nirantk/geneticsQA-train huggingface dataset:
Question: List representatives of the major fungal hypoxanthine-adenine-guanine transporter families.

Context:
Comparative kinetic analysis of AzgA and Fcy21p, prototypes of the two major fungal hypoxanthine-adenine-guanine transporter families
We carried out a comparative kinetic analysis of two prototypes of these transporter families. The first was Fcy21p, a herein characterized protein of Candida albicans, and the second was AzgA, a transporter of Aspergillus nidulans
The azgA gene of Aspergillus nidulans encodes a hypoxanthine-adenine-guanine transporter
In Aspergillus nidulans, loss-of-function mutations in the uapA and azgA genes, encoding the major uric acid-xanthine and hypoxanthine-adenine-guanine permeases, respectively, result in impaired utilization of these purines as sole nitrogen sources
Comparative kinetic analysis of AzgA and Fcy21p, prototypes of the two major fungal hypoxanthine-adenine-guanine transporter families.
The azgA gene of Aspergillus nidulans encodes a hypoxanthine-adenine-guanine transporter.
In Aspergillus nidulans, loss-of-function mutations in the uapA and azgA genes, encoding the major uric acid-xanthine and hypoxanthine-adenine-guanine permeases, respectively, result in impaired utilization of these purines as sole nitrogen sources.
Modelling, substrate docking and mutational analysis identify residues essential for function and specificity of the major fungal purine transporter AzgA.
In Arabidopsis two proteins, AtAzg1 and AtAzg2, show substantial amino acid sequence similarity to the adenine-guanine-hypoxanthine transporter AzgA of Aspergillus nidulans

Answer: AzgA and Fcy21p are prototypes of the two major fungal hypoxanthine-adenine-guanine transporter families.
Exact answer: AzgA, Fcy21p
Question: Which cell type has the protein Chromogranin A as marker?

Context:
Neuroendocrine differentiation (chromogranin A and/or synaptophysin positivity) 
All paragangliomas were universally positive for chromogranin A 
chromogranin A (CGA) is a useful marker for pancreatic neuroendocrine tumors (pNET)
Together with Chromogranin B and Secretogranins, Chromogranin A (CGA) is stored in secretory (chromaffin) granules of the diffuse neuroendocrine system
Chromogranin A (CgA) is the most important general tumour marker used in the diagnosis and follow-up of patients with neuroendocrine tumours (NET).
Chromogranin A (CgA) not only plays an important role in pathologic diagnosis, but is also used as a circulating biomarker in patients with gastroenteropancreatic neuroendocrine neoplasm (GEP-NEN).
numbers of chromogranin A (CHGA)-positive enteroendocrine cells (EEC
 CgA is a reliable serum diagnostic biomarker for PNETs
Chromogranin A (CgA) was considered as the most practical and useful serum tumor marker in PNET patients.
the neuroendocrine markers chromogranin A and synaptophysin;

Answer: Chromogranin A is a marker for neuroendocrine cells
Exact answer: neuroendocrine cells
Question: Is the protein FAK (Focal Adhesion Kinase) phosphorylated?

Context:
Overexpression of NEDD9 led to tyrosine phosphorylation of FAK and SRC oncoproteins, 
yrosine phosphorylated FAK
TNFα contributes for attenuating both Y397FAK and Y416Src phosphorylations in osteoblasts.
 It was possible to show that TNFα provokes attenuation at Y-phosphorylation of both FAK (at Y397 )
ownregulation of G3BP significantly inhibited the phosphorylation of Src, FAK
Periodic mechanical stress significantly induced sustained phosphorylation of FAK at Tyr(397) and Tyr(576/577). 
oss of αSNAP impaired Golgi-dependent glycosylation and trafficking of β1 integrin and decreased phosphorylation of focal adhesion kinase (FAK) and paxillin resulting in FA disassembly.
functional characterization of many of today's best-known Src substrates (for example, p85-Cortactin, p110-AFAP1, p130Cas, p125FAK and p120-catenin)
Western blots were used for P-FAK
e first time, that the EGF-dependent EGFR activation led to increased P-FAKSer732
. P-FAKSer732 presence was crucial for the maintenance of the proliferation rate and its levels were inversely related to the levels of acetylated α-tubulin. P-FAKSer732 localized at the microtubules (MTs) of the spindle, biochemically associated with MTs and contributed to MT depolymerization.
specially, phosphorylation of Tyr925-FAK that is required for full activation of FAK was nearly completely suppressed even with 1nM of methyl violet 2B in A375P cancer cells. 
 The protein expression of PTPN13, focal adhesion kinase (FAK) and phosphorylated FAK (P-FAK) was evaluated using immunohistochemical staining and western blotting.
Curcumin inhibits focal adhesion kinase (FAK) phosphorylation and enhances the expressions of several extracellular matrix components which play a critical role in invasion and metastasis. 
uppressed both the phosphorylation of FAK 
 A GEF-inactive Rgnef mutant rescues FAK-Y397 phosphorylation 

