nirantk/geneticsQA-train huggingface dataset:
Question: List 3 features of IRVAN syndrome.

Context:
Fluorescein photodiagnosis of idiopathic retinal vasculitis, aneurysms, and neuroretinitis (IRVAN) syndrome: A case report and long-term outcome of photocoagulation therapy.
Idiopathic retinal vasculitis, aneurysms, and neuroretinitis (IRVAN) syndrome is a disease characterized by multiple retinal macroaneurysms, neuroretinitis and peripheral capillary non-perfusion, leading to irreversible visual loss.
[Early treatment of idiopathic vasculitis, aneurysms and neuroretinitis (IRVAN). A case report].
CASE REPORT: A 55 year old woman presented with retinal vasculitis, multiple aneurysms, macular exudation and widespread retinal nonperfusion and was diagnosed with IRVAN.
A 7-year-old girl with IRVAN (idiopathic retinal vasculitis, aneurysms, and neuroretinitis) syndrome was monitored for 9 years.
Vision loss associated with the idiopathic retinal vasculitis, aneurysms, and neuroretinitis (IRVAN) syndrome most commonly occurs from macular edema or complications related to neovascularization. 
PURPOSE: To report a case of idiopathic retinal vasculitis, aneurysms and neuroretinitis (IRVAN) syndrome associated with positive perinuclear antineutrophil cytoplasmic antibody (P-ANCA).
PURPOSE: We report our experience in treating 2 patients of idiopathic retinal vasculitis, aneurysm, and neuroretinitis (IRVAN) syndrome with antitumor necrosis factor agent, infliximab, who showed a very favorable response to treatment
Fluorescein angiography delineated saccular aneurysms of the retinal arteriolar vasculature, and IRVAN syndrome was diagnosed.
The authors describe the clinical feature of ten patients with a new syndrome characterized by the presence of retinal vasculitis, multiple macroaneurysms, neuro-retinitis, and peripheral capillary nonperfusion.The authors evaluated ten patients identified to have clinical features compatible with the syndrome of idiopathic retinal vasculitis, aneurysms and neuroretinits (IRVAN)
The authors evaluated ten patients identified to have clinical features compatible with the syndrome of idiopathic retinal vasculitis, aneurysms and neuroretinits (IRVAN).

Answer: Idiopathic retinal vasculitis, aneurysms, and neuroretinitis is coined as IRVAN syndrome.
Exact answer: Idiopathic retinal vasculitis, Aneurysms, Neuroretinitis
Question: Are BBS mutations involved in syndromic Hirschsprung disease?

Context:
Epistasis between RET and BBS mutations modulates enteric innervation and causes syndromic Hirschsprung disease
Here, we report 3 families with BBS and HSCR with concomitant mutations in BBS genes and regulatory RET elements, whose functionality is tested in physiologically relevant assays. Our data suggest that BBS mutations can potentiate HSCR predisposing RET alleles, which by themselves are insufficient to cause disease
Epistasis between RET and BBS mutations modulates enteric innervation and causes syndromic Hirschsprung disease.
Our data suggest that BBS mutations can potentiate HSCR predisposing RET alleles, which by themselves are insufficient to cause disease.
Here, we report 3 families with BBS and HSCR with concomitant mutations in BBS genes and regulatory RET elements, whose functionality is tested in physiologically relevant assays
Our data suggest that BBS mutations can potentiate HSCR predisposing RET alleles, which by themselves are insufficient to cause disease
Here, we report 3 families with BBS and HSCR with concomitant mutations in BBS genes and regulatory RET elements, whose functionality is tested in physiologically relevant assays

Answer: In 3 families with Bardet-Biedl syndrome (BBS) and Hirschsprung disease (HSCR), concomitant mutations in BBS genes and regulatory RET elements have been identified. Analysis of the data suggests that BBS mutations can potentiate HSCR predisposing RET alleles, which by themselves are insufficient to cause disease.
Exact answer: yes
Question: Is the abnormal dosage of ultraconserved elements disfavored in cancer cells?

Context:
Abnormal dosage of ultraconserved elements is highly disfavored in healthy cells but not cancer cells.
We begin by showing that depletion for UCEs characterizes the most recent large-scale human CNV datasets and then find that even newly formed de novo CNVs, which have passed through meiosis at most once, are significantly depleted for UCEs. In striking contrast, CNVs arising specifically in cancer cells are, as a rule, not depleted for UCEs and can even become significantly enriched. This observation raises the possibility that CNVs that arise somatically and are relatively newly formed are less likely to have established a CNV profile that is depleted for UCEs. Alternatively, lack of depletion for UCEs from cancer CNVs may reflect the diseased state. In support of this latter explanation, somatic CNVs that are not associated with disease are depleted for UCEs. Finally, we show that it is possible to observe the CNVs of induced pluripotent stem (iPS) cells become depleted of UCEs over time, suggesting that depletion may be established through selection against UCE-disrupting CNVs without the requirement for meiotic divisions.
Alternatively, lack of depletion for UCEs from cancer CNVs may reflect the diseased state.

