nirantk/geneticsQA-train huggingface dataset:
Question: What is the inheritance pattern of Li–Fraumeni syndrome?

Context:
It therefore appears that the LFS phenotype has been conferred by an aberrant gene, showing a dominant pattern of inheritance, which may be acting to compromise normal p53 function rather than by a mutation in p53 itself.
In addition, there seem to be predispositions to a wider range of different, but well-defined neoplasms: e.g., adenocarcinomatosis of the colon and the endometrium, or the Li-Fraumeni/SBLA syndrome. The latter shows a spectrum of sarcoma, brain tumours, breast cancer, leukaemias, lung and adenocortical cancer. The genes leading to these types of dominantly inherited predispositions appear to be the tentatively so-called tumour suppressor genes, for which the Rb gene serves as a model
he Li-Fraumeni syndrome is a rare autosomal-dominant disease whose hallmark is a predisposition to a wide range of cancers among members of a family.
Li-Fraumeni Syndrome (LFS) is characterized by early-onset carcinogenesis involving multiple tumor types and shows autosomal dominant inheritance.
BACKGROUND: Li-Fraumeni-Syndrome (LFS) is an autosomal-dominant, inherited tumour predisposition syndrome associated with heterozygous germline mutations in the TP53 gene.
Li-Fraumeni syndrome (LFS) is a highly penetrant, autosomal dominant, human familial cancer predisposition
The Li-Fraumeni syndrome is a rare autosomal-dominant disease whose hallmark is a predisposition to a wide range of cancers among members of a family

Answer: Li-Fraumeni syndrome shows autosomal dominant inheritance.
Exact answer: Autosomal dominant
Question: Has the protein SETMAR (Metnase) a transposase domain?

Context:
Metnase (SETMAR) is a SET-transposase fusion protein that promotes nonhomologous end joining (NHEJ) repair in humans.
The transposase domain protein Metnase/SETMAR suppresses chromosomal translocations.
 Metnase (also termed SETMAR) is a fusion of a histone methylase and transposase protein that arose specifically in primates. 
the only intact Hsmar1 transposase gene exists within a chimeric SET-transposase fusion protein referred to as Metnase or SETMAR. 
The Metnase transposase has been remarkably conserved through evolution;
Metnase (also known as SETMAR) is a SET and transposase fusion protein in humans and plays a positive role in double-strand break (DSB) repair. While the SET domain possesses histone lysine methyltransferase activity, the transposase domain is responsible for 5'-terminal inverted repeat (TIR)-specific binding, DNA looping, and DNA cleavage activities. 
Metnase is a fusion gene comprising a SET histone methyl transferase domain and a transposase domain derived from the Mariner transposase.
ulated by the DNA repair component Metnase (also termed SETMAR). Metnase contains a SET histone methylase and transposase nuclease domain
Metnase is a human SET and transposase domain protein 
The human set and transposase domain protein Metnase
 of transposase-related sequences in humans are pseudogenes. We recently isolated and characterized a SET and transposase domain protein termed Metnase that promotes DNA double-strand break (DSB) repair by non-homologous end-joining (NHEJ). Both the SET and transposase domain were required for its NHEJ activity.
Metnase, also known as SETMAR, is a SET and transposase fusion protein with an undefined role in mammalian DNA repair.
Biochemical characterization of a SET and transposase fusion protein, Metnase: i
Metnase (SETMAR) is a SET and transposase fusion protein that promotes in vivo end joining activity and mediates genomic integration of foreign DNA. 
 This transposase coding region is part of the SETMAR gene, in which a histone methylatransferase SET domain is fused to an Hsmar1 transposase domain. 
The human SETMAR protein preserves most of the activities of the ancestral Hsmar1 transposase.
ere we investigate the activity of the human SETMAR protein, a highly expressed fusion between a histone H3 methylase and a mariner family transposase.
SETMAR, a new primate chimeric gene resulting from fusion of a SET histone methyltransferase gene to the transposase gene of a mobile element.
We identified a protein, termed Metnase, that has a SET domain and a transposase/nuclease domain. 
Metnase has a nuclease domain that shares homology with the Transposase family.
Metnase (also called SETMAR) is a SET and transposase domain protein that promotes both DNA double-strand break (DSB) repair and restart of stalled replication forks. 

