported to inhibit simian immunodeficiency deficiency virus potently rather than HIV-1, in absence of viral infectivity factor, Vif. Enhancing A3C's catalytic activity had only a marginal effect on HIV-1 replication (in absence of Vif), the counteractive viral mechanism is unclear. A3C was also shown to inhibit other viruses.

# Function
This gene is a member of the cytidine deaminase gene family. It is one of seven related genes or pseudogenes found in a cluster thought to result from gene duplication, on chromosome 22. Members of the cluster encode proteins that are structurally and functionally related to the C to U RNA-editing cytidine deaminase APOBEC1. Conversely, A3 proteins enzymatically convert cytidine to uridine present in the single stranded DNA.

# Structure
The crystal structure of A3C suggests a putative HIV-1 vif binding region. A3C was found to inhibit LINE-1 elements by directly interacting with ORF1p proteins, in a deaminase-independent manner.
APOBEC3G
APOBEC3G is a human protein belonging to the APOBEC superfamily of proteinsthat interferes with the replication of HIV and other retroviruses. This family of proteins has been suggested to play an important role in innate anti-viral immunity.
APOBEC3G and other proteins in the same family are able to act as a cytidine deaminase, inducing numerous C to U mutations in the negative strand of the HIV DNA. This results in many inviable virions. HIV appears to have evolved the Vif gene in order to counteract this effect. Vif does not halt APOBEC activity: it only down-regulates it, perhaps increasing overall HIV success by elevating the mutation rate. It is also able to function as anti-viral protein when its active site has been mutated so it can no longer mutate retroviral DNA.
It was first identified in 2002 as a cellular factor able to restrict replication of HIV-1 lacking the viral accessory protein Vif.  Soon after, it was shown that APOBEC3G belonged to a family of proteins grouped together due to their homology with the cytidine deaminase APOBEC1.
ARHGAP25
Rho GTPase activating protein 25 is a protein that in humans is encoded by the ARHGAP25 gene. The gene is also known as KAIA0053. ARHGAP25 belongs to a family of Rho GTPase-modulating proteins that are implicated in actin remodeling, cell polarity, and cell migration.

# Model organisms
Model organisms have been used in the study of ARHGAP25 function. A conditional knockout mouse line, called Arhgap25tm1a(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-one tests were carried out on homozygous-mutant mice and one significant abnormality was observed: abnormal retina morphology and pigmentation.
ARHGAP29
ARHGAP29 is a gene located on chromosome 1p22 that encodes Rho GTPase activating protein (GAP) 29, a protein that mediates the cyclical regulation of small GTP binding proteins such as RhoA.

# Function
ARHGAP29 is expressed in the developing face and may act downstream of IRF6 in craniofacial development.

# Structure
ARHGAP29 contains four domains including a coiled-coil region known to interact with Rap2, a C1 domain, the Rho GTPase domain, and a small C-terminal region that interacts with PTPL1.

# Clinical Significance
The 1p22 locus containing ARHGAP29 was associated with nonsydromic cleft lip/palate by genome wide association and meta-analysis.  A follow-up study  identified rare coding variants including a nonsense and a frameshift variant in patients with nonsydromic cleft lip/palate. The finding of ARHGAP29's role in craniofacial development was discovered after the adjacent ABCA4 gene lacked functional or expression data to support it as the etiologic gene for nonsydromic cleft lip/palate even though SNPs in the ABCA4 gene were associated with cleft lip/palate.
ARHGAP31
The Rho GTPase activating protein 31 is encoded in humans by the ARHGAP31 gene. It is a Cdc42/Rac1 GTPase regulator.

# Function
ARHGAP31 encodes a GTPase-activating protein (GAP). A variety of cellular processes are regulated by Rho GTPases which cycle between an inactive form bound to GDP and an active form bound to GTP. This cycling between inactive and active forms is regulated by guanine nucleotide exchange factors and GAPs. The encoded protein is a GAP shown to regulate two GTPases involved in protein trafficking and cell growth.

