Persius/hicric huggingface dataset:
Torso

# Overview
Torso is an anatomical term for the central part of the many animal bodies (including that of the human) from which extend the neck and limbs.  It is sometimes referred to as the trunk. The torso includes the thorax and abdomen.

# Anatomy

## Major organs
Most critical organs are housed within the torso.  In the upper chest, the heart and lungs are protected by the rib cage, and the abdomen contains the majority of organs responsible for digestion: the  liver, which respectively produces bile necessary for digestion; the large and small intestines, which extract nutrients from food; the anus, from which fecal wastes are excreted; the rectum, which stores feces; the gallbladder, which stores and concentrates bile and produces chyme; the ureters, which passes urine to the bladder; the bladder, which stores urine; and the urethra, which excretes urine and passes sperm through the seminal vesicles. Finally, the pelvic region houses both the male and female reproductive organs.

## Major muscle groups
The torso also harbours many of the main muscle groups of the body, including the:
- pectoral muscles
- abdominal muscles
- lateral muscle

## Innervation
The organs and muscles etc. are innervated by various nerves, mainly originating from thoracic vertebral segments. For instance, the cutaneous innervation is provided by:
- Ventral cutaneous branches
- Lateral cutaneous branches
- Dorsal cutaneous branches
Troya
Troya is a brand of hand-made premium cigar owned by Lignum-2, Inc.. The brand was originally a Cuban brand, established in 1932, but the Cuban version is now offered only as an all-machine-made brand of only two vitolas.

# History and Background
This non-Cuban version of the Troya brand was introduced into the U. S. market in 1985. The original medium-bodied blend was discontinued in 2003 and was replaced with a mild blend in 2004.  The line was further extended in 2004 with the introduction of a full-bodied cigar, the Troya X-Tra.
Early 2007 saw the introduction of the Troya Clasico, a cigar blended and manufactured by Don Pepin Garcia at Tabacalera Cubana in Esteli, Nicaragua. Don Pepin had been called upon earlier to aid in the development of the blends for both of the other Troya lines, which were the result of the efforts of several people.

# Troya
This line is manufactured in the Dominican Republic.

## Description
This line comes in two ranges, one with a Cameroon wrapper and the other with a Connecticut wrapper. The Cameroon is a medium-bodied cigar, while the Connecticut is a mild to medium cigar.  The filler and binder in both are Dominican Piloto Cubano and Olor tobaccos. The cigars are presented in boxes of 24.

## Models/Vitolas

# Troya X-Tra
Formerly made in Esteli, Nicaragua, this line is now manufactured in the Dominican Republic at the same factory as the Troya line above.

## Description
Although now made in the Dominican Republic, this line is a Nicaraguan puro. The X-Tra is a medium to full-bodied cigar. The filler is Criollo leaves, and the binder and wrapper are Corojo 99 from the Jalapa valley of Nicaragua. The cigars are presented in boxes of 24.

## Models/Vitolas

# Troya Clasico
This line was introduced to the U. S. market in January of 2007 as a limited edition release. The cigar was blended by Don Pepin Garcia and is manufactured at Tabacalera Cubana in Esteli, Nicaragua.

## Description
This full-bodied cigar is a Nicaraguan puro using tobaccos grown in the Jalapa region of Nicaragua. The wrapper is a Corojo Oscuro and surround a binder and filler of Corojo and Criollo. It is offered in boxes of 20 cigars.

## Models/Vitolas

# Notes
-  Profile of Cuban Troya Perelman's Cyclopedia of Havana Cigars (online version).
-  Jump up to: 2.0 2.1 2.2 2.3 Pereleman, Richard B., comp. Perelman's Pocket Cyclopedia of Cigars, 2007 edn. Los Angeles: Perelman, Pioneer & Co., (2006), p. 500.
-  Press release, Lignum-2, Inc., March 2007.
-  Jump up to: 4.0 4.1 4.2 Tom Irwin, Marketing Manager, Lignum-2, Inc. In litt., 3/23/2007.
no:Troya
U2AF2
Splicing factor U2AF 65 kDa subunit is a protein that in humans is encoded by the U2AF2 gene.

