nirantk/geneticsQA-train huggingface dataset:
Question: Which are the subunits of the transcription factor NF-kappaB in the canonical pathway activation?

Context:
In this study, we demonstrated that the HSV-1 UL42 protein, a DNA polymerase processivity factor, was a novel antagonism of the canonical NF-κB signaling pathway. UL42 was shown to significantly suppress TNF-α mediated NF-κB activation. Co-immunoprecipitation experiment revealed that UL42 bound to the NF-κB subunits p65 and p50. 
Thus, it was first time we demonstrated that HSV-1 UL42 appeared to prevent NF-κB-dependent gene expression by retaining p65 and p50 in the cytoplasm, and UL42-dependent transcriptional activation were inherently coupled to promote HSV-1 lytic replication, which also may contribute to immune evasion and pathogenesis of HSV-1.
The review describes NF-κB and its two pathways: the canonical, mediated by the p65 and p50 subunits, and the non-canonical, mediated by the subunits RelB, p52 and p50. 
The function of the TTV open reading frame (ORF) in the nuclear factor kappaB (NF-kappaB) pathway has not yet been established. In this study, we found for the first time that the TTV ORF2 protein could suppress NF-kappaB activity in a dose-dependent manner in the canonical NF-kappaB pathway. By Western blot analysis, we proved that the TTV ORF2 protein did not alter the level of NF-kappaB expression but prevented the p50 and p65 subunits from entering the nucleus due to the inhibition of IkappaBalpha protein degradation.
Herpes simplex virus 1 DNA polymerase processivity factor UL42 inhibits TNF-α-induced NF-κB activation by interacting with p65/RelA and p50/NF-κB1.

Answer: The NF-κB canonical pathway is mediated by the p65/relA and p50 subunits.
Exact answer: p65, RelA, p50, NF-κB1
Question: Which drug is considered as the first line treatment of fibromyalgia?

Context:
Multimodal approaches seem to be the treatment of choice in fibromyalgia
A multidisciplinary program was developed and implemented for patients with fibromyalgia in the primary care setting. The program included education (seven sessions) and physical therapy (25 sessions).
Amitriptyline for neuropathic pain and fibromyalgia in adults.
Amitriptyline is a tricyclic antidepressant that is widely used to treat chronic neuropathic pain (pain due to nerve damage) and fibromyalgia, and is recommended in many guidelines. 
Amitriptyline should continue to be used as part of the treatment of neuropathic pain or fibromyalgia, but only a minority of patients will achieve satisfactory pain relief.
Valproic acid and its sodium salt (sodium valproate) are antiepileptic drugs that are sometimes used to treat chronic neuropathic pain and fibromyalgia, although they are not licensed for this use. 
Oral pregabalin, a calcium channel alpha(2)delta-subunit ligand with analgesic, anxiolytic and antiepileptic activity, has shown efficacy in the treatment of fibromyalgia.
Pregabalin is, therefore, a valuable option in the first-line treatment of patients with fibromyalgia.

Answer: Pregabalin is, therefore, a valuable option in the first-line treatment of patients with fibromyalgia.
Exact answer: Pregabalin
Question: Describe the applicability of Semantic MediaWiki in the case of FANTOM5

Context:
To make the heterogeneous data set accessible and useful for investigators, we developed a web-based database called Semantic catalog of Samples, Transcription initiation And Regulators (SSTAR). SSTAR utilizes the open source wiki software MediaWiki along with the Semantic MediaWiki (SMW) extension, which provides flexibility to model, store, and display a series of data sets produced during the course of the FANTOM5 project. Our use of SMW demonstrates the utility of the framework for dissemination of large-scale analysis results. SSTAR is a case study in handling biological data generated from a large-scale research project in terms of maintenance and growth alongside research activities
SSTAR utilizes the open source wiki software MediaWiki along with the Semantic MediaWiki (SMW) extension, which provides flexibility to model, store, and display a series of data sets produced during the course of the FANTOM5 project.
SSTAR utilizes the open source wiki software MediaWiki along with the Semantic MediaWiki (SMW) extension, which provides flexibility to model, store, and display a series of data sets produced during the course of the FANTOM5 project.

