nirantk/geneticsQA-train huggingface dataset:
Question: Describe what is the usage of the Theatre software tool for genomic analysis.

Context:
Theatre is a web-based computing system designed for the comparative analysis of genomic sequences, especially with respect to motifs likely to be involved in the regulation of gene expression. Theatre is an interface to commonly used sequence analysis tools and biological sequence databases to determine or predict the positions of coding regions, repetitive sequences and transcription factor binding sites in families of DNA sequences. The information is displayed in a manner that can be easily understood and can reveal patterns that might not otherwise have been noticed. In addition to web-based output, Theatre can produce publication quality colour hardcopies showing predicted features in aligned genomic sequences.
Theatre: A software tool for detailed comparative analysis and visualization of genomic sequence.
Theatre is a web-based computing system designed for the comparative analysis of genomic sequences, especially with respect to motifs likely to be involved in the regulation of gene expression. Theatre is an interface to commonly used sequence analysis tools and biological sequence databases to determine or predict the positions of coding regions, repetitive sequences and transcription factor binding sites in families of DNA sequences. 

Answer: Theatre is a web-based computing system designed for the comparative analysis of genomic sequences, especially with respect to motifs likely to be involved in the regulation of gene expression. Theatre is an interface to commonly used sequence analysis tools and biological sequence databases to determine or predict the positions of coding regions, repetitive sequences and transcription factor binding sites in families of DNA sequences. The information is displayed in a manner that can be easily understood and can reveal patterns that might not otherwise have been noticed. In addition to web-based output, Theatre can produce publication quality colour hardcopies showing predicted features in aligned genomic sequences.
Theatre is a web-based computing system designed for the comparative analysis of genomic sequences, especially with respect to motifs likely to be involved in the regulation of gene expression. The information is displayed in a manner that can be easily understood and can reveal patterns that might not otherwise have been noticed. Theatre can be accessed at http://www.hgmp.mrc.ac.uk/Registered/Webapp/theatre/.
Question: What are the symptoms of Rotor syndrome?

Context:
The mechanistic basis of bilirubin excretion and hyperbilirubinemia syndromes is largely understood, but that of Rotor syndrome, an autosomal recessive disorder characterized by conjugated hyperbilirubinemia, coproporphyrinuria, and near-absent hepatic uptake of anionic diagnostics, has remained enigmatic. 
[A case with Rotor syndrome in hyperbilirubinemic family].
Hyperbilirubinemia syndromes (Gilbert-Meulengracht, Crigler-Najjar, Dubin-Johnson, and Rotor syndrome)
Rotor syndrome is a rare, benign familial disorder characterized by chronic fluctuating, nonhemolytic and predominantly conjugated hyperbilirubinemia with normal hepatic histology
Jaundice is often the first and sometimes the only symptom of liver disease. Besides in parenchymal liver disease jaundice is also observed in chronic non-haemolytic hyperbilirubinemias (Crigler-Najjar type I and II, Gilbert's syndrome) and in hereditary conjugated hyperbilirubinaemias (Dubin-Johnson- and Rotor-syndrome).
 Rotor syndrome is a rare, benign familial disorder characterized by chronic fluctuating, nonhemolytic and predominantly conjugated hyperbilirubinemia with normal hepatic histology. In contrast to Dubin-Johnson syndrome, there is no liver pigmentation in Rotor syndrome.
The mechanistic basis of bilirubin excretion and hyperbilirubinemia syndromes is largely understood, but that of Rotor syndrome, an autosomal recessive disorder characterized by conjugated hyperbilirubinemia, coproporphyrinuria, and near-absent hepatic uptake of anionic diagnostics, has remained enigmatic. Here, we analyzed 8 Rotor-syndrome families and found that Rotor syndrome was linked to mutations predicted to cause complete and simultaneous deficiencies of the organic anion transporting polypeptides OATP1B1 and OATP1B3.
The mechanistic basis of bilirubin excretion and hyperbilirubinemia syndromes is largely understood, but that of Rotor syndrome, an autosomal recessive disorder characterized by conjugated hyperbilirubinemia, coproporphyrinuria, and near-absent hepatic uptake of anionic diagnostics, has remained enigmatic. Here, we analyzed 8 Rotor-syndrome families and found that Rotor syndrome was linked to mutations predicted to cause complete and simultaneous deficiencies of the organic anion transporting polypeptides OATP1B1 and OATP1B3.
Hyperbilirubinemia syndromes (Gilbert-Meulengracht, Crigler-Najjar, Dubin-Johnson, and Rotor syndrome).
Hyperbilirubinemia syndromes (Gilbert-Meulengracht, Crigler-Najjar, Dubin-Johnson, and Rotor syndrome).
[A case with Rotor syndrome in hyperbilirubinemic family].

