nirantk/geneticsQA-train huggingface dataset:
Question: Which is the main calcium pump of the sarcoplasmic reticulum?

Context:
sarcoplasmic reticulum (SR) calcium pump (SERCA)
the sarco/endoplasmic reticulum Ca(2+)-ATPase (SERCA)
SERCA, an endoplasmic reticulum (ER) calcium pump, is solely responsible for transporting cytosolic calcium into the ER lumen.
Sarcoplasmic reticulum Ca(2+)-ATPase (SERCA) is the pump crucial for calcium homeostasis and its impairment results in pathologies such as myopathy, heart failure or diabetes.
Sarcoplasmic reticulum calcium ATPase (SERCA2a), the sarcoplasmic reticulum calcium pump, was found to be a key factor in the alteration of calcium cycling.
The calcium pump SERCA2a (sarcoplasmic reticulum calcium ATPase 2a), which plays a central role in cardiac contraction, shows decreased expression in heart failure (HF).
Calcium is actively accumulated in the endoplasmic reticulum by Sarco/Endoplasmic Reticulum Calcium transport ATPases (SERCA enzymes).
sarco(endo)plasmic reticulum calcium pump (SERCA)
SERCA is a membrane protein that belongs to the family of P-type ion translocating ATPases and pumps free cytosolic calcium into intracellular stores.
Three different SERCA genes were identified-SERCA1, SERCA2, and SERCA3. SERCA is mainly represented by the SERCA2a isoform in the heart.
The sarcoplasmic reticulum Ca�z ATPase (SERCA) is a membrane-bound pump that utilizes ATP to drive calcium ions from the myocyte cytosol against the higher calcium concentration in the sarcoplasmic reticulum.

Answer: Sarcoplasmic reticulum Ca(2+)-ATPase (SERCA) is the pump crucial for calcium homeostasis. SERCA is a membrane protein that belongs to the family of P-type ion translocating ATPases and pumps free cytosolic calcium into intracellular stores.
Exact answer: Sarcoplasmic reticulum Ca(2+)-ATPase
SERCA
serca2
Question: Is PER3 required for CHK2 activation in human cells?

Context:
Per3, a circadian gene, is required for Chk2 activation in human cells.
Depletion of Per3 by siRNA almost completely abolished activation of checkpoint kinase 2 (Chk2) after inducing DNA damage in human cells.
Per3 overexpression induced Chk2 activation in the absence of exogenous DNA damage,
Per3 overexpression also led to the inhibition of cell proliferation and apoptotic cell death.
These combined results suggest that Per3 is a checkpoint protein that plays important roles in checkpoint activation, cell proliferation and apoptosis.
Depletion of Per3 by siRNA almost completely abolished activation of checkpoint kinase 2 (Chk2) after inducing DNA damage in human cells
Per3 overexpression induced Chk2 activation in the absence of exogenous DNA damage, and this activation depended on ATM
In addition, Per3 physically interacted with ATM and Chk2

Answer: Depletion of Per3 by siRNA almost completely abolished activation of checkpoint kinase 2 (Chk2) after inducing DNA damage in human cells.Per3, a circadian gene, is required for Chk2 activation in human cells.
Per3, a circadian gene, is required for Chk2 activation in human cells.  
Per3, a circadian gene, is required for Chk2 activation in human cells.Per3 overexpression induced Chk2 activation in the absence of exogenous DNA damage,
Per3 gene, involved in circadian rhythm control, is required for Chk2 activation in human cells.
Exact answer: yes
Question: Which acetylcholinesterase inhibitors are used for treatment of myasthenia gravis?