# Function
U2 auxiliary factor (U2AF), composed of a large and a small subunit, is a non-snRNP protein required for the binding of U2 snRNP to the pre-mRNA branch site. This gene encodes the U2AF large subunit, which contains a sequence-specific RNA-binding region with 3 RNA recognition motifs and an Arg/Ser-rich domain necessary for splicing. The large subunit binds to the polypyrimidine tract of introns early during spliceosome assembly. Multiple alternatively spliced transcript variants have been detected for this gene, but the full-length natures of only two have been determined to date.
In humans and other tetrapods, it has been shown that without U2AF2, the splicing process is inhibited. However, in zebrafish and other teleosts the RNA splicing process can still occur on certain genes in the absence of U2AF2. This may be because 10% of genes have alternating TG and AC base pairs at the 3' splice site (3'ss) and 5' splice site (5'ss) respectively on each intron, which alters the secondary structure of the RNA and influences splicing.

# Interactions
U2AF2 has been shown to interact with:
- PUF60,
- SF1,
- SFRS11,
- SFRS2IP,
- SRPK2,
- U2 small nuclear RNA auxiliary factor 1  and
- WT1.
UBAP1
Ubiquitin-associated protein 1 is a protein that in humans is encoded by the UBAP1 gene.
This gene is a member of the UBA domain family, whose members include proteins having connections to ubiquitin and the ubiquitination pathway. The ubiquitin associated domain is thought to be a non-covalent ubiquitin binding domain consisting of a compact three helix bundle. This particular protein originates from a gene locus in a refined region on chromosome 9 undergoing loss of heterozygosity in nasopharyngeal carcinoma (NPC). Taking into account its cytogenetic location, this UBA domain family member is being studies as a putative target for mutation in nasopharyngeal carcinomas.

# Model organisms
Model organisms have been used in the study of UBAP1 function. A conditional knockout mouse line, called Ubap1tm1a(EUCOMM)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  at the Wellcome Trust Sanger Institute.
Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Twenty five tests were carried out and two phenotypes were reported. Fewer homozygous mutant embryos were identified during gestation than predicted, and none survived until weaning. The remaining tests were carried out on heterozygous mutant adult mice; no significant abnormalities were observed in these animals.
UBE1C
NEDD8-activating enzyme E1 catalytic subunit is a protein that in humans is encoded by the UBA3 gene.
The modification of proteins with ubiquitin is an important cellular mechanism for targeting abnormal or short-lived proteins for degradation. Ubiquitination involves at least three classes of enzymes: ubiquitin-activating enzymes, or E1s, ubiquitin-conjugating enzymes, or E2s, and ubiquitin-protein ligases, or E3s. This gene encodes a member of the E1 ubiquitin-activating enzyme family. The encoded enzyme associates with AppBp1, an amyloid beta precursor protein binding protein, to form a heterodimer, and then the enzyme complex activates NEDD8, a ubiquitin-like protein, which regulates cell division, signaling and embryogenesis. Multiple alternatively spliced transcript variants encoding distinct isoforms have been found for this gene.
This enzyme contains an E2 binding domain, which resembles ubiquitin, and recruits the catalytic core of the E2 enzyme UBE2M (Ubc12) in a similar manner to that in which ubiquitin interacts with ubiquitin binding domains.

# Interactions
UBE1C has been shown to interact with NEDD8, APPBP1 and UBE2M.
UBE2M
NEDD8-conjugating enzyme Ubc12 is a protein that in humans is encoded by the UBE2M gene.
The modification of proteins with ubiquitin is an important cellular mechanism for targeting abnormal or short-lived proteins for degradation. Ubiquitination involves at least three classes of enzymes: ubiquitin-activating enzymes, or E1s, ubiquitin-conjugating enzymes, or E2s, and ubiquitin-protein ligases, or E3s. This gene encodes a member of the E2 ubiquitin-conjugating enzyme family. The encoded protein is linked with a ubiquitin-like protein, NEDD8, which can be conjugated to cellular proteins, such as Cdc53/culin.

# Interactions
UBE2M has been shown to interact with NEDD8,  PRKAR1A and UBA3.
UBE3A
Ubiquitin-protein ligase E3A (UBE3A) also known as E6AP ubiquitin-protein ligase (E6AP) is an enzyme that in humans is encoded by the UBE3A gene. This enzyme is involved in targeting proteins for degradation within cells.
Protein degradation is a normal process that removes damaged or unnecessary proteins and helps maintain the normal functions of cells.
Ubiquitin protein ligase E3A attaches a small marker protein called ubiquitin to proteins that should be degraded. Cellular structures called proteasomes recognize and digest proteins tagged with ubiquitin.
Both copies of the UBE3A gene are active in most of the body's tissues. In most neurons, however, only the copy inherited from a person's mother (the maternal copy) is normally active; this is known as paternal imprinting. Recent evidence shows that at least some glial cells and neurons may exhibit biallelic expression of UBE3A. Further work is thus needed to delineate a complete map of UBE3A imprinting in humans and model organisms such as mice. 
Silencing of Ube3a on the paternal allele is thought to occur through the Ube3a-ATS part of a lincRNA called "LNCAT", (Large Non-Coding Antisense Transcript).
The UBE3A gene is located on the long (q) arm of chromosome 15 between positions 11 and 13, from base pair 23,133,488 to base pair 23,235,220.