Answer: Rotor syndrome is characterized by conjugated hyperbilirubinemia, coproporphyrinuria, and near-absent hepatic uptake of anionic diagnostics.
Exact answer: conjugated hyperbilirubinemia, coproporphyrinuria, near-absent hepatic uptake of anionic diagnostics
Question: Have Quantitative Trait Loci affecting splicing (splicing QTLs) been linked to disease?

Context:

Answer: Yes, mutations in the DNA that affect the splicing pattern of genes have been linked in transcriptome population studies to a number of diseases.
Exact answer: yes
Question: Which is the substrate of the haspin kinase during mitosis?

Context:
aspin phosphorylates histone H3 at Thr3 (H3T3ph) during mitosis
protein kinase Haspin-mediated spreading of H3T3ph 
Haspin localizes predominantly to chromosomes and phosphorylates histone H3 at threonine-3 during mitosis
haspin/Gsg2 plays an important role in mitosis, where it specifically phosphorylates Thr-3 in histone H3 (H3T3
aspin/Gsg2 is a kinase that phosphorylates histone H3 at Thr-3 (H3T3ph) during mitosis.
H3T3 phosphorylation is catalyzed by Haspin
aspin is an atypical protein kinase that in several organisms phosphorylates histone H3Thr3
histone H3 that is phosphorylated at T3 (H3T3ph) by Aurora B-stimulated Haspin.
phosphorylating Thr3 of histone H3, Haspin promotes centromeric recruitment of the chromosome passenger complex (CPC) during mitosis.
aspin phosphorylates histone H3 at threonine-3 (H3T3ph),
Haspin-dependent histone H3 phosphorylatio
aspin is a serine/threonine kinase that phosphorylates Thr-3 of histone H3 in mitosis
Haspin is a protein kinase the only known target of which is phosphorylation of histone H3 at Thr3 residue (H3T3ph)
Haspin in vitro phosphorylates histone H3 at threonine 3
Haspin is a histone H3 Thr3 kinase that has important roles in chromosome cohesion during mitosis
phosphorylation of histone H3 threonine 3 (H3-pT3) mediated by Haspin
histone H3 specifically when it is phosphorylated at threonine 3, a mark that is placed by the mitotic kinase, haspin
H3T3 kinase haspin
phosphorylation of histone H3-threonine 3 (H3-pT3) mediated by Haspin
kinase activity of Haspin, which phosphorylates H3T3,
istone H3 Thr-3 phosphorylation by Haspin
phosphorylation of histone H3 threonine 3 (H3T3ph) by Haspin
Haspin/Gsg2 is a histone H3 threonine-3 kinase
During mitosis haspin is phosphorylated, associates with the chromosomes, centrosomes and spindle, and is responsible for phosphorylation of histone H3 at threonine-3
haspin, a member of a distinctive group of protein kinases present in diverse eukaryotes, phosphorylates H3 at Thr 3
Haspin phosphorylated histone H3 at both Thr3 and Thr11 in vitro.
Haspin kinase is a histone H3 threonine kinase
Haspin phosphorylated histone H3 at both Thr3 and Thr11 in vitro

Answer: Haspin phosphorylates histone H3 at Thr3 (H3T3ph) during mitosis
Exact answer: Histone 3 at Thr3
Question: What is the mechanism of action of Nalmefene?

Context:
Opioids that stimulate the μ-opioid receptor (MOR1) are the most frequently prescribed and effective analgesics. Here we present a structural model of MOR1. Molecular dynamics simulations show a ligand-dependent increase in the conformational flexibility of the third intracellular loop that couples with the G protein complex. These simulations likewise identified residues that form frequent contacts with ligands. We validated the binding residues using site-directed mutagenesis coupled with radioligand binding and functional assays. The model was used to blindly screen a library of ∼1.2 million compounds. From the 34 compounds predicted to be strong binders, the top three candidates were examined using biochemical assays. One compound showed high efficacy and potency. Post hoc testing revealed this compound to be nalmefene, a potent clinically used antagonist, thus further validating the model. 
The neurobiological mechanism by which opioid modulators affect drinking behavior is based on the strong connection between the endogenous opioid system, the dopamine system and the influence of the CNS stress response.
Naltrexone- and to a lesser extent nalmefene- is an agent that modulates opioidergic transmission in the CNS and it shows a limited but well-studied efficacy in treating alcohol dependence. 
Several derivatives of Naltrexone, Nalmefene (Nal) and JKB-119, exert immunomodulatory activity; however, unlike Nal, JKB-119 does not show significant opioid receptor antagonism. 