Answer: No. Abnormal dosage of ultraconserved elements is highly disfavored in healthy cells but not cancer cells.
Exact answer: no
Question: Can SUMO affect calcium homeostasis?

Context:
Increasing SUMOylation levels correlated inversely with calcium influx in sensory neurons.
CRMP2 deSUMOylation by SUMO proteases SENP1 and SENP2 normalized calcium influx to those in the CRMP2AAA mutant.
Thus, our results identify a novel role for SUMO modification in CRMP2/CaV2.2 signaling pathway
Moreover, SUMO1 overexpression in isolated cardiomyocytes augmented contractility and accelerated Ca(2+) decay.
 RIM1α SUMOylation at lysine residue K502 facilitates the clustering of CaV2.1 calcium channels and enhances the Ca(2+) influx necessary for vesicular release, whereas non-SUMOylated RIM1α participates in the docking/priming of synaptic vesicles and maintenance of active zone structure. 
Identification and characterization of a SUMO-1 conjugation system that modifies neuronal calcium/calmodulin-dependent protein kinase II in Drosophila melanogaster.

Answer: Yes, SUMO proteins can affect calcium homeostasis.
Exact answer: yes
Question: A common problem in proteomics is the contamination of samples with exogenous proteins (often from other species). These proteins can be found in specific databases. List some contaminants.

Context:
protease autolysis or keratin contaminants.
Most of the interfering masses originate from trypsin autolysis and human keratins.
5-15% FBS. Contamination by bovine proteins is difficult to avoid because of adherence to the plastic vessel and the cultured cells.
The main disadvantage of traditional IP and co-IP is that the conditions used to elute the precipitated antigen also release the antibody thus contaminating the antigen
MaConDa: a publicly accessible mass spectrometry contaminants database.

Answer: Some common contaminants in proteomics are proteases (used for the digestion of the proteins), keratins (usually from the skin),  proteins originated from the serum of the culture media and antibodies if used in the experiment.
Exact answer: Proteases, Keratins, Bovine serum proteins, Antibodies
Question: Can chronological age be predicted by measuring telomere length?

Context:
Human somatic cells gradually lose telomeric repeats with age. This study investigated if one could use a correlation between telomere length and age, to predict the age of an individual from their DNA.
Therefore, telomere length measurement by real-time quantitative PCR cannot be used to predict age of a person, due to the presence of large inter-individual variations in telomere lengths.
ur results provide the first clear and unambiguous evidence of a relationship between telomere length and mortality in the wild, and substantiate the prediction that telomere length and shortening rate can act as an indicator of biological age further to chronological age when exploring life history questions in natural conditions.

Answer: No, telomere length measurement by real-time quantitative PCR cannot be used to predict age of a person, due to the presence of large inter-individual variations in telomere lengths.
Exact answer: no
Question: Are people with blood group O protected against severe Malaria?

Context:
Differential carbonylation of cytoskeletal proteins in blood group O erythrocytes: potential role in protection against severe malaria.
. Our findings indicate a possible correlation between the protection against severe malaria in blood group O individuals and a specific pattern of 4-HNE-carbonylation of cytoskeleton proteins.
There is a predominance of blood group O in malaria-endemic regions, and several lines of evidence suggest that ABO blood groups may influence the outcome of P. falciparum infection
These data provide the first evidence that ABO blood group antigens influence macrophage clearance of P. falciparum-infected erythrocytes and suggest an additional mechanism by which blood group O may confer resistance to severe malaria.
Blood group phenotypes A and B are risk factors for cerebral malaria in Odisha, India.
type O is significantly associated with protection against CM, patients with type A and B group had increased risk for developing CM.
Blood group O protects against severe Plasmodium falciparum malaria through the mechanism of reduced rosetting.
Malaria has been a major selective force on the human population, and several erythrocyte polymorphisms have evolved that confer resistance to severe malaria. Plasmodium falciparum rosetting, a parasite virulence phenotype associated with severe malaria, is reduced in blood group O erythrocytes compared with groups A, B, and AB, but the contribution of the ABO blood group system to protection against severe malaria has received little attention
We hypothesized that blood group O may confer resistance to severe falciparum malaria through the mechanism of reduced rosetting.
It appears that individuals who are of blood-group O are relatively resistant to the severe disease caused by P. falciparum infection.

Answer: It appears that individuals who are of blood-group O are relatively resistant to the severe disease caused by P. falciparum infection.
Exact answer: yes
Question: How has the study of ancient DNA (aDNA) been impacted by the use of refined sampling methods such as the inner part of petrous bones and the cementum layer in teeth roots?