Answer: yes, the protein FAK (Focal Adhesion Kinase) is phosphorylated.
Exact answer: yes
Question: Describe a diet that reduces the chance of kidney stones.

Context:
calcium oxalate remains the dominant type accounting for 64% of stones in our dataset,
Uric acid stones contributed 16% of contemporary stone compositions,
Struvite stones showed a decreasing trend from 14% in the 1970s, to 12% in the 1980s and 7% in the current data.
. Given recent concerns that calcium supplements may raise risk for cardiovascular disease and kidney stones,

Answer: People can help prevent kidney stones by making changes in fluid intake and, depending on the type of kidney stone, changes in consumption of sodium, animal protein, calcium, and oxalate.
Drinking enough fluids each day is the best way to help prevent most types of kidney stones. Health care providers recommend that a person drink 2 to 3 liters of fluid a day. People with cystine stones may need to drink even more. Though water is best, other fluids may also help prevent kidney stones, such as citrus drinks.
Exact answer: reducing sodium
Question: How long, in kb (kilobases),  is a "Long interspersed nuclear element"?

Context:
 A combination of molecular hybridization studies and long-range polymerase chain reaction was used to isolate a 6-kb full-length long interspersed nuclear element (LINE or L1)
LINE (7kb long interspersed nuclear element),
The retrotransposon known as long interspersed nuclear element-1 (L1) is 6 kb long, although most L1s in mammalian and other eukaryotic cells are truncated.

Answer: The retrotransposon known as long interspersed nuclear element-1 (L1) is 6-7 kb long,
Exact answer: 6-7 kb
Question: Which heat shock protein is found to be upregulated during Hsp90 inhibition?

Context:
HSP90 inhibition was associated with decreased neuroendocrine ErbB and IGF-I receptor expression, decreased Erk and Akt phospho-rylation and the induction of HSP70 expression.
Inhibition of Hsp90 upregulated the expression of Hsp70 and Hsp70-bound Nox2, 5 and promoted degradation.
Conversely, inhibition of HSP90 significantly increased the expression of both VEGF and HGF mRNA, and induced HSP70 protein in PHH cultures in vitro.

Answer: HSP90 inhibition was found to be associated with induction of HSP70 expression.
Exact answer: HSP70
Question: What is the number of protein coding genes in the human genome?

Context:
Here, seven membrane protein topology prediction methods based on different underlying algorithms, such as hidden Markov models, neural networks and support vector machines, have been used for analysis of the protein sequences from the 21,416 annotated genes in the human genome.
he GENCODE 7 release contains 20,687 protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts not represented in UCSC genes and RefSeq
Current catalogs list a total of approximately 24,500 putative protein-coding genes.
Clustering of these sequences using cross-species relationships suggests that millions of expressed sequences may correspond to only approximately 20,000 distinct protein-coding transcripts.

Answer: The number of protein coding genes in the human genome is currently estimated between 20,000 and 25,000
Exact answer: Between 20,000 and 25,000
Question: What is known about food intolerance and gluten ?

Context:
At present, there is no specific bio-marker of gluten sensitivity.
Emerging research into a syndrome known as nonceliac gluten sensitivity suggests a heterogeneous condition with some features of celiac disease but often categorized as FGIDs, including IBS.
Celiac disease, with a prevalence around 1% of the general population, is the most common genetically-induced food intolerance in the world. Triggered by the ingestion of gluten in genetically predisposed individuals,
Gluten intolerance is a unique model of autoimmune disease in which we can recognize the main environmental factor (gluten) and the more complex genetic background.
Coeliac disease is a multifactorial disease characterized by a dysregulated immune response to ingested wheat gluten and related cereal proteins. With an incidence of about 1% of the general population, it is considered the most common food intolerance disorder.
Coeliac disease is a lifelong intolerance to the gluten found in wheat, barley and rye, and some patients are also sensitive to oats. The disease is genetically determined, with 10% of the first-degree relatives affected and 75% of monozygotic twins being concordant.