Answer: Yes, the protein SETMAR (Metnase) has a transposase domain.
Exact answer: yes
Question: What is the mechanism of action of abiraterone?

Context:
The recognition of sustained androgen dependence of CRPC has led to the identification of more potent and selective inhibitors of androgen synthesis and androgen-receptor signaling, such as abiraterone and enzalutamide, respectively.
This review summarizes the rationale, mechanism of action and relevant clinical data of abiraterone acetate , an oral androgen biosynthesis inhibitor, in the management of CRPC.
Sipuleucel-T, an immunotherapeutic vaccine, is now available in the US for patients with non-metastatic CRPC and abiraterone, an oral enzyme inhibitor of androgen biosynthesis, as well as cabazitaxel, a cytotoxic chemotherapeutic, have been approved for the treatment of metastatic CRPC.
Abiraterone (17-(3-pyridyl)androsta-5,16-dien-3beta-ol, 1) is a potent inhibitor (IC50 4 nM for hydroxylase) of human cytochrome P45017alpha.

Answer: Abiraterone acts by inhibiting cytochrome P450 17α-hydroxylase (CYP17A1), a critical step in androgen biosynthesis, thus leading to inhibition of androgen biosynthesis.
Question: Is there evidence to suggest that triiodothyronine has neuroprotective properties in traumatic brain injury?

Context:
Exogenous T3 administration provides neuroprotection in a murine model of traumatic brain injury.
Treatment with T3 (1.2μg/100g body weight, i.p.) 1h after TBI resulted in a significant improvement in motor and cognitive recovery after CCI, as well as in marked reduction of lesion volumes. 
Western blot analysis revealed the ability of T3 to reduce brain trauma through modulation of cytoplasmic-nuclear shuttling of nuclear factor-κB (NF-κB). Twenty-four hours after brain trauma, T3-treated mice also showed significantly lower number of TUNEL(+) apoptotic neurons and curtailed induction of Bax, compared to vehicle control. In addition, T3 significantly enhanced the post-TBI expression of the neuroprotective neurotrophins (BDNF and GDNF) compared to vehicle. 
The stimulating effect of T3 on peripheral nerve regeneration may have considerable therapeutic potential.
The present study provides evidence that the peripheral nervous system has its own system responsible for the local production of 3,5,3'-triiodothyronine, which may play a key role during the regeneration process.
Although it has been hypothesized that T3 may facilitate neuronal regeneration after CNS injury, the 5'-D2 response to brain injury is unknown.
The outcome after brain injury is closely correlated with the intensity of these changes, particularly with catecholamine plasma levels and the severity of the low triiodothyronine syndrome.
The thyroid hormones triiodothyronine (T3) and L-thyroxine appear to enhance regeneration in the peripheral and central nervous system (CNS). 
T3 treatment influenced the general levels of incorporation of all treated groups over all days postoperation.
T3 effects appear to involve an increased sensitivity of the cells of the injured nervous system to the hormone.
T3, when administered over an 8 week period, stimulated axonal regeneration in the dorsal cortex and corpus callosum and promoted healing of the wound in the corpus callosum. The results of this investigation suggest that the use of T3 in the clinical treatment of injury to the central nervous system may be of less value than the work of earlier authors had indicated.
In addition, T3 significantly enhanced the post-TBI expression of the neuroprotective neurotrophins (BDNF and GDNF) compared to vehicle

Answer: Yes, it has been demonstrated that triiodothyronine exerts neuroprotective properties in traumatic brain injury setting.
Exact answer: yes
Question: What is the Arnold-Chiari syndrome?

Context:
Arnold Chiari syndrome is a condition characterized by herniation of the cerebellar tonsils through the foramen magnum.
The Arnold-Chiari malformation is very rare hindbrain abnormalities characterized by herniation of the hindbrain through the foramen magnum.
The origin of Arnold-Chiari syndrome is connected with narrowness in the posterior fossa, particularly with narrowing of the arachnoid spaces.
Arnold-Chiari Syndrome I is a malformation of the cervicomedullary junction, manifesting usually with downbeat nystagmus, palsy of the caudal cerebral nerves, headache, and vertigo.

