nirantk/geneticsQA-train huggingface dataset:
Question: Is the Drosophila Translational Control Element (TCE) involved in spermatogenesis?

Context:
Gene regulation in Drosophila spermatogenesis: analysis of protein binding at the translational control element TCE.
We have previously identified a 12 nucleotide long sequence element, the TCE, that was demonstrated to be necessary for translational control of expression in the male germ line of Drosophila melanogaster (Schäfer et al., 1990).
Gene regulation in Drosophila spermatogenesis: analysis of protein binding at the translational control element TCE
The Drosophila Translational Control Element (TCE) is required for high-level transcription of many genes that are specifically expressed in testes
Bioinformatic analyses of core promoter sequences from 190 genes that are specifically expressed in testes identified a 10 bp A/T-rich motif that is identical to the translational control element (TCE)
The Drosophila Translational Control Element (TCE) is required for high-level transcription of many genes that are specifically expressed in testes.

Answer: Yes. The Drosophila Translational Control Element (TCE), a 12 nucleotide long sequence element, was demonstrated to be necessary for translational control of expression in the male germ line of Drosophila melanogaster.
Exact answer: yes
Question: Which is the enzymatic activity of the myotubularin family of proteins?

Context:
myotubularin family of phosphatases.
Myotubularin belongs to a large family of conserved lipid phosphatases that include both catalytically active and inactive myotubularin-related proteins (i.e., "MTMRs")
myotubalarin family phosphatase
MTMR2 is a member of the myotubularin family of inositol lipid phosphatases, 
Myotubularin related protein 2 (MTMR2) is a member of the myotubularin family of phosphoinositide lipid phosphatases. 
Myotubularin phosphoinositide phosphatases: cellular functions and disease pathophysiology.
Although myotubularin was thought to be a dual-specificity protein phosphatase, recent results indicate that it is primarily a lipid phosphatase, acting on phosphatidylinositol 3-monophosphate, and might be involved in the regulation of phosphatidylinositol 3-kinase (PI 3-kinase) pathway and membrane trafficking.
Myotubularin is the archetype of a family of highly conserved protein-tyrosine phosphatase-like enzymes. 
we and others have characterized myotubularin as a potent and specific phosphatidylinositol 3-phosphate 3-phosphatase. 
MTMR2 encodes a member of the myotubularin family of phosphoinositide-3-phosphatases, which dephosphorylate phosphatidylinositol 3-phosphate (PI(3)P) and bisphosphate PI(3,5)P2. MTMR13 encodes a large, uncharacterized member of the myotubularin family.
Myotubularin-related proteins are a large subfamily of protein tyrosine phosphatases (PTPs) that dephosphorylate D3-phosphorylated inositol lipids.
Myotubularin, the gene mutated in myotubular myopathy, functions as a lipid phosphatase with specificity for PtdIns(3)P.
The myotubularin family: novel phosphoinositide regulators.
The myotubularins are a large family of inositol polyphosphate 3-phosphatases that
The myotubularin family consists of 16 different proteins, 9 members of which possess catalytic activity, dephosphorylating phosphatidylinositol 3-phosphate [PtdIns(3)P] and phosphatidylinositol 3,5-bisphosphate [PtdIns(3,5)P(2)] at the D-3 position.
Myotubularin phosphoinositide phosphatases in human diseases.
The MTM (myotubularin)/MTMR (myotubularin-related) protein family is comprised of 15 lipid phosphatases, of which nine members are catalytically active. 
The myotubularin family of lipid phosphatases 

Answer: The myotubularin family of proteins are lipid inositol phosphatases
Exact answer: lipid inositol phosphatase activity
Question: Is there a relationship between thyroid hormone altered metabolism and coronary artery disease?