Answer: To make the heterogeneous data set accessible and useful for investigators, a web-based database called Semantic catalog of Samples, Transcription initiation And Regulators (SSTAR) has been developed. SSTAR utilizes the open source wiki software MediaWiki along with the Semantic MediaWiki (SMW) extension, which provides flexibility to model, store, and display a series of data sets produced during the course of the FANTOM5 project. The use of SMW demonstrates the utility of the framework for dissemination of large-scale analysis results. SSTAR is a case study in handling biological data generated from a large-scale research project in terms of maintenance and growth alongside research activities
Question: Is TNNI3K a cardiac-specific protein?

Context:
cardiomyocyte-specific kinase TNNI3K 
We report that cardiac troponin I-interacting kinase (TNNI3K), a cardiomyocyte-specific kinase,
TNNI3K, a cardiac-specific kinase, 
 The cardiac troponin I-interacting kinase (TNNI3K), a novel cardiac specific kinase, is associated with cardiomyocyte hypertrophy
Human cardiac troponin I-interacting kinase (TNNI3K) is a novel cardiac-specific functional kinase that can bind to cTnI in a yeast two-hybrid screen. 
Overexpression of TNNI3K, a cardiac-specific MAPKKK, promotes cardiac dysfunctio
Cardiac troponin I-interacting kinase (TNNI3K) is a cardiac-specific kinase whose biological function remains largely unknown
 Cardiac troponin I-interacting kinase (TNNI3K) is a novel cardiac-specific kinase gene
 a novel cardiac-specific kinase gene (TNNI3K),
 TNNI3K is a novel cardiac troponin I-interacting kinase gene and its overexpression may promote cardiac myogenesis, 
TNNI3K is a new cardiac-specific MAP kinase whose gene is localized to 1p31.1 and that belongs to a tyrosine kinase-like branch in the kinase tree of the human genome.
The cardiac ankyrin repeat kinase (CARK) gene, also named TNNI3K for its interaction with cardiac troponin I, is both a unique expression and heart-enriched gene
Molecular cloning of cardiac troponin I-interacting kinase (TNNI3K), a novel cardiac-specific protein kinase containing seven N-terminal ankyrin (ANK) repeats followed by a protein kinase domain and a C-terminal Ser-rich domain, has previously been reported.
 TNNI3K is highly expressed in heart, but is undetectable in other tissues. Immunohistochemical analysis predominantly localized TNNI3K in the nucleus of cardiac myocytes. 

Answer: Yes, TNNI3K is highly expressed in heart but is undetectable in other tissues.
Exact answer: yes
Question: What is the role of TAD protein domain?

Context:
 Thus, nuclear ERK5 activates transcription factors by either direct phosphorylation or acting as co-activator thanks to a unique transcriptional activation TAD domain located at its C-terminal tail. 
Although lacking kinase activity, these forms activate transcription by interacting with transcription factors through the TAD domain. 
Myc has an N-terminal transcription activation domain (TAD) that interacts with various coactivators and a C-terminal basic-helix-loop-helix-leucine zipper (bHLHZip) domain required for E box-specific DNA-binding and heterodimerization with its obligatory bHLHZip protein partner Max. 
p300 worked synergistically with MRTF-A to activate the transcription of MYH9, MYL9 and CYR61. As identified by co-IP, p300 interacted with the C-terminal TAD domain of MRTF-A.
To investigate further the role of cytoplasmic sequestration of p53 in its inhibition by the E1B 55-kDa protein we systematically examined domains in both the Ad12 55-kDa protein and p53 that underpin their colocalization in the cytoplasmic body and show that the N-terminal transactivation domain (TAD) of p53 is essential for retaining p53 in the cytoplasmic body.
Physical interaction between the transactivation domain (TAD) of the mixed-lineage leukemia protein (MLL) and the KIX domain of the cyclic-AMP response element binding protein (CREB) binding protein (CBP) is necessary for MLL-mediated transcriptional activation.
The IE62 possesses several domains essential for trans-activation, including an acidic trans-activation domain (TAD), a serine-rich tract (SRT), and binding domains for USF, TFIIB, and TATA box binding protein (TBP)
To investigate further the role of cytoplasmic sequestration of p53 in its inhibition by the E1B 55-kDa protein we systematically examined domains in both the Ad12 55-kDa protein and p53 that underpin their colocalization in the cytoplasmic body and show that the N-terminal transactivation domain (TAD) of p53 is essential for retaining p53 in the cytoplasmic body.
We have characterized two transcription activation domains (TADs) in Da, called activation domain 1 (AD1) and loop-helix (LH), and have evaluated their roles in promoting peripheral neurogenesis.
Particularly, the intrinsic histone acetyltransferase (HAT) activity and transactivation domains (TAD) play essential roles for their coactivating function.

