nirantk/geneticsQA-train huggingface dataset:
Question: List processes which are under the control of the YAP protein.

Context:
in which YAP appears to regulate cell proliferation 
YAP and TAZ oncoproteins confer malignancy and drug resistance to various cancer types. 
Yes-associated protein (YAP), a transcription coactivator, is the major downstream effector of the Hippo pathway, which plays a critical role in organ size control and cancer development
YAP (Yes-associated protein) and TAZ (transcriptional coactivator with PDZ-binding motif) are major downstream effectors of the Hippo pathway that influences tissue homeostasis, organ size, and cancer development. 
The Hippo signaling pathway converges on YAP to regulate growth, differentiation, and regeneration.
Yes associated protein (YAP) and transcriptional co-activator with PDZ-binding motif (TAZ) are its targets and terminal effectors: inhibition of the pathway promotes YAP/TAZ translocation to the nucleus, where they interact with transcriptional enhancer associate domain (TEAD) transcription factors and coactivate the expression of target genes, promoting cell proliferation. 
Intracellular molecules Yap, Akt, mTOR, and Erk are signaling pathway members that regulate the proliferation of tumor cells

Answer: Yes-associated protein (YAP), a transcription coactivator, is the major downstream effector of the Hippo pathway, which plays a critical role in organ size control, cell poliferation and cancer development and tissue homeostasis and differentiation.
Exact answer: cell proliferation, organ size control, cancer development, tissue homeostasis, cell differentiation
Question: What is the major adverse effect of adriamycin(doxorubicin)?

Context:
It remains to be seen whether inhibition by adriamycin of these systems is related to the severe cardiotoxicity, the major adverse effect of the drug that limits its clinical usefulness.
Leukocytopenia was the major adverse effect among patients undergoing systemic THP administration
The major adverse effect was bone-marrow suppression;
The major adverse effect was bone marrow suppression;
Cardiotoxicity is a major adverse effect of the anthracycline antibiotics and can be acute or chronic;
chronic cardiotoxicity represents a serious adverse effect that may be lethal due to the development of irreversible, cumulative dose-dependent, congestive cardiomyopathy
Myelosuppression, predominantly neutropenia and leucopenia, is the dose-limiting toxicity; in addition to this, mucositis, nausea, vomiting and alopecia are frequent, whereas hepatopathy, characterised by elevated bilirubin concentrations, occurs less frequently
In spite of the routine use of this drug its major adverse effect, the dose-dependent cardiotoxicity, cannot be prevented yet
The major adverse effect was myelosuppression
Cardiac toxicity is a major adverse effect caused by doxorubicin (DOX) therapy
Antioxidative and cardioprotective effects of Phyllanthus urinaria L. on doxorubicin-induced cardiotoxicity
The major adverse effect of DOX treatment in cancer patients is the onset of cardiomyopathy and heart failure

Answer: Cardiac toxicity is a major adverse effect caused by doxorubicin (DOX) therapy  
Cardiac toxicity is a major adverse effect caused by doxorubicin (DOX) therapy. In spite of the routine use of this drug its major adverse effect, the dose-dependent cardiotoxicity, cannot be prevented yet. Cardiotoxicity is a major adverse effect of the anthracycline antibiotics and can be acute or chronic.
Exact answer: Cardiotoxicity, Cardiac toxicity
Question: What is the triple screening test performed during pregnancy measuring?

Context:
AFP--1.18 MoM and estriol--1.29 MoM and significantly higher mean median value for the free beta-hCG
alpha-fetoprotein (AFP), 1.02 for human chorionic gonadotropin (hCG) and 1.01 for unconjugated estriol (uE3
alpha fetoprotein (AFP), beta human chorionic gonadotropin (beta-hCG), and unconjugated estriol (uE3) 
alpha-fetoprotein (AFP), intact HCG and unconjugated estriol (uE3)
lpha-fetoprotein (AFP), total beta human chorionic gonadotrophin (hCG) and estriol (uE(3)
alpha feto-protein, HCG and unconjugated estriol
maternal serum alpha-fetoprotein, human chorionic gonadotropin and unconjugated oestriol 
maternal serum alpha fetoprotein, unconjugated oestriol and human chorionic gonadotrophin

Answer: Alpha-fetoprotein (AFP), human chorionic gonadotropin (hCG) and unconjugated estriol (uE3)
Exact answer: AFP, Estriol, hCG
Question: Approximately how many recombination hotspots have been found in the yeast genome?