Context:
The results showed that higher levels of TSH within the reference range were independently associated with the presence of CAD only among subjects less than or equal to 65 years old, suggesting age might influence the relationship.
FT3 levels within the normal range were inversely correlated with the presence and severity of CAD. Moreover, lower FT3 concentrations were correlated with the Gensini score and independently predicted the presence and severity of CAD.
High TSH within the reference range was associated with increased risk of coronary death in women (P(trend) 0·005), but not in men. The risk of coronary death was also increased among women with subclinical hypothyroidism or subclinical hyperthyroidism, compared to women with TSH of 0·50-1·4 mU/l. 
 Prevalence of CHD was more common in hypothyroid and moderate SCH patients.
The angiographic results were as follows: significant coronary disease (SH 28.1% vs. non-SH 43.8%; p=0.087); three-vessel disease (9.4% vs. 9.9%; p=0.919); two-vessel disease (12.5% vs. 13.4%; p=0.892); single-vessel disease (6.3% vs. 29.5%; p=0.051); minimal lesions (9.4% vs. 10.9%; p=0.794); and no coronary disease (62.4% vs, 45.3%; p=0.064).
Lower fT3 levels were predictive of both single-vessel (p = 0.012) and multivessel (p = 0.009) CAD. Through a multivariate logistic regression analysis, fT3 was still linked to the presence of CAD (hazard ratio [HR]: 0.48, 95% confidence interval [CI]: 0.34-0.68, p < 0.001).
Our study showed that FT(4) levels were associated with the presence and the severity of CAD. Also, this study suggests that elevated serum FT(4) levels even within normal range could be a risk factor for CAD. 
The present meta-analysis indicates that sub-clinical hypothyroidism is associated with both, a significant risk of CHD at baseline and at follow-up.
The incidence of multi-vessel disease was higher in patients with high TSH level (p=0.026). TSH level showed a significant correlation with age (r=0.109, p=0.044) and Gensini's score (r=0.117, p=0.045). The multivariate analysis revealed that age (OR 2.39, p=0.001), diabetes (OR 3.74, p=0.001), creatinine (OR 2.06, p=0.008), and smoking (OR 1.85, p=0.045) were independent predictors for significant coronary artery disease, but TSH level did not predict coronary artery stenosis.
These data in patients referred for coronary angiography suggest that variation of thyroid function within the statistical normal range may influence the presence and severity of coronary atherosclerosis.

Answer: The major part of the studies and metaanalysis data show that hypothyroidism, both primary and secondary forms, is associated with higher incidence and severity of coronary artery disease.
Exact answer: yes
Question: Does the protein mTOR regulate autophagy?

Context:
autophagy is negatively regulated by the mammalian target of rapamycin receptor (mTOR)
Subjecting cells to starvation or rapamycin efficiently induces autophagy by inhibiting the MTOR signaling pathway triggering increased autophagic flux. 
Several pathways, including mTOR, have been shown to regulate autophagy.
these results provide insights into the mechanism by which hyperactivation of mTORC1 promotes breast cancer progression through increasing autophagy and Akt activation in vivo.
 the canonical mTOR-controlled autophagy pathway
mTOR inhibition severely impairs liver regeneration and increases autophagy after PH
mTOR remains at a high level and inhibits autophagy.
AKT is involved in granulosa cell autophagy regulation via mTOR signaling during rat follicular development and atresia.
mammalian target of rapamycin (mTOR), a major negative regulator of autophagy.
mTOR suppresses granulosa cell autophagy
Mammalian target of rapamycin (mTOR), a potent suppressor of autophagy,
The mTOR signaling pathway integrates inputs from a variety of upstream stimuli to regulate diverse cellular processes including proliferation, growth, survival, motility, autophagy, protein synthesis and metabolism
The activation of mammalian target of rapamycin (mTOR) signaling pathway blocks the effects of ghrelin-induced autophagy and apoptosis,
 inducing apoptosis and autophagy via the mTOR signaling pathway
 The mTOR gene regulates cell growth by controlling mRNA translation, ribosome biogenesis, autophagy, and metabolism.

Answer: mammalian target of rapamycin (mTOR)  is a major negative regulator of autophagy.
Exact answer: yes
Question: Other than protein coding potential, what features set apart long non-coding RNAs from protein coding genes?

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.
In contrast to protein-coding genes, however, lncRNAs display a striking bias toward two-exon transcripts
hey are predominantly localized in the chromatin and nucleus, and a fraction appear to be preferentially processed into small RNAs.
They are under stronger selective pressure than neutrally evolving sequences-particularly in their promoter regions, which display levels of selection comparable to protein-coding genes.
Comprehensive analysis of their expression in multiple human organs and brain regions shows that lncRNAs are generally lower expressed than protein-coding genes, and display more tissue-specific expression patterns, with a large fraction of tissue-specific lncRNAs expressed in the brain.
he proportion of conserved sequence (4.1%-5.5%) in these macroRNAs is comparable to the density of exons within protein-coding transcripts (5.2%). These macroRNAs, taken together, thus possess the imprint of purifying selection, thereby indicating their functionality.