Answer: Celiac disease, with a prevalence around 1% of the general population, is the most common genetically-induced food intolerance in the world. Triggered by the ingestion of gluten in genetically predisposed individuals.
Emerging research into a syndrome known as nonceliac gluten sensitivity suggests a heterogeneous condition with some features of celiac disease but often categorized as FGIDs, including IBS.
Coeliac disease is a multifactorial disease characterized by a dysregulated immune response to ingested wheat gluten and related cereal proteins. With an incidence of about 1% of the general population, it is considered the most common food intolerance disorder.Emerging research into a syndrome known as nonceliac gluten sensitivity suggests a heterogeneous condition with some features of celiac disease but often categorized as FGIDs, including IBS.
Question: Is protein CXCR4 used as a prognostic marker of cancer?

Context:
Aberrant overexpression of CXCR4 is associated with worse overall survival, adenocarcinoma histology, distant metastasis, lymph node involvement in NSCLC.
CXCR4 belongs to a family of G protein-coupled cell surface receptors and has been proved to a prognostic marker in a various tumors, including esophageal squamous cell cancer. 
The chemokine C-X-C motif receptor 4 (CXCR4) has been found to be a prognostic marker in various types of cancer, being involved in chemotaxis, stemness and drug resistance. 
The chemokine receptor CXCR4 that has been shown to be implicated in PDAC tumorigenicity and aggressiveness could serve as a prognostic marker for survival after a curative-intent surgery and was associated with the pattern of tumour recurrence (distant versus local relapse).
XCR4 promotes tumor growth, angiogenesis and metastasis, and is a prognostic marker in a number of different types of tumors.
CXCR4 has been identified as a prognostic marker for acute myeloid leukemia (AML) and other malignancies. 
The chemokine receptor CXCR4 has been found to be a prognostic marker in various types of cancer, including breast cancer. 
Upregulated expression of C-X-C chemokine receptor 4 is an independent prognostic predictor for patients with gastric cancer.
detection of CXCR4 expression will be helpful for predicting prognosis for patients with gastric cancer.
The chemokine receptor CXCR4 is a marker of metastatic disease.
High CXCR4 level in cancer specimens independently predicts a poor outcome for patients with node-positive breast cancer.
Univariate and multivariate analyses demonstrated that the high levels of nuclear CXCR4 and CXCL12 expression in hepatocytes were significantly better prognostic factors for overall and hepatic disease-free survival in patients with CLM.
The chemokine receptor CXCR4 has been implicated in sarcoma development and has been found to be a prognostic marker for poor clinical outcome. 
high CXCR4 expression is correlated to shorter DFS and could be used as a prognostic marker in order to stratify melanoma patients at higher progression risk.

Answer: Yes, the chemokine C-X-C motif receptor 4 (CXCR4) has been found to be a prognostic marker in various types of cancer.
Exact answer: yes
Question: Are chromomethylases present in animal genomes?

Context:
Many plant, animal, and fungal genomes contain cytosine DNA methylation in asymmetric sequence contexts (CpHpH, H = A, T, C).
However, at the SUPERMAN locus, asymmetric methylation was only completely abolished in drm1 drm2 chromomethylase 3 (cmt3) triple mutant plants.
Although neither the drm1 drm2 double mutants nor the cmt3 single mutants show morphological defects, drm1 drm2 cmt3 triple mutant plants show pleiotropic effects on plant development.
Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene.
The lack of CMT homologs in animal genomes could account for the observation that in contrast to plants, animals maintain primarily CG methylation.
Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants.
A role for CHROMOMETHYLASE3 in mediating transposon and euchromatin silencing during egg cell reprogramming in Arabidopsis.
During embryogenesis there is a major switch from dependence upon maternally-deposited products to reliance on products of the zygotic genome.
Expression analysis of eight putative tomato DNA methyltransferases encoding genes showed that one chromomethylase (CMT) and two rearranged methyltransferases (DRMs) are preferentially expressed in the pericarp during fruit growth and could be involved in the locus-specific increase of methylation observed at this developmental phase in the pericarp.
Natural variation for alleles under epigenetic control by the maize chromomethylase zmet2.
Arabidopsis has two types of methyltransferases with demonstrated maintenance activity: MET1, which maintains CpG methylation and is homologous to mammalian DNMT1, and CHROMOMETHYLASE 3 (CMT3), which maintains CpNpG (N = A, T, C, or G) methylation and is unique to the plant kingdom.
Maize chromomethylase Zea methyltransferase2 is required for CpNpG methylation.
A cytosine DNA methyltransferase containing a chromodomain, Zea methyltransferase2 (Zmet2), was cloned from maize. The sequence of ZMET2 is similar to that of the Arabidopsis chromomethylases CMT1 and CMT3, with C-terminal motifs characteristic of eukaryotic and prokaryotic DNA methyltransferases.
We have detected a chromodomain embedded within the catalytic region of a predicted Arabidopsis DNA methyltransferase that is diverged from other eukaryotic enzymes. The 791 residue "chromomethylase" (CMT1) is encoded by a floral transcript that is spliced from 20 exons and is present at only approximately 1/10(-7) of total mRNA.