# Clinical relevance
ARHGAP31 mutations result in a loss of available active Cdc42 and consequently disrupt actin cytoskeletal structures, causing syndromic cutis aplasia and limb anomalies.
ARHGEF11
Rho guanine nucleotide exchange factor 11 is a protein that in humans is encoded by the ARHGEF11 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 a complex with G proteins and stimulate Rho-dependent signals. A similar protein in rat interacts with glutamate transporter EAAT4 and modulates its glutamate transport activity. Expression of the rat protein induces the reorganization of the actin cytoskeleton and its overexpression induces the formation of membrane ruffling and filopodia. Two alternative transcripts encoding different isoforms have been described.

# Interactions
ARHGEF11 has been shown to interact with PLXNB3, PLXNB1, PLXNB2 and RHOA.
ARHGEF12
Rho guanine nucleotide exchange factor 12 is a protein that in humans is encoded by the ARHGEF12 gene.

# Function
Rho GTPases play a fundamental role in numerous cellular processes that are initiated by extracellular stimuli that work through G protein coupled receptor . The encoded protein may form a complex with G proteins and stimulate Rho-dependent signals.

# Clinical significance
This protein is observed to form myeloid/lymphoid fusion partner in acute myeloid leukemia.

# Interactions
ARHGEF12 has been shown to interact with:
- GNA12,
- GNA13,
- IGF1R,
- PLXNB1,
- RHOA, and
- TEC.
ATP6V0A2
V-type proton ATPase 116 kDa subunit a isoform 2 also known as V-ATPase 116 kDa isoform a2 is an enzyme that in humans is encoded by the ATP6V0A2 gene.

# Function
V-ATPase 116 kDa isoform a2 is a subunit of the vacuolar ATPase (v-ATPase), an heteromultimeric enzyme that is present in intracellular vesicles and in the plasma membrane of specialized cells, and which is essential for the acidification of diverse cellular components. V-ATPase consists of a membrane peripheral V(1) domain for ATP hydrolysis, and an integral membrane V(0) domain for proton translocation. The subunit encoded by this gene is a component of the V(0) domain.

# Clinical significance
Mutations in this gene are a cause of both cutis laxa type II and wrinkly skin syndrome.
ATP6V1B2
V-type proton ATPase subunit B, brain isoform is an enzyme that in humans is encoded by the ATP6V1B2 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, three B, and two G subunits, as well as a C, D, E, F, and H subunit. The V1 domain contains the ATP catalytic site. The protein encoded by this gene is one of two V1 domain B subunit isoforms and is the only B isoform highly expressed in osteoclasts.
In melanocytic cells ATP6V1B2 gene expression may be regulated by MITF.
ATP6V1C1
V-type proton ATPase subunit C 1 is an enzyme that in humans is encoded by the ATP6V1C1 gene.
This gene encodes a component of vacuolar ATPase (V-ATPase), a multisubunit enzyme that mediates acidification of intracellular compartments of eukaryotic cells. V-ATPase dependent 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 gene is one of two genes that encode the V1 domain C subunit proteins and is found ubiquitously. This C subunit is analogous but not homologous to gamma subunit of F-ATPases. Previously, this gene was designated ATP6D.
In melanocytic cells ATP6V1C1 gene expression may be regulated by MITF.
ATP6V1G2
V-type proton ATPase subunit G 2 is an enzyme that in humans is encoded by the ATP6V1G2 gene.
This gene encodes a component of vacuolar ATPase (V-ATPase), a multisubunit enzyme that mediates acidification of intracellular compartments of eukaryotic cells. V-ATPase dependent 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 double prime, 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 one of three V1 domain G subunit proteins. This gene had previous gene symbols of ATP6G and ATP6G2. Alternatively spliced transcript variants encoding different isoforms have been described.
Ataxin 3
Ataxin-3 is a protein that in humans is encoded by the ATXN3 gene.

# Clinical significance
Machado-Joseph disease, also known as spinocerebellar ataxia-3, is an autosomal dominant neurologic disorder. The protein encoded by the ATXN3 gene contains (CAG)n repeats in the coding region, and the expansion of these repeats from the normal 13-36 to 68-79 is the cause of Machado-Joseph disease. There is an inverse correlation between the age of onset and CAG repeat numbers. Alternatively spliced transcript variants encoding different isoforms have been described for this gene.