Answer: Compared to protein coding genes, long non-coding RNAs (lncRNAs) display a bias towards two-exon transcripts. They are predominantly localized in the chromatin and nucleous. They are lower expressed and display a more tissue-specific expression pattern. LncRNAs are overall more weakly conserved than protein coding genes.
Question: Which sports have a risk for commotio cordis?

Context:
This study sought to characterize the demographics of commotio cordis globally in comparison to the U.S. experience.
Not unexpectedly, the groups differed with baseball/softball and football predominant in the United States (55% of events) and soccer, cricket, and hockey most common internationally (47% of events). 
The authors reviewed 41 incidents of baseball injuries reported to the National Center for Catastrophic Sports Injury Research from 1982 until 2002.
Catastrophic injuries included 23 severe head injuries, 8 cervical injuries, 3 cases of commotio cordis, and 2 cases each of a collapsed trachea and facial fractures.
Commotio cordis events occurred most commonly during organized sporting events (79 [62%]), such as baseball, but 49 (38%) occurred as part of daily routine and recreational activities.
Twenty-two (28%) participants were wearing commercially available chest barriers, including 7 in whom the projectile made direct contact with protective padding (baseball catchers and lacrosse/hockey goalies), and 2 in whom the projectile was a baseball specifically designed to reduce risk.
In a recent study of fatal chest impacts by baseballs, 28% of the children were wearing a chest protector. This study evaluates the effectiveness of chest protectors in reducing the risk of commotio cordis. 
It has been described after blows to the chest from baseballs, softballs, hockey pucks, and other objects.
Commotio cordis due to blunt trauma to the precordium is a rare cause of death in young athletes, occurring less frequently than all of the other athletics-related deaths. Several measures, such as the use of safety baseballs and the use of chest protectors, can help protect young athletes from commotio cordis. 

Answer: Participation in sports such as baseball, football, soccer, cricket, hockey and lacrosse has a risk for commotio cordis.
Exact answer: baseball, football, soccer, cricket, hockey, lacrosse
Question: Which genetic defects are observed in Prader-Willi syndrome?

Context:
Prader-Willi syndrome is a complex genetic disease caused by lack of expression of paternally inherited genes on chromosome 15q11-q13.
Prader-Willi syndrome (PWS) is caused by the disturbed expression of genes from the imprinted region of 15q11-q13, but the specific contributions of individual genes remain unknown.
Prader-Willi syndrome (PWS) is a rare disorder caused by genetic defects in certain regions of chromosome 15q11-13.
Prader-Willi syndrome (PWS) is an example of a human genetic disorder that involves imprinting genes on the proximal long arm of chromosome 15 and SNRPN gene as a candidate gene for this syndrome.
Genomic imprinting plays an important role in the molecular pathogenesis of PWS that caused by paternal microdeletions of 15q11-q13 or maternal UPD of chromosome 15. The basic defect seemed to be an absence of function of PWS genes that are normally expressed only from the paternal chromosome 15.
Abnormalities in imprinted inheritance occur in several genetic diseases and cancer, and are exemplified by the diverse genetic defects involving chromosome 15q11-q13 in Prader-Willi (PWS) and Angelman (AS) syndromes.
The predominant genetic defects in PW are 15q11-13 deletions of paternal origin and maternal chromosome 15 uniparental disomy.
In both disorders, these mutations are associated with parent-of-origin specific methylation at several 15q11-13 loci.
Prader-Willi syndrome (PWS) is caused by absence of a paternal contribution of the chromosome region 15q11-q13, resulting from paternal deletions, maternal uniparental disomy, or rare imprinting mutations.
Because methylation analysis can detect all three major classes of genetic defects associated with PWS (deletion, UPD, or imprinting mutations), methylation analysis with either PW71 or SNRPN is an efficient primary screening test to rule out a diagnosis of PWS.
The predominant genetic defects in Prader-Willi syndrome (PWS) are 15q11-q13 deletions of paternal origin and maternal chromosome 15 uniparental disomy (UPD).
In both disorders, these mutations are associated with parent-of-origin specific methylation at several 15q11-q13 loci. The critical PWS region has been narrowed to a approximately 320-kb region between D15S63 and D15S174, encoding several imprinted transcripts, including PAR5, IPW, PAR1 (refs 7,8) and SNRPN, which has so far been considered a strong candidate for the PWS gene.
The genetic defects in Prader-Willi syndrome (PWS) and Angelman syndrome (AS) map to 15q11-13.