Context:
Pyridostigmine is the most widely used acetylcholinesterase inhibitor.
For more than 50 years the acetylcholinesterase inhibitor pyridostigmine bromide has been the drug of choice in the symptomatic therapy for myasthenia gravis. 
The switch to SR-Pyr ameliorated the total quantified myasthenia gravis (QMG) score from 0.9 ± 0.5 to 0.6 ± 0.4 (p<0.001) in all patients and in the younger subgroup. This was accompanied by a significant improvement in the quality of life parameters. The health status valued by EuroQoL questionnaire improved from 0.626 ± 0.286 to 0.782 ± 0.186 (p<0.001). 
Our results support the usefulness of SR-Pyr in an individualized therapeutic regimen to improve quality of life regardless of the patient's age in myasthenia gravis.
This review focuses on treatment of MG, mainly on the use of the AChE inhibitor pyridostigmine.
Despite a lack of data from well controlled clinical trials to support their use, AChE inhibitors, of which pyridostigmine is the most commonly used, are recommended as first-line therapy for MG. 
Novel AChE inhibitors with oral antisense oligonucleotides have been developed and preliminary results appear to be promising.
Except for one small and inconclusive trial of intranasal neostigmine, no randomised controlled trial has been conducted on the use of acetylcholinesterase inhibitors in myasthenia gravis. Response to acetylcholinesterase inhibitors in observational studies is so clear that a randomised controlled trial depriving participants in the placebo arm of treatment would be difficult to justify.
 Current guidelines and recommendations for MG treatment are based largely on clinical experience, retrospective analyses and expert consensus. Available therapies include oral acetylcholinesterase (AChE) inhibitors for symptomatic treatment, and short- and long-term disease-modifying treatments.
Pyridostigmine has been used as a treatment for MG for over 50 years and is generally considered safe. It is suitable as a long-term treatment in patients with generalized non-progressive milder disease, and as an adjunctive therapy in patients with severe disease who are also receiving immunotherapy. 
Acetylcholinesterase inhibitors provide temporary, symptomatic treatment for all forms of myasthenia gravis. 

Answer: Pyridostigmine and neostygmine are acetylcholinesterase inhibitors that are used as first-line therapy for symptomatic treatment of myasthenia gravis. Pyridostigmine is the most widely used acetylcholinesterase inhibitor. Extended release pyridotsygmine and novel acetylcholinesterase inhibitors inhibitors with oral antisense oligonucleotides are being studied.
Exact answer: neostigmine, pyridostigmine
Question: What is the results of inactivated ANGPLT3?

Context:
Although it appears by now that the main lipid pathways have been uncovered, and that only modulators or adaptor proteins such as those encoded by LDLRAP1, APOA5, ANGPLT3/4, and PCSK9 are currently being discovered
Angptl3 knockout mice have marked hypolipidemia, and heterozygous carriers of ANGPLT3, loss-of-function mutations were found among individuals in the lowest quartile of plasma triglycerides in population studies. 
 4 related individuals with primary hypolipidemia were found to be compound heterozygotes for ANGPTL3 loss-of-function mutations.
Complete ANGPTL3 deficiency caused by loss-of-function mutations of ANGPTL3 is associated with a recessive hypolipidemia

Answer: Complete ANGPTL3 deficiency caused by loss-of-function mutations of ANGPTL3 is associated with a recessive hypolipidemia
Exact answer: Recessive hypolipidemia
Question: What is DeepCAGE?

Context:
The cap analysis of gene expression (CAGE) technology has been established to detect transcriptional starting sites (TSSs) and expression levels by utilizing 5' cDNA tags and PCR. It has been reported that the amount of templates is proportional to the amplification efficiency of PCR. CAGE has been used as a key technique for analyzing promoter activity and finding new transcripts including alternative spliced products and noncoding transcripts. Here, we introduce more powerful tools such as deepCAGE, which can be utilized for high-throughput next-generation sequencing technology. DeepCAGE can produce much deeper transcriptome datasets and can reveal more details of the regulatory network.
Here, we present a new method for high-throughput sequencing of 5' cDNA tags-DeepCAGE: merging the Cap Analysis of Gene Expression method with ultra-high-throughput sequence technology. 
DeepCAGE can also detect promoters used only in a small subset of cells within the complex tissue
DeepCAGE can produce much deeper transcriptome datasets and can reveal more details of the regulatory network.
DeepCAGE can also detect promoters used only in a small subset of cells within the complex tissue.
Here, we introduce more powerful tools such as deepCAGE, which can be utilized for high-throughput next-generation sequencing technology.
Mammalian cells have at least 5-10 magnitudes more TSS than previously believed, and deeper sequencing is necessary to detect all active promoters in a given tissue. Here, we present a new method for high-throughput sequencing of 5' cDNA tags-DeepCAGE: merging the Cap Analysis of Gene Expression method with ultra-high-throughput sequence technology. 
Here, we introduce more powerful tools such as deepCAGE, which can be utilized for high-throughput next-generation sequencing technology. 
Using these data, we present evidence indicating a key role for the Arnt2 transcription factor in hippocampus gene regulation. DeepCAGE can also detect promoters used only in a small subset of cells within the complex tissue.
Here, we introduce more powerful tools such as deepCAGE, which can be utilized for high-throughput next-generation sequencing technology. DeepCAGE can produce much deeper transcriptome datasets and can reveal more details of the regulatory network.