Answer: Nalmefene shows opioid receptor antagonism, binds the μ-opioid receptor (MOR1) and modulates opioidergic transmission in the CNS.
Question: Which DNA repair system is involved in HNPCC?

Context:
The HNPCC syndrome (hereditary non polyposis colon cancer) or Lynch syndrome stands for an autosomic dominant condition leading to the most prevalent hereditary colo-rectal cancers (CCR). MMR (mismatch repair)'s genes are involved in carcinogenesis as they play a role in ADNA mismatch repair.
Mutations in the genes of the mismatch DNA repair system and of the TGF-beta-II-receptor, the main defects of the HNPCC (hereditary nonpolyposis colorectal cancer), are exclusively identified in sequences of microsatellites. 
In HNPCC families, germline mutations in any of four genes encoding proteins of a specialized DNA repair system, the mismatch repair, predispose to cancer development. 

Answer: In HNPCC families, germline mutations in any of four genes encoding proteins of a specialized DNA repair system, the mismatch repair, predispose to cancer development.
Exact answer: In HNPCC, the mismatch DNA repair system is involved.
Question: Which are the most frequent syndromes associated with inherited bone marrow failure?

Context:
Ocular and orbital manifestations of the inherited bone marrow failure syndromes: Fanconi anemia and dyskeratosis congenita
The inherited bone marrow failure syndromes (IBMFS) are a heterogeneous group of genetic disorders that share the inability of the bone marrow to produce an adequate number of blood cells. The 4 most frequent syndromes are Fanconi anemia (FA), dyskeratosis congenita (DC), Diamond-Blackfan anemia (DBA), and Shwachman-Diamond syndrome (SDS)
The major inherited bone marrow failure syndromes associated with development of pancytopenia include Fanconi anemia, dyskeratosis congenita, Shwachman-Diamond syndrome, and amegakaryocytic thrombocytopenia.
The major inherited bone marrow failure syndromes associated with development of pancytopenia include Fanconi anemia, dyskeratosis congenita, Shwachman-Diamond syndrome, and amegakaryocytic thrombocytopenia

Answer: The inherited bone marrow failure syndromes (IBMFS) are a heterogeneous group of genetic disorders that share the inability of the bone marrow to produce an adequate number of blood cells. The 4 most frequent syndromes are Fanconi anemia (FA), dyskeratosis congenita (DC), Diamond-Blackfan anemia (DBA), and Shwachman-Diamond syndrome (SDS)  
The inherited bone marrow failure syndromes (IBMFS) are a heterogeneous group of genetic disorders that share the inability of the bone marrow to produce an adequate number of blood cells. The 4 most frequent syndromes are Fanconi anemia (FA), dyskeratosis congenita (DC), Diamond-Blackfan anemia (DBA), and Shwachman-Diamond syndrome (SDS).
Exact answer: Fanconi anemia, Dyskeratosis congenita, Diamond-Blackfan anemia, Shwachman-Diamond syndrome
Question: Is nucleosome eviction ATP-dependent?

Context:
ATP-dependent chromatin remodeling and nucleosome-depleted 'barriers' co-operate to determine the kinetics of nucleosome organization
ATP-dependent nucleosome-remodeling factors endow chromatin with structural flexibility by promoting assembly or disruption of nucleosomes and the exchange of histone variants.
remodeling takes place in an ATP-independent manner. Binding of distamycin to the linker and nucleosomal DNA culminates in eviction of the linker histone and the formation of a population of off-centered nucleosomes.
which promotes histone deposition onto DNA, and a novel activity, which prevents nucleosome eviction but not remodeling mediated by the ATP-dependent RSC complex
ATP-dependent chromatin remodeling complex SWI/SNF regulates transcription and has been implicated in promoter nucleosome eviction
ATP-dependent nucleosome-remodeling enzyme involved in transcription, replication, and the DNA damage response
Iec1-Ino80 complex promotes transcription through nucleosome eviction
Ino80 complex from fission yeast mediates ATP-dependent nucleosome remodeling in vitro
reconstitution of nucleosome disassembly using the ATP-dependent chromatin remodeler Rsc and Vps75 revealed that these proteins can cooperate to remove H2A/H2B dimers from nucleosomes.
TP-dependent chromatin-remodeling complexes, such as RSC, can reposition, evict or restructure nucleosome
TP-dependent chromatin remodeling complexes play a critical role in chromatin dynamics
 activity of SWI/SNF to histone eviction in trans from gene promoters.