Answer: The predominant genetic defects in Prader-Willi syndrome are 15q11-13 deletions of paternal origin and maternal chromosome 15 uniparental disomy, or rare imprinting mutations, combined with monoallelic expression of the paternal alleles.
Exact answer: 15q11-13 deletions of paternal origin, maternal chromosome 15 uniparental disomy, rare imprinting mutations, monoallelic expression of the paternal alleles
Question: Describe the usefulness of CAMUR in The Cancer Genome Atlas (TCGA)

Context:
CAMUR: Knowledge extraction from RNA-seq cancer data through equivalent classification rules
CAMUR, a new method that extracts multiple and equivalent classification models. CAMUR iteratively computes a rule-based classification model, calculates the power set of the genes present in the rules, iteratively eliminates those combinations from the data set, and performs again the classification procedure until a stopping criterion is verified. CAMUR includes an ad-hoc knowledge repository (database) and a querying tool.We analyze three different types of RNA-seq data sets (Breast, Head and Neck, and Stomach Cancer) from The Cancer Genome Atlas (TCGA) and we validate CAMUR and its models also on non-TCGA data. Our experimental results show the efficacy of CAMUR: we obtain several reliable equivalent classification models, from which the most frequent genes, their relationships, and the relation with a particular cancer are deduced
CAMUR includes an ad-hoc knowledge repository (database) and a querying tool.We analyze three different types of RNA-seq data sets (Breast, Head and Neck, and Stomach Cancer) from The Cancer Genome Atlas (TCGA) and we validate CAMUR and its models also on non-TCGA data.
CAMUR: Knowledge extraction from RNA-seq cancer data through equivalent classification rules.
We propose CAMUR, a new method that extracts multiple and equivalent classification models.

Answer: CAMUR is a new method that extracts multiple and equivalent classification models. CAMUR iteratively computes a rule-based classification model, calculates the power set of the genes present in the rules, iteratively eliminates those combinations from the data set, and performs again the classification procedure until a stopping criterion is verified. CAMUR includes an ad-hoc knowledge repository (database) and a querying tool. Three different types of RNA-seq data sets (Breast, Head and Neck, and Stomach Cancer) were analyzed from The Cancer Genome Atlas (TCGA) and CAMUR and its models were validated also on non-TCGA data. Experimental results show the efficacy of CAMUR by obtaining several reliable equivalent classification models, from which the most frequent genes, their relationships, and the relation with a particular cancer are deduced.
Question: Are Sidekick proteins members of the immunoglobulin superfamily?

Context:
Here we show that four closely related immunoglobulin superfamily (IgSF) adhesion molecules--Dscam (Down's syndrome cell adhesion molecule), DscamL (refs 6-9), Sidekick-1 and Sidekick-2
Sidekick-1, a cell adhesion molecule of the immunoglobulin superfamily, is up-regulated in glomerular podocytes in the collapsing glomerulopathy of HIV-associated nephropathy (HIVAN).

Answer: Yes, sidekick are cell adhesion molecules of the immunoglobulin superfamily.
Exact answer: yes
Question: Is the ACE inhibitor indicated for lung cancer treatment?