Answer: TAD domain is a transcription activation domain found in transcription factors.
Exact answer: transcription activation domain, transactivation domain, trans-activating domain
Question: How are looped genes identified in yest?

Context:
Gene-loop formation is dependent on regulatory proteins localized at the 5' and 3' ends of genes, such as TFIIB.
Instead, activators physically interacted with the general transcription factor TFIIB when the genes were activated and in a looped configuration.

Answer: Gene-loop formation is dependent on regulatory proteins localized at the 5' and 3' ends of genes, such as TFIIB.
gene-loop formation is dependent on regulatory proteins localized at the 5' and 3' ends of genes, such as tfiib.
Gene-loop formation is dependent on regulatory proteins localized at the 5' and 3' ends of genes, such as TFIIB
Gene-loop formation is dependent on regulatory proteins localized at the 5' and 3' ends of genes, such as TFIIB. . . . .
Question: What is the localization of the protein encoded by the gene DNAJC11?

Context:
 DnaJC11, respectively. The first three are outer membrane proteins, CHCHD3 has been assigned to the matrix space, and the other two proteins have not been described in mitochondria previously.

Answer: mitochondrial inner membrane
Exact answer: mitochondrial inner membrane
Question: Is Beta-Thalassemia is associated with a mutation or deletion of the gene that codes for alpha globin?

Context:
Beta-thalassemia, one of the most common single-gene disorders, is the result of reduced or absent production of β-globin chains
The beta-thalassemia syndromes are a heterogeneous group of genetic disorders characterized by reduced or absent expression of the beta-globin gene

Answer: Beta-thalassemia, one of the most common single-gene disorders, is the result of reduced or absent production of β-globin chains
beta-thalassemia, one of the most common single-gene disorders, is the result of reduced or absent production of β-globin chains.
Beta-thalassemia, one of the most common single-gene disorders, is the result of reduced or absent production of -globin chains. 
Beta-thalassemia, one of the most common single-gene disorders, is the result of reduced or absent production of β-globin chains.
Exact answer: no
Question: List clinical trials that have directly compared microsurgical clipping with endovascular coiling for treatment of ruptured brain aneurysms?

Context:
The authors report the 3-year results of the Barrow Ruptured Aneurysm Trial (BRAT). The objective of this ongoing randomized trial is to compare the safety and efficacy of microsurgical clip occlusion and endovascular coil embolization for the treatment of acutely ruptured cerebral aneurysms and to compare functional outcomes based on clinical and angiographic data. 
We report the design of the FIAT study, a clinical care trial aiming to compare angiographic and clinical outcomes following treatment with a Flow-Diverter or with the best conventional treatment option. The FIAT study will include both a randomized and a registry portion. Patients will be proposed randomization to either FD stenting or best conventional treatment option (observation, coiling, stenting, or clipping) as determined by the treating physician. 
The effect of clipping and coiling in acute severe subarachnoid hemorrhage after international subarachnoid aneurysmal trial (ISAT) results.
A critical appraisal of the ISAT of microsurgical clipping versus coiling is used for comparison of our results.
International subarachnoid aneurysm trial (ISAT) of neurosurgical clipping versus endovascular coiling in 2143 patients with ruptured intracranial aneurysms: a randomised comparison of effects on survival, dependency, seizures, rebleeding, subgroups, and aneurysm occlusion.
International Subarachnoid Aneurysm Trial (ISAT) of neurosurgical clipping versus endovascular coiling in 2143 patients with ruptured intracranial aneurysms: a randomised trial.

Answer: Barrow Ruptured Aneurysm Trial (BRAT) and international subarachnoid aneurysmal trial (ISAT) have directly compared microsurgical clipping with endovascular coiling for treatment of ruptured brain aneurysms. FIAT study, a clinical care trial aiming to compare angiographic and clinical outcomes following treatment with a Flow-Diverter or with the best conventional treatment option (including clipping) is underway.
Exact answer: Barrow Ruptured Aneurysm Trial (BRAT)
international subarachnoid aneurysmal trial (BRAT)
FIAT study
Question: How does apolipoprotein E in HDL help with anti-inflammatory and anti-atherogenic effects?