Answer: Arnold Chiari syndrome is a condition characterized by herniation of the cerebellar tonsils through the foramen magnum, manifesting usually with downbeat nystagmus, palsy of the caudal cerebral nerves, headache, and vertigo.
Question: List sclerostin interaction partners.

Context:
 Several previously unidentified full-length sclerostin-interacting proteins such as alkaline phosphatase, carbonic anhydrase, gremlin-1, fetuin A, midkine, annexin A1 and A2, and collagen α1, which have established roles in bone formation or resorption processes, were bound to the sclerostin-MBP amylose resin but not to the MBP amylose resin. Other full-length sclerostin-interacting proteins such as casein kinase II and secreted frizzled related protein 4 that modulate Wnt signaling were identified. Several peptides derived from proteins such as Phex, asporin and follistatin that regulate bone metabolism also bound sclerostin. 
We identified an interaction between sclerostin and the carboxyl-terminal portion of the receptor tyrosine-protein kinase erbB-3.
Sclerostin, SOST, the gene affected in this disease, has been postulated to exert its activity by functioning as a BMP antagonist. However, recent evidence indicates that SOST is highly related to Wise, which can also modulate the Wnt pathway by binding to LRP5 and LRP6.
Bone density ligand, Sclerostin, directly interacts with LRP5 but not LRP5G171V to modulate Wnt activity.
We show that recombinant sclerostin and noggin bound to each other with high affinity (K(D) = 2.92 nm).

Answer: alkaline phosphatase
carbonic anhydrase
gremlin-1
fetuin A
midkine
annexin A1 
annexin A2
collagen α1
casein kinase II 
secreted frizzled related protein 4
Phex
asporin
follistatin
erbB-3
LRP5 
noggin
Exact answer: alkaline phosphatase, carbonic anhydrase, gremlin-1, fetuin A, midkine, annexin A1, annexin A2, collagen α1, casein kinase II, secreted frizzled related protein 4, Phex, asporin, follistatin, erbB-3, LRP5, noggin
Question: Is  farnesoid X receptor (FXR) a nuclear receptor?

Context:
Farnesoid X receptor (FXR) belongs to the ligand-activated nuclear receptor superfamily, and functions as a transcription factor regulating the transcription of numerous genes involved in bile acid homeostasis, lipoprotein and glucose metabolism
 Farnesoid X receptor (FXR) is an ascending target for metabolic and inflammatory diseases. As a nuclear receptor, FXR exhibits many physiological effects in transcription control of several genes.
 FXR is a member of the nuclear receptor superfamily which is also highly expressed in the liver. 
Farnesoid X receptor (FXR) is a bile acid nuclear receptor described through mouse knockout studies as a tumor suppressor for the development of colon adenocarcinomas
Farnesoid X receptor (FXR, Nr1h4) is a ligand-activated transcription factor belonging to the nuclear receptor superfamily.
the nuclear receptor farnesoid X receptor 
 farnesoid X receptor (FXR), a nuclear receptor activated by bile acid ligands. 
T-β-MCA is an farnesoid X receptor (FXR) nuclear receptor antagonist,
 Farnesoid X receptor (FXR), a nuclear receptor (NR) and originally considered as a bile acid-activated transcriptional factor, 
 The nuclear receptor farnesoid X receptor (FXR) plays a major role in the enterohepatic cycling of bile acids
Liver X receptors, LXRs, are ligand-activated transcription factors that belong to the group H nuclear receptor (NR) superfamily. 
The intracellular nuclear receptor farnesoid X receptor and the transmembrane G protein-coupled receptor TGR5 respond to bile acids by activating transcriptional networks and/or signalling cascades.
ncluding those of nuclear receptors, primarily farnesoid X receptor (FXR), 
ile acids and their cognate nuclear receptor, FXR,
Farnesoid X receptor (FXR, Nr1h4) and small heterodimer partner (SHP, Nr0b2) are nuclear receptors that are critical to liver homeostasis.
he activation of the nuclear receptor farnesoid X receptor (FXRα)
bile acid-activated nuclear receptor farnesoid X receptor (FXR)
 nuclear receptor signaling, notably by the farnesoid X receptor (FXR
FXR (farnesoid X receptor, NRIH4), a nuclear receptor, plays a major role in the control of cholesterol metabolism.
The role of the nuclear receptor FXR is unclear.
nuclear receptor FXR 
a member of the nuclear receptor superfamily of ligand-activated transcription factors,
Farnesoid X receptor (FXR) is a nuclear receptor that functions as a bile acid sensor controlling bile acid homeostasis.