Answer: No. Multiple lines of experimental evidence suggest that chromomethylases (CMTs) have been hitherto identified in plant genomes(Arabidopsis, maize, tomato). CMTs maintain CpNpG (N = A, T, C, or G) methylation and they are unique to the plant kingdom. The lack of CMT homologs in animal genomes could be explained based on the fact that, in contrast to plants, animals maintain primarily CG methylation. Therefore, the presence of CMTs is not required in the animal genomes.
Exact answer: no
Question: Which is the molecular weight of the protein angiogenin?

Context:
Angiogenin is a potent blood-vessel-inducing polypeptide with a molecular weight of 14,000 that has a unique ribonucleolytic activity.
 Bovine angiogenin is a single-chain protein of 125 amino acids; it contains six cysteines and has a calculated molecular weight of 14,595.
The amino acid composition of this basic (isoelectric point greater than 9.5), single-chain protein of molecular weight approximately 14 400 has been determined.
was found to have a molecular weight of 15 kDa on SDS-PAGE, and the sequence of the N-terminal 25 amino acid residues was identical to that of bovine angiogenin
Human angiogenin is a 14-kDa plasma protein with angiogenic and ribonucleolytic activities. 
 angiogenin-1 (15 kDa). 
This protein is 14 kD in molecular weight, and is identical to the angioplastic factor angiogenin. 
 angiogenin (M(r) = 14,120),

Answer: The molecular weight of angiogenin is 14,120 Da. The bovine angiogenin is 14,595 Da
Exact answer: 14,120 Da
Question: Do thyroid hormone receptors change after brain injury?

Context:
For example, the T3 receptor alpha was predominantly expressed in stroke-tissue, indicating that regeneration of nerves in stroke tissue may be facilitated by increased T3 receptor alpha expression.
TRα expression was also increased in human infants with IVH. 
Thus, in infants with IVH the combined elevation in deiodinase-3 and reduction in deiodinase-2 decreases TH signaling that can be worsened by an increase in unliganded TRα. 
A rapid increase of the total number of binding sites for T3 appeared within 30 min of ischemia and reached over 40% by 3 h. During the same 3-h period, the relative binding affinity was reduced by 25%. Upon recirculation after 30 min or 3 h of ischemia, a rapid reversal of measured T3 binding sites occurred, which progressed to 20-30% below the control value by the recirculation period of 3 h. 

Answer: thyroid hormone receptors increase after brain injury
Exact answer: yes
Question: What is membrane scission?

Context:
To promote membrane scission, dynamin proteins polymerize, wrap around, and constrict the membrane; however, the mechanism underlying their role in membrane fusion remains unclear.
 Its role in endocytosis may be mediated by its reported interaction with dynamin 2, a 100 kDa GTPase that polymerizes around the necks of budding vesicles and catalyzes membrane scission
Because the neck's radius is, in general, finite, membrane scission and the consequent pinching off of the vesicle can only occur if it is narrowed to permit the necessary membrane topological reformation.
Dynamin recruitment and membrane scission at the neck of a clathrin-coated pit.
ESCRT-III is the final complex in the pathway that assembles on endosomes and executes membrane scission of intraluminal vesicles.
The scission of biological membranes is facilitated by a variety of protein complexes that bind and manipulate lipid bilayers. 
Dynamin-2 is a pleiotropic GTPase whose best-known function is related to membrane scission during vesicle budding from the plasma or Golgi membranes. 
 Force produced by actin similarly contributes in membrane scission in endocytosis or Golgi remodeling.
Dynamin 2 (Dyn2) is a ~100kDa GTPase that assembles around the necks of nascent endocytic and Golgi vesicles and catalyzes membrane scission. 
membrane scission protein dynamin-2.
 Finally, a membrane scission event must occur to release the free virion
 Furthermore, GTP-dependent membrane scission by dynamin was dramatically elevated by BAR domain proteins. 
few can mediate membrane scission to complete the budding process.