Context:
In the fission yeast genome DSBs are located within 194 prominent peaks separated on average by 65-kbp intervals of DNA that are largely free of DSBs
Most meiotic recombination is positioned at hotspots, but knowledge of the mechanisms is nebulous
meiotic recombination is initiated by double-strand DNA breaks (DSBs) which occur at relatively high frequencies in some genomic regions (hotspots) and relatively low frequencies in others (coldspots)

Answer: In the fission yeast genome DSBs are located within 194 prominent peaks separated on average by 65-kbp intervals of DNA that are largely free of DSBs.
Exact answer: Approximately 200, 200, ~200
Question: Are there focused databases from which you can retrieve gene expression data on renal disease?

Context:
Proteomics database in chronic kidney disease
Naturally occurring human urinary peptides for use in diagnosis of chronic kidney disease

Answer: Biological databases are used to store and edit large amount of data, created from genomics data. In the most of the cases the data are stored according to their type but there are cases of focused databases that store database on a specific disease. In the case of renal disease there are plenty of databases, for example KUPKB a collection of omics datasets, Nephromine a renal genome-wide gene expression dataset based in transcriptomics, CDKD and Proteomics Database in Chronic Kidney Disease.
Exact answer: yes
Question: Are ultraconserved elements depleted among copy number variants (CNVs)?

Context:
We have demonstrated that nonexonic UCEs are depleted among segmental duplications (SDs) and copy number variants (CNVs) and proposed that their ultraconservation may reflect a mechanism of copy counting via comparison. Here, we report that nonexonic UCEs are also depleted among 10 of 11 recent genomewide data sets of human CNVs, including 3 obtained with strategies permitting greater precision in determining the extents of CNVs
Interestingly, human UCEs have been reported to be strongly depleted among segmental duplications and benign copy number variants (CNVs)
We propose that these elements may be interpreted as hallmarks for dose-sensitive genes, particularly for those genes whose gain or loss may be directly implied in neurodevelopmental disorders. Therefore, their presence in genomic imbalances of unknown effect might be suggestive of a clinically relevant condition
Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants.
Ultraconserved elements (UCEs) are strongly depleted from segmental duplications and copy number variations (CNVs) in the human genome, suggesting that deletion or duplication of a UCE can be deleterious to the mammalian cell.
Interestingly, human UCEs have been reported to be strongly depleted among segmental duplications and benign copy number variants (CNVs).
We have demonstrated that nonexonic UCEs are depleted among segmental duplications (SDs) and copy number variants (CNVs) and proposed that their ultraconservation may reflect a mechanism of copy counting via comparison.
We have demonstrated that nonexonic UCEs are depleted among segmental duplications (SDs) and copy number variants (CNVs) and proposed that their ultraconservation may reflect a mechanism of copy counting via comparison
Interestingly, human UCEs have been reported to be strongly depleted among segmental duplications and benign copy number variants (CNVs)
Here, we show that UCEs are significantly depleted among segmental duplications and copy number variants
The depletion of UCEs among copy number variation as well as the significant under-representation of single-nucleotide polymorphisms (SNPs) within UCEs have also revealed their evolutional and functional importance indicating their potential impact on disease, such as cancer

Answer: Yes. Interestingly, human ultraconserved elements (UCEs) have been reported to be strongly depleted among segmental duplications and benign copy number variants (CNVs). These elements may be interpreted as hallmarks for dose-sensitive genes, particularly for those genes whose gain or loss may be directly implied in neurodevelopmental disorders. Therefore, their presence in genomic imbalances of unknown effect might be suggestive of a clinically relevant condition
Exact answer: yes
Question: Is MammaPrint cleared by the United States Food and Drug Administration? 

Context:
Real-time RT-PCR confirmed the 5-gene prognostic signature that was distinct from an FDA-cleared 70-gene signature of MammaPrint panel and from the Oncotype DX recurrence score assay panel.

Answer: Yes. MammaPrint is cleared by the FDA for breast cancer recurrence.
Exact answer: yes
Question: Which are the common symptoms of Cushing's syndrome?