# Interactions
Ataxin 3 has been shown to interact with:
- RAD23A,
- RAD23B, and
- VCP.

# Model organisms
Model organisms have been used in the study of ATXN3 function. A conditional knockout mouse line called Atxn3tm1a(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
Acrolein

# Overview
In organic chemistry, the compound CH2=CH-CHO, more often called acrolein than the IUPAC name 2-propenal, is the simplest unsaturated aldehyde. It is produced widely but is most often immediately reacted with other products due to its instability and toxicity. It has a piercing, disagreeable, acrid smell similar to that of burning fat.

# Synthesis
Acrolein is prepared industrially by oxidation of propene. Efforts are underway to use propane as feedstock for the synthesis, however, this is more difficult.
Several million tonnes of acrolein are produced each year.
When glycerol is heated to 280 C, it decomposes into acrolein.
Acrolein may also be produced on lab scale by the reaction of approximately 1 part sodium bisulfate on 3 parts glycerine by weight.

# Uses
Acrolein is used in the preparation of polyester resin, polyurethane, propylene glycol, acrylic acid, acrylonitrile, and glycerol.
Acrolein tends to polymerize when left at room temperature, leaving a gummy yellowish residue with a putrid odor. It is also thought to be an intermediate in the Skraup synthesis of quinolines, but is rarely used as such due to its instability.

# Health risks
Acrolein is a severe pulmonary irritant and lacrimating agent. It has been used as a chemical weapon during World War I. It is, however, not outlawed by the Chemical Weapons Convention.
Acrolein is also a metabolite of the chemotherapy drug cyclophosphamide, and is associated with hemorrhagic cystitis.
Skin exposure to acrolein causes serious damage.  Acrolein concentrations of 2 ppm are immediately harmful.
Acrolein is a suspected human carcinogen.
 In October 2006, researchers found connections between acrolein in the smoke from tobacco cigarettes and the risk of lung cancer.

# Acrolein test
Acrolein test is a test for the presence of glycerin or fats. A sample is heated with potassium bisulfate, and acrolein is released if the test is positive. When a fat is heated strongly in the presence of a dehydrating agent such as KHSO4, the glycerol portion of the molecule is dehydrated to form the unsaturated aldehyde, acrolein (CH2=CH-CHO), which has the peculiar odor of burnt grease.
Actinide
The actinoid (according to IUPAC terminology) (previously actinide) series encompasses the 15 chemical elements that lie between actinium and lawrencium included on the periodic table, with atomic numbers 89 - 103.  The actinoid series derives its name from the first element in the series, actinium, and ultimately from the Greek  (aktis), "ray," reflecting the elements' radioactivity.
The actinoid series (An) is included in some definitions of the rare earth elements. IUPAC is currently recommending the name actinoid rather than actinide, as the suffix "-ide" generally indicates ions (moreover, from Latin, the suffix -ide means "sons of actinium", while -oid means "similar to actinium").  There are alternative arrangements of the periodic table that exclude actinium or lawrencium from appearing together with the other actinoids.
The actinoids  display less similarity in their chemical properties than the lanthanoid series (Ln), exhibiting a wider range of oxidation states, which initially led to confusion as to whether actinium, thorium, and uranium should be considered d-block elements. All actinoids are radioactive.
Only thorium and uranium occur naturally in the earth's crust in anything more than trace quantities. Neptunium and plutonium have been known to show up naturally in trace amounts in uranium ores as a result of decay or bombardment. The remaining actinides were discovered in nuclear fallout, or were synthesized in particle colliders. The latter half of the series possess exceedingly short  half-lives.
The actinoids are typically placed below the main body of the periodic table (below the lanthanoid series), in the manner of a footnote. The full-width version of the periodic table shows the position of the actinoids more clearly.
An organometallic compound of an actinoid is known as an organoactinoid.