Context:
 have previously reported that apolipoprotein E (apoE), a protein component of very-low-density lipoproteins (VLDL) and high-density lipoproteins and a potent plasma-borne atheroprotective factor, exerts anti-inflammatory activity in macrophages by switching the activation profile from M1 ("classic") to M2 ("alternative") in a process involving signaling via low-density lipoprotein receptor 
anti-inflammatory activity in macrophages 
Small peptides corresponding to the receptor-binding region of apoE mimic the anti-inflammatory activity of the apoE 
Apolipoprotein (apo) E-containing high-density lipoprotein (HDL) has antioxidant, anti-inflammatory and anti-atherogenic properties
 have previously reported that apolipoprotein E (apoE), a protein component of very-low-density lipoproteins (VLDL) and high-density lipoproteins and a potent plasma-borne atheroprotective factor, exerts anti-inflammatory activity in macrophages by switching the activation profile from M1 ("classic") to M2 ("alternative") in a process involving signaling via low-density lipoprotein receptor 
anti-inflammatory activity in macrophages 
Small peptides corresponding to the receptor-binding region of apoE mimic the anti-inflammatory activity of the apoE 
Apolipoprotein (apo) E-containing high-density lipoprotein (HDL) has antioxidant, anti-inflammatory and anti-atherogenic properties

Answer: Apolipoprotein (apo) E-containing high-density lipoprotein (HDL) has antioxidant, anti-inflammatory and anti-atherogenic properties
Question: Is the protein β1-integrin recycled?

Context:
Pathways selectively regulating β1-integrin recycling are implicated in cancer invasion and metastasis,
integrin-positive early and recycling endosomes 
LPA-induced recycling of β1 integrin,
RCP-mediated recycling of α5β1 integrin 
CycD1 overexpression increased β1 integrin recycling 
inhibition of autophagy slowed down the lysosomal degradation of internalized β1 integrins and promoted its membrane recycling
recycling pathway for β1-integrin
 β1 integrin recycling
 β1 integrin recycling
 controlling β1 integrin recycling to the plasma membrane 
integrin recycling pathway
Distinct recycling of active and inactive β1 integrins.
Integrin functions are controlled by regulating their affinity for ligand, and by the efficient recycling of intact integrins through endosomes.
 β1 integrins, resulting in their recycling to the cell surface where they can be reused.

Answer: Yes, the β1-integrin is recycled.
Exact answer: yes
Question: Are long non coding RNAs spliced?

Context:
Our analyses indicate that lncRNAs are generated through pathways similar to that of protein-coding genes, with similar histone-modification profiles, splicing signals, and exon/intron lengths.
For alternative exons and long noncoding RNAs, splicing tends to occur later, and the latter might remain unspliced in some cases.
bosome-mapping data to identify lncRNAs of Caenorhabditis elegans. We found 170 long intervening ncRNAs (lincRNAs), which had single- or multiexonic structures that did not overlap protein-coding transcripts, and about sixty antisense lncRNAs (ancRNAs), which were complementary to protein-coding transcripts
We introduce an approach to predict spliced lncRNAs in vertebrate genomes combining comparative genomics and machine learning.
Owing to similar alternative splicing pattern to mRNAs, the concept of lncRNA genes was put forward to help systematic understanding of lncRNAs. 
Our synthesis of recent studies suggests that neither size, presence of a poly-A tail, splicing, direction of transcription, nor strand specificity are of importance to lncRNA function.

Answer: Long non coding RNAs appear to be spliced through the same pathway as the mRNAs
Exact answer: yes
Question: Is there a genome-wide technique for the detection of R-loop formation?

Context:
Genome-wide analysis of fragile sites by chromatin immunoprecipitation (ChIP) and microarray (ChIP-chip) of phosphorylated H2A in these mutants supported a transcription-dependent mechanism of DNA damage characteristic of R loops
We have used a bisulfite-sensitivity assay to demonstrate genome-wide increase in the occurrence of RNA-DNA hybrids (R-loops), including from antisense and read-through transcripts, in a nusG missense mutant defective for Rho-dependent termination.
The results demonstrate a key function of FACT in the resolution of R-loop-mediated transcription-replication conflicts, likely associated with a specific chromatin organization.
Previous work revealed that GC skew and R-loop formation associate with a core set of unmethylated CpG island (CGI) promoters in the human genome