Answer: Yes, nucleosome eviction and chromatin remodelling depends on ATP
Exact answer: yes
Question: What role do Kupffer cells play in innate immunity and inflammation?

Context:
Kupffer cells (KCs) play a role in the development of drug induced liver injury (DILI).
Hepatic macrophages consist of Kupffer cells, which are originated from the fetal yolk-sack, and infiltrated bone marrow-derived monocytes/macrophages. 
Kupffer cells (KCs) are the main source of MMP.
liver, both Kupffer cells and recruited hepatic macrophages can contribute to decreased hepatic insulin sensitivity.
Macrophages such as Kupffer cells in the liver are multifunctional cells.
Kupffer cells--the resident macrophages of the liver--are able to release a tremendous array of mediators upon inflammatory conditions, such as infection, and their role in innate immunity is well described in the literature.
Kupffer cells are the tissue macrophages in the liver and play an important role in the defense mechanisms of the body

Answer: Kupffer cells are able to release a tremendous array of mediators upon inflammatory conditions, such as infection, and their role in innate immunity is well described in the literature.
Question: Is factor XI deficient in Hemophilia C?

Context:
Factor XI deficiency is a rare hematologic disorder. Hemophilia C (factor XI deficiency) affects both genders and it is usually asymptomatic,
Congenital factor XI deficiency (also known as the Rosenthal syndrome or hemophilia C)
rare case of an acute cerebral aneurysm rupture in a patient with a known factor XI deficiency. Aneurysmal subarachnoid hemorrhage (SAH) accounts for a high mortality and morbidity rate. When SAH is associated with an inherited coagulation disorder such as hemophilia C
Factor XI deficiency (Hemophilia C)
Factor XI deficiency, also called hemophilia C,

Answer: Factor XI deficiency is associated with a bleeding tendency called Hemophilia C.
Exact answer: yes
Question: Which mushroom is poisonous, Amanita phalloides or Agaricus Bisporus

Context:
Seventeen edible mushrooms commercially available in Korea were analysed for their umami taste compounds (5'-nucleotides: AMP, GMP, IMP, UMP, XMP; free amino acids: aspartic, glutamic acid) and subjected to human sensory evaluation and electronic tongue measurements. Amanita virgineoides featured the highest total 5'-nucleotide content (36.9 ± 1.50 mg/g), while monosodium glutamate-like components (42.4 ± 6.90 mg/g) were highest in Agaricus
liver transplantation improves patients' short-term post liver transplantation survival in Amanita phalloides poisoning

Answer: The well-known cultivated species Agaricus bisporus is safe to eat while Amanita Phalloides is poisonous.
Exact answer: Amanita phalloides
Question: List mouse models for autism spectrum disorder (ASD).

Context:
maternal immune activation (MIA) mouse model that is known to display features of ASD.
BTBR T+tf/J (BTBR), a model of ASD with cognitive deficits,
C58/J mouse strain, a model of ASD core symptoms. 
the C58/J mouse model of autism
Both C58/J and Grin1 knockdown mice, another model of ASD-like behavior, 
Mice injected subcutaneously with 600 mg/kg valproic acid (VPA600) at gestational day 12.5 show reduced social interaction in adulthood (at 8 weeks of age), and they have been proposed as a mouse model of autism.
BTBR T+tf/J (BTBR), a commonly-used model presenting all core autism-related phenotypes 
The Autism ProSAP1/Shank2 mouse model 
Shank3-deficient mice
a panel of Shank mutant mouse models
maternal immune activation (MIA) mouse model of gestational poly(IC) exposure 
poly(IC) mouse model of autism spectrum disorders
BTBR T+ tf/J strain, a mouse model of autism.
The inbred BTBR T+ tf/J (BTBR) strain, a putative mouse model of autism,
C57BL/6J strain
SYNGAP1 mouse model of ID/ASD
Tsc2f/-;Cre mice demonstrated increased repetitive behavior as assessed with marble burying activity
BTBR T+ tf/J mouse model for autism spectrum disorders
Furthermore, maternal infection (maternal immune activation, MIA) is a risk factor for ASD.
NR1(neo-/-) mice
mice heterozygous for the Gabrb3 gene
Gestational immune activation and Tsc2 haploinsufficiency
novel transgenic mouse, MALTT,
sing a mouse model, CD38, a transmembrane protein expressed in immune cells but also in brain, was found to be critical for social behavior via regulation of oxytocin secretion. 
fmr1 knockout mouse model
TS2-neo mouse
Congenic Tbx1 heterozygous (HT) mice 
the valproic acid (VPA) mouse model of autism
 indicates that the MeCP2+/- model may be useful for preclinical development targeting specific cortical processing abnormalities in RTT with potential relevance to ASD.
(Dp(11)17/+) 
BTBR T+tf/J (BTBR) inbred mice are frequently used as a model of autism spectrum disorders (ASD)
Intact and impaired executive abilities in the BTBR mouse model of autism.