Context:
Cushing syndrome is the constellation of signs and symptoms caused by protracted exposure to glucocorticoids. The most common cause of Cushing syndrome in children and adolescents is exogenous administration of glucocorticoids. Presenting features commonly include weight gain, growth retardation, hirsutism, obesity, striae, acne and hypertension
This is a rare syndrome and its main endocrine manifestation, primary pigmented nodular adrenal disease (PPNAD), is an uncommon cause of adrenocorticotropic hormone-independent Cushing's syndrome.We report the case of a 20-year-old patient with a history of weight gain, hirsutism, acne, secondary amenorrhea and facial lentiginosis.

Answer: Cushing syndrome is the constellation of signs and symptoms caused by protracted exposure to glucocorticoids. Presenting features commonly include weight gain, growth retardation, hirsutism, obesity, striae, acne and hypertension.
Exact answer: weight gain, growth retardation, hirsutism, obesity, striae, acne, hypertension
Question: What is apelin?

Context:
Apelin, a small regulatory peptide, is the endogenous ligand for the apelin receptor (APJ) receptor.
Apelin is an adipocyte-derived hormone that plays important roles in energy metabolism.
Apelin, as the endogenous ligand of G protein-coupled receptor APJ, participates in a number of physiological and pathological processes. 
Apelin is a novel bioactive peptide as the endogenous ligand for APJ.
adipokine apelin 
Apelin is the endogenous ligand of the APJ receptor, a member of the G protein-coupled receptor family.
To date four adipokines (leptin, visfatin, apelin and ghrelin) have been investigated and all affect myometrial contractility, but some more potently than others.
The adipocytokine apelin is a peptide, Apelin and its receptor are abundantly expressed in the nervous and cardiovascular systems.
The aim of this study was to determine the levels of regulatory peptides apelin
Apelin is a vaso-dilatory peptide that also has a modulatory role in pain processing. 

Answer: Apelin, a small regulatory peptide, is the endogenous ligand for the apelin receptor (APJ) receptor.
Exact answer: Apelin, a small regulatory peptide, is the endogenous ligand for the apelin receptor (APJ) receptor.
Question: Has the fungus Ashbya gossypii got many nuclei that share cytoplasm?

Context:
multinucleated Ashbya gossypii cells.
multinucleated Ashbya gossypii fungal cells
Nuclei in the filamentous, multinucleated fungus Ashbya gossypii divide asynchronously. 
multinucleated Ashbya gossypii cells
We analyzed a unique asynchronous nuclear division cycle in a multinucleated filamentous fungus, Ashbya gossypii.
 multinucleated hyphae in Ashbya gossypii.
We have followed the migration of GFP-labelled nuclei in multinucleate hyphae of Ashbya gossypii
multinucleate fungus Ashbya gossypii
Ashbya gossypii grows as multinucleated and constantly elongating hyphae
multinucleated hyphae of Ashbya gossypii.
We report the mechanistic basis guiding the migration pattern of multiple nuclei in hyphae of Ashbya gossypii. 
multinucleate fungal cells
multinucleate Ashbya gossypii cells relies on a minimal network of genes
Clustering of nuclei in multinucleated hyphae is prevented by dynein-driven bidirectional nuclear movements and microtubule growth control in Ashbya gossypii.
In the multinucleate fungus Ashbya gossypii, cytoplasmic microtubules (cMTs) emerge from the spindle pole body outer plaque (OP) in perpendicular and tangential directions.
multinucleated hyphae of Ashbya gossypii.
multiple nuclei in Ashbya gossypii hyphae
Ashbya gossypii has a budding yeast-like genome but grows exclusively as multinucleated hyphae.

Answer: Yes, Ashbya gossypii has a budding yeast-like genome but grows exclusively as multinucleated hyphae.
Exact answer: yes
Question: Could transcription factors act as cell-cell signalling molecules?