Answer: Yes, farnesoid X receptor (FXR) is a nuclear receptor.
Exact answer: yes
Question: How many periods of regulatory innovation led to the evolution of vertebrates?

Context:
Three periods of regulatory innovation during vertebrate evolution.
To investigate the gain of regulatory elements throughout vertebrate evolution, we identified genome-wide sets of putative regulatory regions for five vertebrates, including humans. These putative regulatory regions are conserved nonexonic elements (CNEEs), which are evolutionarily conserved yet do not overlap any coding or noncoding mature transcript. We then inferred the branch on which each CNEE came under selective constraint. Our analysis identified three extended periods in the evolution of gene regulatory elements. Early vertebrate evolution was characterized by regulatory gains near transcription factors and developmental genes, but this trend was replaced by innovations near extracellular signaling genes, and then innovations near posttranslational protein modifiers.
Early vertebrate evolution was characterized by regulatory gains near transcription factors and developmental genes, but this trend was replaced by innovations near extracellular signaling genes, and then innovations near posttranslational protein modifiers.
Our analysis identified three extended periods in the evolution of gene regulatory elements. 
Our analysis identified three extended periods in the evolution of gene regulatory elements. Early vertebrate evolution was characterized by regulatory gains near transcription factors and developmental genes, but this trend was replaced by innovations near extracellular signaling genes, and then innovations near posttranslational protein modifiers.
Our analysis identified three extended periods in the evolution of gene regulatory elements. Early vertebrate evolution was characterized by regulatory gains near transcription factors and developmental genes, but this trend was replaced by innovations near extracellular signaling genes, and then innovations near posttranslational protein modifiers.
We then inferred the branch on which each CNEE came under selective constraint. Our analysis identified three extended periods in the evolution of gene regulatory elements.
Our analysis identified three extended periods in the evolution of gene regulatory elements.
Early vertebrate evolution was characterized by regulatory gains near transcription factors and developmental genes, but this trend was replaced by innovations near extracellular signaling genes, and then innovations near posttranslational protein modifiers.

Answer: Investigators proposed that there have been three extended periods in the evolution of gene regulatory elements. Early vertebrate evolution was characterized by regulatory gains near transcription factors and developmental genes, but this trend was replaced by innovations near extracellular signaling genes, and then innovations near posttranslational protein modifiers.
Exact answer: Three
Question: Are there any Decision support systems for chronic pain management ?

Context:
a project to operationalize the 2003 VA/DOD Clinical Practice Guideline for Opioid Therapy for Chronic Non-Cancer Pain into a computerized decision support system (DSS)
We based the DSS on the existing ATHENA-DSS
Use of this iterative process led to development of a multifunctional DSS
interactive decision dashboard format
We created a computerized, interactive clinical decision dashboard 
Interactive decision dashboards can be adapted for clinical use and have the potential to foster informed decision making.
Clinical decision support systems are promising tools for improving behavioral medicine care for chronic pain.
Improving Patient Safety Using ATHENA-Decision Support System Technology: 
ATHENA-DSS is an automated decision support system developed in a collaboration between Stanford University and the U.S. Department of Veterans Affairs (VA) to increase guideline-adherent prescribing and to change physician behavior.
The use of a computer-based decision support system facilitates primary care physicians' management of chronic pain.
The use of a CBDS system may improve the ability of PCPs to manage chronic pain and may also facilitate screening of consults to optimize specialist utilization.