# Clinical significance
Mutations within the UBE3A gene are responsible for some cases of Angelman syndrome and Prader-Willi syndrome. Most of these mutations result in an abnormally short, nonfunctional version of ubiquitin protein ligase E3A. Because the copy of the gene inherited from a person's father (the paternal copy) is normally inactive in the brain, a mutation in the remaining maternal copy prevents any of the enzyme from being produced in the brain. This loss of enzyme function likely causes the characteristic features of these two conditions.
The UBE3A gene lies within the human chromosomal region 15q11-13.  Other abnormalities in this region of chromosome 15 can also cause Angelman syndrome.  These chromosomal changes include deletions, rearrangements (translocations) of genetic material, and other abnormalities. Like mutations within the gene, these chromosomal changes prevent any functional ubiquitin protein ligase E3A from being produced in the brain.

# Interactions
UBE3A has been shown to interact with:
- BLK,
- Lck,
- MCM7,
- MECP2,
- Progesterone receptor,
- TSC2,
- UBE2D1,
- UBE2D2,
- UBE2L3,
- UBQLN1,  and
- UBQLN2.
UBXD5
UBX domain-containing protein 11 is a protein that in humans is encoded by the UBXN11 gene.

# Function
This gene encodes a protein with a divergent C-terminal UBX domain. The homologous protein in the rat interacts with members of the Rnd subfamily of Rho GTPases at the cell periphery through its C-terminal region. It also interacts with several heterotrimeric G proteins through their G-alpha subunits and promotes Rho GTPase activation. It is proposed to serve a bidirectional role in the promotion and inhibition of Rho activity through upstream signaling pathways. The 3' coding sequence of this gene contains a polymoprhic region of 24 nt tandem repeats. Several transcripts containing between 1.5 and five repeat units have been reported. Multiple transcript variants encoding different isoforms have been found for this gene.

# Interactions
UBXD5 has been shown to interact with Rnd1, Rnd2 and Rnd3.
UHMK1
U2AF homology motif (UHM) kinase 1, also known as UHMK1, is a protein which in humans is encoded by the UHMK1 gene.

# Function
UHMK1 is a kinase enzyme which phosphorylates the protein stathmin and has an RNA recognition motif of unknown function.

# Clinical significance
UHMK1 is highly expressed in the brain and has been genetically implicated in schizophrenia in two genetic studies.   Mice with the gene encoding stathmin knocked out, so that they do not express this protein in the brain, show abnormal fear responses. This effect could be developed as an animal model for schizophrenia.  UHMK1 also phosphorylates the CNS proteins myelin basic protein (MBP) and synapsin I so that genetic abnormalities in UHMK1 could contribute to the genetic cause of schizophrenia through several different brain pathways.
UHRF1
Ubiquitin-like, containing PHD and RING finger domains, 1, also known as UHRF1, is a protein which in humans is encoded by the UHRF1 gene.

# Function
This gene encodes a member of a subfamily of RING-finger type E3 ubiquitin ligases. The protein binds to hemi-methylated DNA during S-phase and recruits the main DNA methyltransferase gene, DNMT1, to regulate chromatin structure and gene expression. Its expression peaks at late G1 phase and continues during G2 and M phases of the cell cycle. It plays a major role in the G1/S transition, and functions in the p53-dependent DNA damage checkpoint. Multiple transcript variants encoding different isoforms have been found for this gene. It was originally identified as a direct regulator of topoisomerase 2a, but this has subsequently been disproven.  Uhrf1 has been extensively studied in vivo using zebrafish.

# Clinical significance
UHRF1 has recently been identified as a novel oncogene in hepatocellular carcinoma, the primary type of liver cancer.
UQCC2
Ubiquinol-cytochrome c reductase complex assembly factor 2 is a protein that in humans is encoded by the UQCC2 gene. Located in the mitochondrial nucleoid, this protein is a complex III assembly factor, playing a role in cytochrome b biogenesis along with the UQCC1 protein. It regulates insulin secretion and mitochondrial ATP production and oxygen consumption. In the sole recorded case, a mutation in the UQCC2 gene caused Complex III deficiency, characterized by intrauterine growth retardation, neonatal lactic acidosis, and renal tubular dysfunction.