# History of the actinoid series
From the earlier known chemical properties of actinium (89) up to uranium (92), indicating a relation to the transition metals, it was generally assumed that the transuraniums would have similar qualities. During his Manhattan Project research in 1944, Glenn T. Seaborg experienced unexpected difficulty isolating americium (95) and curium (96). He began wondering if these elements more properly belonged to a different series than the transition metals, which would explain why the expected chemical properties of the new elements were different. In 1945, he went against the advice of colleagues and proposed the most significant change to Mendeleev's periodic table to have been accepted universally by the scientific community: the actinide series.
In 1945, Seaborg published his actinide concept of heavy element electronic structure, predicting that the actinides would form a transition series analogous to the rare earth series of lanthanoid elements.
In 1961, Antoni Przybylski discovered a star that contained unusually high amounts of actinides.
AdaBoost
AdaBoost, short for Adaptive Boosting, is a machine learning algorithm, formulated by Yoav Freund and Robert Schapire. It is a meta-algorithm, and can be used in conjunction with many other learning algorithms to improve their performance. AdaBoost is adaptive in the sense that subsequent classifiers built are tweaked in favor of those instances misclassified by previous classifiers. AdaBoost is sensitive to noisy data and outliers. Otherwise, it is less susceptible to the overfitting problem than most learning algorithms.
AdaBoost calls a weak classifier repeatedly in a series of rounds  t = 1,\ldots,T. For each call a distribution of weights D_{t} is updated that indicates the importance of examples in the data set for the classification. On each round, the weights of each incorrectly classified example are increased (or alternative, the weights of each correctly classified example are decreased), so that the new classifier focuses more on those examples.

# The algorithm for the binary classification task
Given: (x_{1},y_{1}),\ldots,(x_{m},y_{m}) where x_{i} \in X,\, y_{i} \in Y = \{-1, +1\}
Initialise D_{1}(i) = \frac{1}{m}, i=1,\ldots,m.
For t = 1,\ldots,T:
- Find the classifier h_{t} : X \to \{-1,+1\} that minimizes the error with respect to the distribution D_{t}: h_{t} = \arg \min_{h_{j} \in \mathcal{H}} \epsilon_{j}, where  \epsilon_{j} = \sum_{i=1}^{m} D_{t}(i)
- Prerequisite: \epsilon_{t} , otherwise stop.
- Choose \alpha_{t} \in \mathbf{R}, typically \alpha_{t}=\frac{1}{2}\textrm{ln}\frac{1-\epsilon_{t}}{\epsilon_{t}} where \epsilon_{t} is the weighted error rate of classifier h_{t}.
- Update:
D_{t+1}(i) = \frac{ D_{t}(i) \, e^{- \alpha_{t} y_{i} h_{t}(x_{i})} }{ Z_{t} }
where Z_{t} is a normalization factor (chosen so that D_{t+1} will be a probability distribution, i.e. sum one over all x).
Output the final classifier:
H(x) = \textrm{sign}\left( \sum_{t=1}^{T} \alpha_{t}h_{t}(x)\right)
The equation to update the distribution D_{t} is constructed so that:
e^{- \alpha_{t} y_{i} h_{t}(x_{i})} \begin{cases} 1, & y(i) \ne h_{t}(x_{i}) \end{cases}
Thus, after selecting an optimal classifier h_{t} \, for the distribution D_{t} \,, the examples x_{i} \, that the classifier h_{t} \, identified correctly are weighted less and those that it identified incorrectly are weighted more.  Therefore, when the algorithm is testing the classifiers on the distribution D_{t+1} \,, it will select a classifier that better identifies those examples that the previous classifer missed.

# Statistical Understanding of Boosting
Boosting can be seen as minimization of a convex loss function over a convex set of functions.  Specifically, the loss being minimized is the exponential loss
and we are seeking a function
Agenesis
Agenesis is the medical term for the failure of an organ to develop during embryonic growth and development.

# Conditions
Many specific examples of agenesis are referred to by individual names, depending on the organ affected.
- Agenesis of the corpus callosum- failure of the Corpus callosum to develop.
- Renal agenesis- failure of one or both of the kidneys to develop.
- Phocomelia- failure of the arms or legs to develop, often caused by the drug thalidomide.
- Penile agenesis- failure of penis to develop.

# Alternate Definition
In theology and origins science, agenesis means to have no beginning or to have no creator.  To come into existence without the influence of an outside intelligence.
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