Answer: Numerous mouse models exists for autism spectrum disorder, such as: BTBR T+tf/J (BTBR), maternal immune, activation (MIA) mouse model of gestational poly(IC) exposure, C58/J and ProSAP1/Shank2.
Exact answer: maternal immune activation (MIA) mouse model of gestational poly(IC) exposure
C58/J
Grin1
Shank3-deficient mice
C57BL/6J
SYNGAP1
Tsc2f/-
MALTT
(Dp(11)17/+)
NR1(neo-/-)
TS2-neo mouse
Tbx1 heterozygous (HT) mice
BTBR T+tf/J (BTBR)
VPA600
ProSAP1/Shank2
Question: Is TREM2 associated with Alzheimer's disease in humans?

Context:
Genetic deficits and loss of function for the triggering receptor expressed in myeloid cells 2 (TREM2; encoded at chr6p21.1), a transmembrane spanning stimulatory receptor of the immunoglobulin/lectin-like gene superfamily, have been associated with deficiencies in phagocytosis and the innate immune system in Alzheimer's disease.
Recent works have demonstrated a rare functional variant (R47H) in triggering receptor expressed on myeloid cells (TREM) 2 gene, encoding TREM2 protein, increase susceptibility to late-onset Alzheimer's disease (AD),
possible involvement of TREM2 in AD pathogenesis.
TREM2 is associated with the risk of Alzheimer's disease in Spanish population.
Two recent studies have reported the association of rs75932628-T in the TREM2 gene with the risk for Alzheimer's disease (AD).
we report the first positive replication study in a Spanish population and confirm that TREM2 rs75932628-T is associated with the risk for AD.
(TREM2) has recently been identified as a rare risk factor for late-onset Alzheimer's disease (AD).
In this study we examined the association between TREM2 exon 2 variants and early-onset AD in a sample of Caucasian subjects of French origin including 726 patients with age of onset ≤65 years and 783 controls.
We found significantly more variants in exon 2 of TREM2 in patients with Alzheimer's disease than in controls in the discovery set
The most commonly associated variant, rs75932628 (encoding R47H), showed highly significant association with Alzheimer's disease (P<0.001).
Our findings strongly implicate variant TREM2 in the pathogenesis of Alzheimer's disease. Given the reported antiinflammatory role of TREM2 in the brain, the R47H substitution may lead to an increased predisposition to Alzheimer's disease
Recent works have demonstrated a rare functional variant (R47H) in triggering receptor expressed on myeloid cells (TREM) 2 gene, encoding TREM2 protein, increase susceptibility to late-onset Alzheimer's disease (AD), with an odds ratio similar to that of the apolipoprotein E ε4 allele.
The rs75932628-T variant of the gene encoding the triggering receptor expressed on myeloid cells 2 (TREM2) has recently been identified as a rare risk factor for late-onset Alzheimer's disease (AD).
BACKGROUND: Homozygous loss-of-function mutations in TREM2, encoding the triggering receptor expressed on myeloid cells 2 protein, have previously been associated with an autosomal recessive form of early-onset dementia.
CONCLUSIONS: Heterozygous rare variants in TREM2 are associated with a significant increase in the risk of Alzheimer's disease.
RESULTS: A rare missense mutation (rs75932628-T) in the gene encoding the triggering receptor expressed on myeloid cells 2 (TREM2), which was predicted to result in an R47H substitution, was found to confer a significant risk of Alzheimer's disease in Iceland (odds ratio, 2.92; 95% confidence interval [CI], 2.09 to 4.09; P=3.42×10(-10)).

Answer: TREM2 variants have been found to be associated with early as well as with late onset Alzheimer's disease.
Exact answer: yes