# Structure
The UQCC2 gene is located on the p arm of chromosome 6 in position 21.31 and spans 14,990 base pairs. The gene produces a  14.9 kDa protein composed of 126 amino acids. This protein has no homologous domains with other known proteins. It is associated with the mitochondrial nucleoid, likely located in the peripheral region. This protein's distribution pattern is similar to other components of the mitochondrial nucleoid, like mtSSB and PHB1/PHB2.

# Function
This gene encodes a nucleoid protein localized to the mitochondrial inner membrane and sublocalized to the mitochondrial matrix. The encoded protein permissively regulates insulin secretion in pancreatic beta cells, positively regulates mitochondrial ATP production and oxygen consumption, and is involved in late skeletal muscle differentiation through modulation of mitochondrial respiratory chain activity. This protein is required for the assembly of the Complex III. Expression of this protein is decreased in cells with low mtDNA.

# Clinical Significance
In the sole recorded case, a homozygous mutation in intron 2 of the UQCC2 gene caused a splicing disruption; the patient presented with symptoms of nuclear type 7 Complex III deficiency, including neonatal lactic acidosis, renal tubulopathy, and severe intrauterine growth retardation. Additional clinical features included a dysmorphic facial appearance, delayed psychomotor development, autistic features, aggressive behavior, and mild sensorineural hearing loss. Additionally, the patient had decreased levels of UQCC1.

# Interactions
This protein interacts with UQCC1.
UQCRQ
Ubiquinol-cytochrome c reductase, complex III subunit VII, 9.5kDa is a protein that in humans is encoded by the UQCRQ gene. This ubiqinone-binding protein is a subunit of mitochondrial Complex III in the electron transport chain. A mutation in the UQCRQ gene has been shown to cause severe neurological disorders. Infection by Trypanosoma cruzi can cause oxidative modification of this protein in cardiac muscle tissue.

# Structure
The UQCRQ gene is located on the q arm of chromosome 5 in position 31.1 and spans 2,217 base pairs. The gene produces a  9.9 kDa protein composed of 82 amino acids. This protein is transmembranous, with more mass on the matrix side of the membrane.

# Function
This gene encodes a ubiquinone-binding protein of low molecular mass. It is a small core-associated protein and a subunit of ubiquinol-cytochrome c reductase complex III, which is part of the mitochondrial respiratory chain.

# Clinical significance
Variants of UQCRQ have been associated with complex III deficiency. One set of twenty consanguineous cases of a Ser45Phe mutation in the UQCRQ gene, and a different homozygous 4-bp deletion at p.338-341, have been linked to this disease. In an inbred Israeli Bedouin family, the mutations, inherited in an autosomal recessive pattern, displayed the phenotype of mitochondrial Complex III deficiency, nuclear type 4, accompanied by severe neurological symptoms. Other symptoms of complex III deficiency linked to these mutations have included hypoglycemia, lactic acidosis, and hypotonia.
In another study of cardiac muscle tissue in individuals infected by Trypanosoma cruzi, an oxidative modification of the UQCRQ subunit was present, along with oxidative modification of subunits UQCRC1 and UQCRC2 of the same core complex and UQCRH and CYC1 of the neighboring subcomplex.

# Interactions
The protein encoded by UQCRQ has protein-protein interactions with UQCRC1, OPTN, ERCC8, GRINL1A, Dctn1, K8.1, XRCC3, PML, RAB7A, HNRNPA1L2, CDC73, NLRP3, HAUS2, TMEM248, and GOLT1B.
USP11
Ubiquitin carboxyl-terminal hydrolase or Ubiquitin specific protease 11 is an enzyme that in humans is encoded by the USP11 gene. USP11 belongs to the Ubiquitin specific proteases family (USPs) which is a sub-family of the Deubiquitinating enzymes (DUBs).USPs are multiple domain proteases and belong to the C19 cysteine proteases subfamily. Depending on their domain architecture and position there is different homology between the various members. Generally the largest domain is the catalytic domain which harbours the three residue catalytic triad that is included inside conserved motifs (Cys and His boxes). The catalytic domain also contains sequences that are not related with the catalysis function and their role is mostly not clearly understood at present, the length of these sequences varies for each USP and therefore the length of the whole catalytic domain can range from approximately 295 to 850 amino acids. Particular sequences inside the catalytic domain or at the Nterminus of some USPs have been characterised as UBL (Ubiquitin like) and DUSP (domain present in ubiquitinspecific proteases) domains respectively. In some cases, regarding the UBL domains, it has been reported to have a catalysis enhancing function as in the case of USP7. In addition, a socalled DU domain module is the combination of a DUSP domain followed by a UBL domain separated by a linker and is found in USP11 as well as in USP15 and USP4.
USP11 is 963aa protein with a MW of approximately 109.8 kDa and a pI of ~5.28; it shares significant homology with USP15 and along with USP4 forms the DU subfamily. Nevertheless, alignment of the three USPs confirms that USP15 and USP4 are the closest homologues with the identity reaching ~73 % between their UBL1 domains whereas USP11 is the most distant member with an identity of only ~32.3 % when compared to USP15. An UBL2 domain insertion (285aa) is present within the catalytic domain, which encompasses amino acids 310931, and the catalytic triad consists of a cysteine, a histidine and an aspartic acid.