Context:
Pax6 is a transcription factor essential for the development of tissues including the eyes, central nervous system and endocrine glands of vertebrates and invertebrates. It regulates the expression of a broad range of molecules, including transcription factors, cell adhesion and short-range cell-cell signalling molecules, hormones and structural proteins
Recent data support the view that transcription factors - in particular, homeoproteins - can be transferred from cell to cell and have direct non-cell-autonomous (and therefore paracrine) activities

Answer: Yes. Recent data support the view that transcription factors - in particular, homeoproteins - can be transferred from cell to cell and have direct non-cell-autonomous (and therefore paracrine) activities.
Pax6 is a transcription factor essential for the development of tissues including the eyes, central nervous system and endocrine glands of vertebrates and invertebrates. It regulates the expression of a broad range of molecules, including transcription factors, cell adhesion and short-range cell-cell signalling molecules, hormones and structural proteins
Exact answer: yes
Question: Which ones are the ESKAPE organisms?

Context:
The aim of this study was to test in the clinic whether antimicrobial diversity affects resistance of Enterococcus faecium, Staphylococcus aureus, Klebsiella species, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species (ESKAPE) pathogens in ventilator-associated pneumonia (VAP).
Despite important geographical variations, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species (ESKAPE) pathogens constitute more than 80% of ventilator-associated pneumonia (VAP) episodes. 
Multidrug resistance among the 'ESKAPE' organisms - encompassing Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp. - is of particular concern because they are responsible for many serious infections in hospitals.
Patients recovering from traumatic injuries or surgery often require weeks to months of hospitalization, increasing the risk for wound and surgical site infections caused by ESKAPE pathogens, which include A. baumannii (the ESKAPE pathogens are Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species).
'ESKAPE' (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acintobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) pathogens play a major role in the rapidly changing scenario of antimicrobial resistance in the 21st century.
Although bacteremias caused by the 6 ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) have recently been highlighted as a serious complication in solid organ transplant (SOT), more information is urgently needed. 
Multidrug resistance among the 'ESKAPE' organisms - encompassing Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.
Multidrug resistance among the 'ESKAPE' organisms - encompassing Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp. - is of particular concern because they are responsible for many serious infections in hospitals. 

Answer: The 6 ESKAPE pathogens are Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species.
Exact answer: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter species
Question: Have the promoter regions of the genes implicated in Rett Syndrome been characterized with CAGE?

Context:
CAGE-defined promoter regions of the genes implicated in Rett Syndrome.
Mutations in three functionally diverse genes cause Rett Syndrome. Although the functions of Forkhead box G1 (FOXG1), Methyl CpG binding protein 2 (MECP2) and Cyclin-dependent kinase-like 5 (CDKL5) have been studied individually, not much is known about their relation to each other with respect to expression levels and regulatory regions. Here we analyzed data from hundreds of mouse and human samples included in the FANTOM5 project, to identify transcript initiation sites, expression levels, expression correlations and regulatory regions of the three genes.RESULTS: Our investigations reveal the predominantly used transcription start sites (TSSs) for each gene including novel transcription start sites for FOXG1. We show that FOXG1 expression is poorly correlated with the expression of MECP2 and CDKL5. We identify promoter shapes for each TSS, the predicted location of enhancers for each gene and the common transcription factors likely to regulate the three genes. Our data imply Polycomb Repressive Complex 2 (PRC2) mediated silencing of Foxg1 in cerebellum.CONCLUSIONS: Our analyses provide a comprehensive picture of the regulatory regions of the three genes involved in Rett Syndrome.
CAGE-defined promoter regions of the genes implicated in Rett Syndrome
CAGE-defined promoter regions of the genes implicated in Rett Syndrome.

Answer: Yes. Promoter regions of the genes implicated in Rett Syndrome have been characterized using CAGE.
Exact answer: yes
Question: Which syndrome is NHE6 associated with?