Context:
The angiotensin converting enzyme (ACE) inhibitors are used widely as antihypertensive agents, and it has been suggested that they decrease the risk of some cancers, although available data are conflicting. 
Using cell viability and fluorescent activated cell sorting analysis tests, we demonstrated that captopril inhibited the viability of LNM35 cells by inducing apoptosis, providing insight about the mechanisms underlying its antitumorigenic activities. In view of these experimental findings, we conclude that captopril could be a promising option for the treatment of lung cancer.
In order to determine the mechanism by which captopril inhibited tumor growth, we investigated the impact of this drug on cell proliferation, apoptosis, and angiogenesis. Immunohistochemical analysis demonstrated that captopril treatment significantly reduced the number of proliferating cells (Ki-67) in the tumor samples but was not associated with inhibition of tumor angiogenesis (CD31).
Using this model, we demonstrated that daily IP administration of captopril (2.8 mg/mouse) for 3 weeks resulted in a remarkable reduction of tumor growth (58%, P < 0.01) and lymph node metastasis (50%, P= 0.088). 
Angiotensin-converting enzyme (ACE) inhibitors have been shown to mitigate radiation-induced lung injury in preclinical models
ACE inhibitors may decrease the incidence of radiation pneumonitis in patients receiving thoracic radiation for lung cancer.

Answer: No, the angiotensin converting enzyme (ACE) inhibitors are used widely as antihypertensive agents. On the contrary, it has been suggested that they decrease the risk of some cancers, although available data are conflicting. One study proposes that captopril could be a promising option for the treatment of lung cancer. Furthermore, angiotensin-converting enzyme (ACE) inhibitors have been shown to mitigate radiation-induced lung injury in preclinical models
Exact answer: no
Question: List genes that have been found mutated in CMT1A (Charcot-Marie-Tooth disease type 1 A).

Context:
Most cases of CMT are caused by mutations in PMP22,
 structural myelin protein PMP22
Duplication of the gene encoding the peripheral myelin protein of 22 kDa (PMP22) underlies the most common inherited neuropathy, Charcot-Marie-Tooth 1A (CMT1A), a disease without a known cure.
. Two patients showed rearrangements in the PMP22 gene, which is commonly associated with CMT1
Many PMP22 mutants accumulate in excess in the endoplasmic reticulum (ER) and lead to the inherited neuropathies of Charcot-Marie-Tooth (CMT) disease. 
The T118M mutation in PMP22 gene is associated with Charcot Marie Tooth, type 1A (CMT1A).
In CMT1, PMP22 duplication was the most common mutation while the second gene in order of frequency was MPZ in familial and SH3TC2 in isolated cases. 
CMT1A/PMP22 duplication
he most frequent subtype is type 1A (CMT1A) caused by duplication in chromosome 17p12 that includes PMP22.

Answer: PMP22 is the common gene found mutated through a duplication in CMT1A. Other genes are
MPZ and SH3TC2
Exact answer: PMP22, MPZ, SH3TC2
Question: In which genomic regions are Alu enriched?

Context:
There are regions such as the four homeobox gene clusters, which are nearly devoid of these repeats that contrast with repeat dense regions in other transcriptionally active regions of the genome.
These elements are more clustered in genes which are involved in metabolism, transport, and signaling processes. In contrast, they are significantly fewer in genes coding for information pathway components as well as structural proteins.
This bias in Alu distribution is independent of the effect of Alu density of the flanking genomic region and is also not affected by the GC content of the gene and its upstream and downstream regions.
The relative proportions of Alu subfamilies (Alu J, Alu S, and Alu Y) are not significantly different in genes with high Alu density belonging to the functional categories of transport, metabolism, and signaling.
We suggest that Alu elements might be involved in regulatory mechanisms and are therefore differentially selected in primate genomes.
Sequence analysis demonstrated these "young" Alu insertions represented gene conversion events of pre-existing ancient Alu elements or independent parallel insertions of older Alu elements in the same genomic region. 
This study suggests that the majority of Alu insertions in primate genomes are the products of unique evolutionary events.
Our screening of the Alu insertion loci also resulted in the recovery of several "young" Alu elements that resided at orthologous positions in nonhuman primate genomes.

Answer: There are regions such as the four homeobox gene clusters, which are nearly devoid of these repeats that contrast with repeat dense regions in other transcriptionally active regions of the genome. Alu elements are more clustered in genes which are involved in metabolism, transport, and signaling processes. In contrast, they are significantly fewer in genes coding for information pathway components as well as structural proteins.
This bias in Alu distribution is independent of the effect of Alu density of the flanking genomic region and is also not affected by the GC content of the gene and its upstream and downstream regions.
There are regions such as the four homeobox gene clusters, which are nearly devoid of these repeats that contrast with repeat dense regions in other transcriptionally active regions of the genome.
Exact answer: genes which are involved in metabolism, transport, and signaling processes, gene conversion-prone regions