Answer: Genome-wide analysis of fragile sites by chromatin immunoprecipitation (ChIP) and microarray (ChIP-chip) of phosphorylated H2A in these mutants supported a transcription-dependent mechanism of DNA damage characteristic of R loops. Here we show that recombination factors are required for the survival of yeast FACT mutants, consistent with an accumulation of DNA breaks that we detected by Rad52 foci and transcription-dependent hyperrecombination. The latter pathway operates on nascent transcripts that are not simultaneously translated and requires factors Rho, NusG, and NusA, each of which is essential for viability of WT Escherichia coli. DNA replication in Escherichia coli is normally initiated at a single origin, oriC, dependent on initiation protein DnaA.
Genome-wide analysis of fragile sites by chromatin immunoprecipitation (ChIP) and microarray (ChIP-chip) of phosphorylated H2A in these mutants supported a transcription-dependent mechanism of DNA damage characteristic of R loops
A bisulfite-sensitivity assay may demonstrate genome-wide increase in the occurrence of RNA-DNA hybrids (R-loops).
Exact answer: yes
Question: What is the function of caspases?

Context:
Caspases are the ultimate executors of the apoptotic programmed cell death pathway.
Members of the caspase family of cysteine proteases coordinate the morphological and biochemical events that typify apoptosis. 
Caspase function is known to be essential for cell death by apoptosis,
Caspases, initially identified as a family of proteases regulating cell death, have been found to have nonapoptotic functions as well.
. As in other organisms, apoptosis is executed by caspases.
Caspases are intracellular proteases that propagate programmed cell death, proliferation, and inflammation. 
Apoptosis is dependent upon caspase activation leading to substrate cleavage and, ultimately, cell death.
Caspases are a family of evolutionarily conserved cysteine proteases that constitute the effector arm of the apoptotic machinery.
Caspases are critical mediators of apoptosis, the principle mechanism by which extra and harmful cells are eliminated to ensure proper development and maintain cellular homeostasis in all multicellular organisms. 
Caspases (cysteine-containing aspartate-specific proteases) are at the core of the cell's suicide machinery. These enzymes, once activated, dismantle the cell by selectively cleaving key proteins after aspartate residues. 
Programmed cell death plays an important role in maintaining homeostasis during animal development, and has been conserved in animals as different as nematodes and humans. 

Answer: Caspases are intracellular proteases that propagate programmed cell death, proliferation, and inflammation.
Exact answer: Caspases are intracellular proteases that propagate programmed cell death, proliferation, and inflammation.
Question: Has silicon been used in treatment of  incontinence ?

Context:
an artificial anal sphincter. Worldwide, there are two established devices on the market: the artificial bowel sphincter® (ABS) from A. M. S. (Minnetonka, MN, USA) and the soft anal band® from A. M. I. (Feldkirch, Austria). How to implant the artificial anal sphincter? Both devices consist of a silicon cuff which can be filled with fluid.
The InVance™ system uses a silicon-coated polyester sling positioned under the bulbar urethra via a perineal incision.
Through a perineal incision three titanium screws with a polipropylene suture were inserted in each ischiopubic rami, and a silicon/polipropylene mesh (Invance) is affixed to them, compressing the bulbar urethra
surgical treatment of female stress urinary incontinence with a trans-obturator sub-urethral tape of Uratape (Porgés). METHODS: Treatment and follow up of their complication were performed at the CHRU of Lille. RESULTS: In both cases, this complication is related to prolonged vaginal exposition of the tape. Vaginal erosion always occurs next to the silicon coated section of the tape
A non-elastic, polypropylene tape (UraTape, Mentor-Porgès) with a silicon coated central part was placed under the mid-urethra.
 Stress incontinence is a rare complication in men, usually following prostatic surgery. It can be treated conservatively with pelvic floor training and alpha-adrenergic receptor agonists and if necessary surgically with submucosal collagen or silicon injections in the sphincter area or implantation of a sphincter prosthesis
The Femassist is a medical-grade silicon dome-shaped device, worn over the urethra and held securely via suction and a commercially available adhesive lotion.
To examine the performance of a silicon urinary control device for nonsurgical management of women with genuine stress incontinence
The "FemAssist" is a dome-shaped medical grade silicon device intended to be worn over the external urethral meatus and held in place by suction and an adhesive gel. Thirty eight women with varying degrees of genuine stress urinary incontinence (GSUI) or mixed incontinence on multichannel urodynamic testing were fitted with one of two sizes of "FemAssist

Answer: Yes
Exact answer: yes