Answer: Membrane scission is the final step in order to complete the budding process, pinching off of the vesicle. To promote membrane scission, dynamin proteins polymerize, wrap around, and constrict the membrane. The scission of biological membranes is facilitated by a variety of protein complexes that bind and manipulate lipid bilayers.
Question: Which is the enzyme that degrades decapped mRNAs?

Context:
The removal of the 5'-cap structure by the decapping enzyme DCP2 and its coactivator DCP1 shuts down translation and exposes the mRNA to 5'-to-3' exonucleolytic degradation by XRN1
DCP2 activation by DCP1 occurs preferentially on the EDC4 scaffold, which may serve to couple DCP2 activation by DCP1 with 5'-to-3' mRNA degradation by XRN1 in human cells
XRN1 is a 5' → 3' processive exoribonuclease that degrades mRNAs after they have been decapped

Answer: The removal of the 5'-cap structure by the decapping enzyme DCP2 and its coactivator DCP1 shuts down translation and exposes the mRNA to 5'-to-3' exonucleolytic degradation by XRN1
The removal of the 5'-cap structure by the decapping enzyme DCP2 and its coactivator DCP1 shuts down translation and exposes the mRNA to 5'-to-3' exonucleolytic degradation by XRN1.
Exact answer: XRN1
Question: Is the long non- coding RNA malat-1 up or downregulated in cancer?

Context:
lncRNA MALAT-1 expression is upregulated in some tumors.
Metastasis-Associated-in-Lung-Adenocarcinoma-Transcript-1 (MALAT-1) is an ncRNA that is highly expressed in several tumor types
metastasis-associated lung adenocarcinoma transcript (MALAT)-1 is known to be consistently upregulated in several epithelial malignancies
MALAT-1 was up-regulated in human prostate cancer tissues and cell lines.
Genome-wide profiling revealed that MALAT-1 and prostate cancer gene 3 (PCA3) are overexpressed in PCa tissues
The level of MALAT-1 in LSCC was significantly higher than that in the corresponding adjacent non-neoplastic tissues
metastasis-associated lung adenocarcinoma transcript 1, MALAT1, is a long non-coding RNA (lncRNA) that has been discovered as a marker for lung cancer metastasis. It is highly abundant,
(MALAT1), a long non-coding RNA (lncRNA), is up-regulated in many solid tumors and associated with cancer metastasis and recurrence
 Quantitative analyses indicated a 6-7-fold increased RNA level in HCCs versus uninvolved liver,
(hcn), encoding a 7-kb mRNA-like transcript. The gene appears to be the murine ortholog of the human alpha gene, that is, MALAT-1.
After suppression subtractive hybridization and differential screening, we detected the metastasis-associated lung adenocarcinoma transcript 1 (MALAT-1) gene as one of the major genes upregulated in ESS
a novel non-coding RNA (MALAT-1) to be expressed at significantly higher levels in stage-I and stage-II NSCLC primary tumours that subsequently metastasised
quantitative RT-PCR verified overexpression in metastasizing samples. Several of the identified genes (eIF4A1, thymosin beta4 and a novel transcript named MALAT-1) were demonstrated to be significantly associated with metastasis in NSCLC patients 
Σ RNA is a class of conserved large non-coding RNAs (murine Hepcarcin; human MALAT-1) up-regulated in carcinomas
To date, most known NCTs studied have been relatively short, but several important regulatory NCTs, including XIST, MALAT-1, BC1 and BC200, are considerably larger in length
These NCTs were among the most abundantly expressed transcripts detected
The nuclear transcript MALAT-1 has been functionally associated with gene regulation and alternative splicing and its regulation has been shown to impact proliferation, apoptosis, migration and invasion

Answer: Malat-1 expression is upregulated in several tumor types
Exact answer: upregulated