Answer: The cap analysis of gene expression (CAGE) technology has been established to detect transcriptional starting sites (TSSs) and expression levels by utilizing 5' cDNA tags and PCR. It has been reported that the amount of templates is proportional to the amplification efficiency of PCR. CAGE has been used as a key technique for analyzing promoter activity and finding new transcripts including alternative spliced products and noncoding transcripts. DeepCAGE can be utilized for high-throughput next-generation sequencing technology. DeepCAGE can produce much deeper transcriptome datasets and can reveal more details of the regulatory network.
Question: What is the mechanism of DNA replication termination in vertebrates?

Context:
Eukaryotic DNA replication terminates when replisomes from adjacent replication origins converge. Termination involves local completion of DNA synthesis, decatenation of daughter molecules and replisome disassembly.
We show that DNA synthesis does not slow detectably as forks approach each other, and that leading strands pass each other unhindered before undergoing ligation to downstream lagging strands. Dissociation of the replicative CMG helicase (comprising CDC45, MCM2-7 and GINS) occurs only after the final ligation step, and is not required for completion of DNA synthesis, strongly suggesting that converging CMGs pass one another and dissociate from double-stranded DNA. This termination mechanism allows rapid completion of DNA synthesis while avoiding premature replisome disassembly

Answer: Eukaryotic DNA replication terminates when replisomes from adjacent replication origins converge. Termination involves local completion of DNA synthesis, decatenation of daughter molecules and replisome disassembly. DNA synthesis does not slow detectably as forks approach each other, and leading strands pass each other unhindered before undergoing ligation to downstream lagging strands. Dissociation of the replicative CMG helicase (comprising CDC45, MCM2-7 and GINS) occurs only after the final ligation step, and is not required for completion of DNA synthesis, strongly suggesting that converging CMGs pass one another and dissociate from double-stranded DNA. This termination mechanism allows rapid completion of DNA synthesis while avoiding premature replisome disassembly.
Question: Describe ATR-16 syndrome.

Context:
ATR-16 syndrome is due to alterations on chromosome 16p13.3, and is usually accompanied by alpha-thalassemia, mild-moderate mental retardation, dysmorphic facial features, skeletal and genitourinary malformations.
Alpha thalassemia retardation associated with chromosome16 (ATR-16 syndrome) is defined as a contiguous gene syndrome resulting from haploinsufficiency of the alpha-globin gene cluster and genes involved in mental retardation (MR). 
This is the fifth reported case of the ATR-16 syndrome (alpha-thalassemia retardation-16) not complicated by duplication or deletion of other chromosomes.
Familial mental retardation syndrome ATR-16 due to an inherited cryptic subtelomeric translocation, t(3;16)(q29;p13.3).

Answer: ATR-16 syndrome is due to alterations on chromosome 16p13.3, and is usually accompanied by alpha-thalassemia, mild-moderate mental retardation, dysmorphic facial features, skeletal and genitourinary malformations.
Question: What gene is mutated in Sickle Cell Anemia?

Context:
Sickle cell anemia (SCA) is an inherited blood disorder. SCA patients present clinical and hematologic variability that cannot be only explained by the single mutation in the beta-globin gene.
Sickle cell anemia (SCA) is an autosomal recessive disease caused by the HBB:c.20A>T mutation that leads to hemoglobin S synthesis.
Sickle cell anemia is caused by a single type of mutation, a homozygous A→T substitution in the ß globin gene.
Implementation of this approach for disorders resulting from mutations affecting the beta-globin gene (e.g., beta-thalassemia and sickle cell anemia), however, has been hampered by the inability to generate recombinant viruses able to efficiently and faithfully transmit the necessary sequences for appropriate gene expression.
The allele-specific PCR approach has been modified by introducing a second mismatch at the 3'-penultimate link of the primer and used to identify the sickle cell anemia mutation (A-->T transversion in the sixth codon of the human beta-globin gene causing Glu-->Val substitution in the protein), thus obviating the problem of an interpretationally ambiguous 3'-terminal mismatch including T residue.
Sickle-cell anemia results from an A leads to T transversion in the second nucleotide of codon 6 of the beta-globin gene.
Sickle cell anemia is a genetic blood disorder arising from a point mutation in the beta-globin gene that leads to the replacement of glutamic acid residue by valine at the sixth position of the beta--chain of hemoglobin.
Sickle cell anemia is a genetic blood disease resulting from production of mutant beta-globin (beta(S)) and has severe clinical consequences. 

Answer: Sickle cell anemia (SCA) is an autosomal recessive disease caused by by the HBB:c.20A>T mutation that leads to hemoglobin S synthesis.
 sca patients present clinical and hematologic variability that cannot be only explained by the single mutation in the beta-globin gene.
Exact answer: HBB
Question: Is the JNK pathway activated during liver regeneration?