Answer: Yes, there is a variety of decision support systems for chronic pain management.
Clinical decision support systems are promising tools for improving behavioral medicine care for chronic pain.The use of a computer-based decision support system facilitates primary care physicians' management of chronic pain.
Exact answer: yes
Question: From which tissue was the NCI-H520 cell-line derived?

Context:
The nanostructures target the cells with high affinity and specificity via the specific interaction between the aptamer (a 45-base oligonucleotide) and the cell, and distinguish A549 cells from other types of cancer cells (HeLa and MCF-7 cells) and subtypes of lung cancer cells (NCI-H157, NCI-H520, NCI-H1299, and NCI-H446 cells). 
Functional studies in A549 bronchioalveolar carcinoma and NCI-H520 squamous cell carcinoma cells revealed that Msi1 was enriched in spheroid cultures of tumor cells and in the CD133+ cell population. 
BHLHB3 gene overexpression inhibited colony formation of A549, NCI-H520 and NCI-H596 lung cancer cells. 
Cellular proliferation was inhibited in non-small cell lung cancer (NSCLC) cell lines NCI-H460, NCI-H520, NCI-H1299, and SK-MES-1 by CTGF overexpression.
Human NCI-H520 cancer cells transfected with PDCD5 cDNA showed decreased colony-forming ability. 
In 4 lung cancer cell strains, BNIP3L protein was not detected in A549, NCI-H460, NCI-H446, except for NCI-H520, in which the protein expression level was slightly lower than that in immortal bronchial epithelial cell strain HBE4-E6/E7.
We show that CLN3 mRNA and protein are overexpressed in glioblastoma (U-373G and T98g), neuroblastoma (IMR-32 and SK-N-MC), prostate (Du145, PC-3, and LNCaP), ovarian (SK-OV-3, SW626, and PA-1), breast (BT-20, BT-549, and BT-474), and colon (SW1116, SW480, and HCT 116) cancer cell lines but not in pancreatic (CAPAN and As-PC-1) or lung (A-549 and NCI-H520) cancer cell lines.
NSCLC cell lines NCI-H520 and H460, which have no endogenous Cyr61, formed 60-90% fewer colonies after being transfected with a Cyr61 cDNA expression vector than cells transfected with the same amount of empty vector.
Importantly, the non-small cell lung carcinoma cell lines expressed either liver-specific (non-neuronal) mRNA (cell line A549) or predominantly the neuronal (cell line NCI-H520) AADC message. 
The antitumor effect of CGP41251 (4'-N-benzoyl staurosporine), a selective protein kinase C (PKC) inhibitor, was examined on two kinds of human non-small cell lung cancer (NSCLC) cell lines (adenocarcinoma: A549 and squamous cell carcinoma: NCI-H520).

Answer: Non-small cell lung cancer (NSCLC) cell line NCI-H520. 
Squamous cell carcinoma cell line NCI-H520.
The NCI-H520 cell-line is derived from human non-small cell lung cancer tissue.
Exact answer: Squamous cell carcinoma, Non-small cell lung cancer, Lung
Question: List Parkin binding partners

Context:
In addition to two known binding partners (HSP90, CDC37), 12 proteins were identified using the TAP assay; four of which are mitochondrially localized (GRP75, HSP60, LRPPRC, and TUFM).
We find that parkin binds PICK1 via a PDZ-mediated interaction, which predominantly promotes PICK1 monoubiquitination rather than polyubiquitination. 
We have identified the 20S proteasomal subunit alpha4 (synonyms: PSMA7, XAPC7, subunit alpha type 7) as a new interacting partner of parkin.
we cloned parkin-binding protein using a yeast two-hybrid system and identified a putative G protein-coupled receptor protein,which we named the Pael receptor (Pael-R)
, whose interactions with CASK are reviewed here, include the Parkinson's disease molecule parkin, 

Answer: HSP90
CDC37
GRP75
HSP60
LRPPRC
TUFM
PICK1
PSMA7
Pael receptor
Exact answer: HSP90, CDC37, GRP75, HSP60, LRPPRC, TUFM, PICK1, PSMA7, XAPC7, Pael receptor