Context:
A novel mutation in the endosomal Na+/H+ exchanger NHE6 (SLC9A6) causes Christianson syndrome with electrical status epilepticus during slow-wave sleep (ESES)
Mutations in the solute carrier family 9, subfamily A member 6 (SLC9A6) gene, encoding the endosomal Na+/H+ exchanger 6 (NHE6) are associated with Christianson syndrome, a syndromic form of X-linked intellectual disability characterized by microcephaly, severe global developmental delay, autistic behavior, early onset seizures and ataxia.
Genetic and phenotypic diversity of NHE6 mutations in Christianson syndrome.
Recently, Christianson syndrome (CS) has been determined to be caused by mutations in the X-linked Na(+) /H(+) exchanger 6 (NHE6).
Christianson syndrome protein NHE6 modulates TrkB endosomal signaling required for neuronal circuit development.
Recently, Christianson syndrome (CS) has been determined to be caused by mutations in the X-linked Na(+) /H(+) exchanger 6 (NHE6).
A novel mutation in the endosomal Na+/H+ exchanger NHE6 (SLC9A6) causes Christianson syndrome with electrical status epilepticus during slow-wave sleep (ESES).
Mutations in the solute carrier family 9, subfamily A member 6 (SLC9A6) gene, encoding the endosomal Na+/H+ exchanger 6 (NHE6) are associated with Christianson syndrome, a syndromic form of X-linked intellectual disability characterized by microcephaly, severe global developmental delay, autistic behavior, early onset seizures and ataxia. 
OBJECTIVE: Recently, Christianson syndrome (CS) has been determined to be caused by mutations in the X-linked Na(+) /H(+) exchanger 6 (NHE6). 
Mutations in the solute carrier family 9, subfamily A member 6 (SLC9A6) gene, encoding the endosomal Na+/H+ exchanger 6 (NHE6) are associated with Christianson syndrome, a syndromic form of X-linked intellectual disability characterized by microcephaly, severe global developmental delay, autistic behavior, early onset seizures and ataxia.
encoding the endosomal Na+/H+ exchanger 6 (NHE6) are associated with Christianson syndrome,

Answer: Mutations in the solute carrier family 9, subfamily A member 6 (SLC9A6) gene, encoding the endosomal Na+/H+ exchanger 6 (NHE6) are associated with Christianson syndrome, a syndromic form of X-linked intellectual disability characterized by microcephaly, severe global developmental delay, autistic behavior, early onset seizures and ataxia.
Exact answer: Christianson syndrome
Question: What is the gold standard treatment for Iatrogenic male incontinence?

Context:
The initial treatment for SUI that persists after 12 months consists of conservative measures such as pelvic floor muscle exercises and behavioral therapy. Properly selected and informed patients can also be treated efficiently with minimally invasive procedures such as the implantation of a male suburethral sling, although the experience with such devices is not extensive. However, the implantation of artificial urinary sphincter is the gold standard therapy.
treatments such as periurethral injection of bulking agents, artificial urinary sphincter (AUS) implantation, and sub-urethral sling positioning. The artificial urethral sphincter has represented, until today, the gold standard but, in the recent years, sling systems have been investigated as minimally invasive alternative options.
Today, three different sling procedures are commonly performed: bone-anchored, readjustable, and trans-obturator slings systems.
The bone anchored suburethral synthetic sling is a simple and attractive procedure that can produce immediate good results with low morbidity, especially when strictly selected patients are treated. 
BAUS implantation is a safe, effective, minimally invasive option for iatrogenic male incontinence due to ISD. It compares favourably with AUS.

Answer: The artificial urethral sphincter has represented, until today, the gold standard but, in the recent years, sling systems have been investigated as minimally invasive alternative options.
Exact answer: Artificial urethral sphincter, AUS
Question: What is the incidence of sudden cardiac death among young athletes?

Context:
Sudden cardiac death is the leading cause of mortality among young athletes with an incidence of 1-2 per 100,000 athletes per annum.
The incidence of SCD is expected at one case for each 200,000 young athletes per year.
The incidence of sudden cardiac death (SCD) among young athletes is estimated to be 1-3 per 100,000 person years, and may be underestimated. 
Sudden cardiac death in a young athlete is a tragic and marking event, even though the media attention it gets is more important than its incidence (1-2/100000 per year). 
The sudden death of athletes under 35 years engaged in competitive sports is a well-known occurrence; the incidence is higher in athletes (approximately 2/100,000 per year) than in non-athletes (2.5 : 1), and the cause is cardiovascular in over 90%.

Answer: the incidence of sudden cardiac death among young athletes ranges from 0.5  to 3  per 100,000 athletes per year  .
Exact answer: 0.5  to 3  per 100,000 athletes per year
Question: Which is the protein encoded by the human gene GRIK?

Context:
GRIK = glutamate receptor, ionotropic, kainate
 To this end, the effects of chronic ethanol self-administration on glutamate receptor ionotropic AMPA (GRIA) subunit variant and kainate (GRIK)

Answer: Glutamate Receptor Ionotropic Kainate
Exact answer: glutamate receptor ionotropic kainate