Context:
analysis of the role of JNK signaling pathway in regulating cell proliferation and apoptosis of rat liver regeneration
paths of JNK signaling pathway regulate cell proliferation and apoptosis in both LR
c-jun is not mandatory for mouse hepatocyte proliferation 
Mice lacking c-jun in the liver display impaired regeneration after partial hepatectomy (PH)
initial activity of the JNK pathway
use of Drosophila for the study of regeneration 
Loss of macroautophagy led to overactivation of the c-Jun N-terminal kinase (JNK)/c-Jun signaling pathway that induced cell death.
stress induced during intermittent selective clamping accelerates rat liver regeneration through JNK pathway
JNK2 promotes injury after mouse LT via the MPT
Jun N-terminal kinase 2 promotes graft injury via the mitochondrial permeability transition after mouse liver transplantation
add45beta promotes hepatocyte survival during liver regeneration in mice by modulating JNK signaling
basis for JNK suppression during liver regeneration and identify Gadd45beta as a potential therapeutic target in liver diseases
 genetic inactivation of the JNK pathway results in impaired proliferation of fetal hepatoblasts in vitro and defective adult liver regeneration in vivo
enhancement of the activation of Jun N-terminal kinase and p38 mitogen-activated protein kinase caused by partial hepatectomy
 arsenite induced apoptosis in the hepatocytes in vivo, through the enhancement of the activation of JNK and p38 MAPK caused by partial hepatectomy
Jun N-terminal kinase and p38 MAPK, but not Akt, was altered.
Although mechanical stress has been implicated in hepatic cirrhosis and liver regeneration following hepatectomy, the signaling pathway(s) that may be activated in hepatocytes in response to mechanical stress have not been determined
 JNK, ERK and JAK2 inhibitors partially abrogated apoptosis and when used in combination reduced it to basal levels
induction of CD40-mediated cholangiocyte apoptosis requires JAK2-mediated phosphorylation of STAT3 as well as sustained JNK1/2, ERK1/2 activation
Jun-N-terminal kinase drives cyclin D1 expression and proliferation during liver regeneration
c-Jun-N-terminal kinase (JNK) pathway is strongly activated after partial hepatectomy (PH)
growth factors and cytokines are involved in liver regeneration
JAB1 (Jun activation domain-binding protein 1), a co-activator of AP-1, which is essential for liver regeneration, specifically interacts with intracellular HPO

Answer: Yes, the Jun-N-terminal kinase (JNK) pathway is strongly activated after partial hepatectomy.
Exact answer: yes
Question: The MMR vaccine protects against what 3 viruses?

Context:
 measles, mumps and rubella (MMR) vaccine 
Measles, mumps, rubella (MMR) vaccine is a live vaccine preparation containing attenuated strains of all 3 viruses.

Answer: The MMR vaccine provides immunity to measles, mumps and rubella.
 measles, mumps and rubella (mmr) vaccine .
Exact answer: Measles, Mumps, Rubella
Question: Patients of which disease could be treated by utilizing knowledge obtained from experiments suppressing TDP-43 toxicity in yeast?

Context:
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease primarily affecting motor neurons. Mutations in the gene encoding TDP-43 cause some forms of the disease, and cytoplasmic TDP-43 aggregates accumulate in degenerating neurons of most individuals with ALS. Thus, strategies aimed at targeting the toxicity of cytoplasmic TDP-43 aggregates may be effective
The strongest suppressor of TDP-43 toxicity was deletion of DBR1, which encodes an RNA lariat debranching enzyme. We show that, in the absence of Dbr1 enzymatic activity, intronic lariats accumulate in the cytoplasm and likely act as decoys to sequester TDP-43, preventing it from interfering with essential cellular RNAs and RNA-binding proteins. Knockdown of Dbr1 in a human neuronal cell line or in primary rat neurons is also sufficient to rescue TDP-43 toxicity. Our findings provide insight into TDP-43-mediated cytotoxicity and suggest that decreasing Dbr1 activity could be a potential therapeutic approach for ALS

Answer: Amyotrophic lateral sclerosis (ALS).
The strongest suppressor of TDP-43 toxicity was deletion of DBR1, which encodes an RNA lariat debranching enzyme. We show that, in the absence of Dbr1 enzymatic activity, intronic lariats accumulate in the cytoplasm and likely act as decoys to sequester TDP-43, preventing it from interfering with essential cellular RNAs and RNA-binding proteins. Knockdown of Dbr1 in a human neuronal cell line or in primary rat neurons is also sufficient to rescue TDP-43 toxicity. Our findings provide insight into TDP-43-mediated cytotoxicity and suggest that decreasing Dbr1 activity could be a potential therapeutic approach for ALS  
Exact answer: Amyotrophic lateral sclerosis (ALS)
Question: What is the number of long non coding RNAs in the human genome