# Function
Protein ubiquitination controls many intracellular processes, including cell cycle progression, transcriptional activation, and signal transduction. This dynamic process, involving ubiquitin conjugating enzymes and deubiquitinating enzymes, adds and removes ubiquitin. Deubiquitinating enzymes are cysteine proteases that specifically cleave ubiquitin from ubiquitin-conjugated protein substrates. This gene encodes a deubiquitinating enzyme which lies in a gene cluster on chromosome Xp11.23

# Interactions
USP11 has been shown to interact with RANBP9.

# Model organisms
Model organisms have been used in the study of USP11 function. A conditional knockout mouse line called Usp11tm1(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
USP48
Ubiquitin carboxyl-terminal hydrolase 48 is an enzyme that in humans is encoded by the USP48 gene.
This gene encodes a protein containing domains that associate it with the peptidase family C19, also known as family 2 of ubiquitin carboxyl-terminal hydrolases. Family members function as deubiquitinating enzymes, recognizing and hydrolyzing the peptide bond at the C-terminal glycine of ubiquitin. Enzymes in peptidase family C19 are involved in the processing of poly-ubiquitin precursors as well as that of ubiquitinated proteins. Alternate transcriptional splice variants, encoding different isoforms, have been characterized.
In melanocytic cells USP48 gene expression may be regulated by MITF.
USP53
Inactive ubiquitin carboxyl-terminal hydrolase 53 is a protein that in humans is encoded by the USP53 gene.
Although USP53 is classified as a deubiquitinating enzyme based on sequence homology to other proteases from this group, it lacks a functionally essential histydine in the catalytic domaine and activity assays suggest that USP53 is catalytically inactive.
 Even though USP53 is devoid of catalytic activity, USP53 serves important physiological functions:
mutations in Usp53 have been shown to cause progressive hearing loss in mice, as well as late-onset hearing loss and cholestasis in humans.
USP53 localizes at cellular tight junctions and interacts with tight junction protein 2 (TJP2). Mutations in TJP2 have also been shown to cause hearing impairments  and cholestasis.
USP9X
Probable ubiquitin carboxyl-terminal hydrolase FAF-X is an enzyme that in humans is encoded by the USP9X gene.

# Function
This gene is a member of the peptidase C19 family and encodes a protein that is similar to ubiquitin-specific proteases. Though this gene is located on the X chromosome, it escapes X-inactivation.
Depletion of USP9X from two-cell mouse embryos halts blastocyst development and results in slower blastomere cleavage rate, impaired cell adhesion and a loss of cell polarity. It has also been implicated that USP9X is likely to influence developmental processes through signaling pathways of Notch, Wnt, EGF, and mTOR. USP9X has been recognized in studies of mouse and human stem cells involving embryonic, neural and hematopoietic stem cells. High expression is retained in undifferentiated progenitor and stem cells and decreases as differentiation continues. USP9X is a protein-coding gene that has been implicated either directly through mutations or indirectly in a number of neurodevelopmental and neurodegenerative disorders. Three mutations have been connected with X-linked intellectual disability and disrupt neuronal growth and cell migration. Neurodegenerative disorders, such as Alzheimer's, Parkinson's and Huntington's disease, have also been linked to USP9X. Specifically, USP9X has been implicated in the regulation of the phosphorylation and expression of the microtule-associated protein tau, which forms pathological aggregates in Alzheimer's and other tauopathies. Scientists have generated a knockout model where they isolated hippocampal neurons from an USP9X-knockout male mouse, which showed a 43% reduction in axonal length and aborization compared to wildtype.

# Interactions
USP9X has been shown to interact with:
- Beta-catenin,
- MARK4,
- MLLT4, and
- NUAK1.
- ERG.
- CEP131