Context:
The recent ENCODE (Encyclopedia of DNA Elements) study reported 9,640 lncRNA loci in the human genome, which corresponds to around half the number of protein-coding genes. 
Over 18,000 transcripts are presently annotated as lncRNA, and encompass previously annotated classes of noncoding transcripts including large intergenic noncoding RNA, antisense RNA and processed pseudogenes
BACKGROUND: Over 10,000 long intergenic non-coding RNAs (lincRNAs) have been identified in the human genome.

Answer: Different estimates put currently the number of human long non coding RNAs between 10,000 and 20,000
Exact answer: between 10,000 and 20,000
Question: Which deiodinases are best known to be present in brain?

Context:
In brain, the presence of type III iodothyronine deiodinase (D3) seems to be important to maintain homeostasis of T(3) levels.
We were able to detect a protein fragment corresponding to the expected molecular mass (30 kDa) for type III deiodinase by means of Western blot analysis. RT-PCR as well as Northern blot analysis confirmed the presence of D3 mRNA in the cerebellum.
The presence of 5D (type-III) together with our previous report of 5'-deiodinase (type-I in euthyroidism and type-II in hypothyroidism) shows that the isozymes of deiodinases in the neurohypophysis are quite similar to those in the brain.

Answer: All the 3 deiodinases (Type 1, Type 2 and Type 3 deiodinase) are present in the "brain" but Type 1 deiodinase  is only found in neurohypophysis that cannot be actually considered true "brain tissue".
Exact answer: Type 2 deiodinase, Type 3 deiodinase
Question: What is promoted by ERAP1-ERAP2 dimerization?

Context:
ERAP1-ERAP2 dimerization increases peptide-trimming efficiency.
In this study, we produced stabilized ERAP1-ERAP2 heterodimers and found that they produced several mature epitopes more efficiently than a mix of the two enzymes unable to dimerize. Physical interaction with ERAP2 changes basic enzymatic parameters of ERAP1 and improves its substrate-binding affinity. Thus, by bringing the two enzymes in proximity and by producing allosteric effects on ERAP1, dimerization of ERAP1/2 creates complexes with superior peptide-trimming efficacy. Such complexes are likely to enhance Ag presentation by cells displaying coordinated expression of the two enzymes.
In this study, we produced stabilized ERAP1-ERAP2 heterodimers and found that they produced several mature epitopes more efficiently than a mix of the two enzymes unable to dimerize.
Formation of heterodimers by ERAP1 and ERAP2 has been proposed to facilitate trimming of epitope precursor peptides, but the effects of dimerization on ERAP function remain unknown.
ERAP1-ERAP2 dimerization increases peptide-trimming efficiency
In this study, we produced stabilized ERAP1-ERAP2 heterodimers and found that they produced several mature epitopes more efficiently than a mix of the two enzymes unable to dimerize. 
In this study, we produced stabilized ERAP1-ERAP2 heterodimers and found that they produced several mature epitopes more efficiently than a mix of the two enzymes unable to dimerize.
ERAP1-ERAP2 dimerization increases peptide-trimming efficiency.

Answer: ERAP1-ERAP2 dimerization increases peptide-trimming efficiency.
ERAP1-ERAP2 dimerization increases peptide-trimming efficiency. ERAP1-ERAP2 heterodimers produce several mature epitopes more efficiently than a mix of the two enzymes unable to dimerize. Physical interaction with ERAP2 changes basic enzymatic parameters of ERAP1 and improves its substrate-binding affinity. Thus, by bringing the two enzymes in proximity and by producing allosteric effects on ERAP1, dimerization of ERAP1/2 creates complexes with superior peptide-trimming efficacy. Such complexes are likely to enhance Ag presentation by cells displaying coordinated expression of the two enzymes.
The endoplasmic reticulum aminopeptidases (ERAP)1 and ERAP2 play a critical role in the production of final epitopes presented by MHC class I molecules.
Question: What is the function of R-spondin 1 and noggin in non-damaged gallbladders?

Context:
R-spondin 1 and noggin facilitate expansion of resident stem cells from non-damaged gallbladders.
R-spondin 1 and noggin facilitate expansion of resident stem cells from non-damaged gallbladders.

Answer: R-spondin 1 and noggin facilitate expansion of resident stem cells from non-damaged gallbladders.
Exact answer: The expansion of resident stem cells.