Context:
Large-scale genomic analyses of ancient human populations have become feasible partly due to refined sampling methods. The inner part of petrous bones and the cementum layer in teeth roots are currently recognized as the best substrates for such research.
Ancient DNA (aDNA) research involves invasive and destructive sampling procedures that are often incompatible with anthropological, anatomical, and bioarcheological analyses requiring intact skeletal remains. The osseous labyrinth inside the petrous bone has been shown to yield higher amounts of endogenous DNA than any other skeletal element; however, accessing this labyrinth in cases of a complete or reconstructed skull involves causing major structural damage to the cranial vault or base.
first genome-wide ancient DNA from Anatolian Neolithic farmers, whose genetic material we obtained by extracting from petrous bones,

Answer: The study of ancient DNA (aDNA) has been impacted by the use of refined sampling methods such as the inner part of petrous bones and the cementum layer in teeth roots by making large-scale genomic analyses of ancient human populations feasible. These substrates are recognized as the best for such research, allowing for the extraction of genetic material from petrous bones of Anatolian Neolithic farmers.
Question: What memory problems are reported in the " Gulf war syndrome"

Context:
memory loss
loss of memory,
 loss of memory
dysmnesia
memory problems
"impaired cognition," characterized by problems with attention, memory, and reasoning, as well as insomnia, depression, daytime sleepiness, and headaches

Answer: memory loss
Exact answer: memory loss
Question: Which gene mutations are predictive of response to anti-TNF therapy in Rheumatoid Arthritis patients?

Context:
Genetic Variations in Pattern Recognition Receptor Loci Are Associated with Anti-TNF Response in Patients with Rheumatoid Arthritis
Six of twenty successfully genotyped polymorphisms were nominally associated with EULAR treatment response. Three of these were in weak to moderate linkage disequilibrium with polymorphisms previously reported associated with anti-TNF treatment response. TLR5(rs5744174) variant allele carriers (odds ratio(OR) = 1.7(1.1-2.5),p = 0.010,q = 0.46) and TLR1(rs4833095) homozygous variant carriers (OR = 2.8(1.1-7.4),p = 0.037,q = 0.46) had higher odds for a positive treatment response. NLRP3(rs10754558) variant allele carriers (odds ratio(OR) = 0.6(0.4-1.0),p = 0.045,q = 0.46) were more likely to have a negative treatment response. The association in TLR5(rs5744174) remained significant after correction for multiple comparisons among patients negative for RF (OR = 6.2(2.4-16.3),p = 0.0002,q = 0.024). 
Variation at FCGR2A and functionally related genes is associated with the response to anti-TNF therapy in rheumatoid arthritis
We aimed to validate this genetic association in a patient cohort from the Spanish population, and also to identify new genes functionally related to FCGR2A that are also associated with anti-TNF response.
A total of 348 RA patients treated with an anti-TNF therapy were included and genotyped for FCGR2A polymorphism rs1081274.
 Using gene expression profiles from macrophages obtained from synovial fluid of RA patients, we searched for genes highly correlated with FCGR2A expression.
We found a significant association between FCGR2A and the response to adalimumab (P=0.022). Analyzing the subset of anti-CCP positive RA patients (78%), we also found a significant association between FCGR2A and the response to infliximab (P=0.035). DHX32 and RGS12 were the most consistently correlated genes with FCGR2A expression in RA synovial fluid macrophages (P<0.001).
We found a significant association between the genetic variation at DHX32 (rs12356233, corrected P=0.019) and a nominally significant association between RGS12 and the response to adalimumab (rs4690093, uncorrected P=0.040).
In the anti-CCP positive group of patients, we also found a nominally significant association between RGS12 and the response to infliximab (rs2857859, uncorrected P=0.042).

Answer: Μutations in TLR5 and TLR1 genes contribute to differential response to anti-TNF treatment in RA. Variation at FCGR2A and functionally related genes such as DHX32 and RGS12 is also associated with the response to anti-TNF therapy in rheumatoid arthritis.
Exact answer: TLR5, TLR1, FCGR2A, DHX32, RGS12
Question: How can Human Hsp70 Disaggregase potentially reverse Parkinson's-linked α-Synuclein amyloid fibrils, given the need for therapeutic agents to address neurodegenerative disorders caused by protein misfolding and aggregation, and the role of disaggregases in resolubilizing protein aggregates?

Context:
Therapeutic agents are urgently required to cure several common and fatal neurodegenerative disorders caused by protein misfolding and aggregation, including amyotrophic lateral sclerosis (ALS), Parkinson's disease (PD), and Alzheimer's disease (AD).
Human Hsp70 Disaggregase Reverses Parkinson's-Linked α-Synuclein Amyloid Fibrils.
Disaggregases, molecular chaperones that resolubilize protein aggregates.
The structural basis by which Hsp104 dissolves disordered aggregates and prions is unknown.

Answer: Human Hsp70 Disaggregase can potentially reverse Parkinson's-linked α-Synuclein amyloid fibrils by resolubilizing protein aggregates. Disaggregases, such as Hsp70, are molecular chaperones that can dissolve protein aggregates, including those linked to neurodegenerative disorders like Parkinson's disease. This process is crucial in addressing the protein misfolding and aggregation that underlie conditions such as ALS, PD, and AD.
Question: What kind of affinity purification would you use in order to isolate soluble lysosomal proteins?

Context:
Most luminal lysosomal proteins are synthesized as precursors containing mannose 6-phosphate (Man6-P) and a number of recent studies have conducted affinity purification of Man6-P containing proteins as a step toward defining the composition of the lysosome
This chapter describes the process of production, purification, separation, and mass spectrometry identification of soluble lysosomal proteins. The rationale for purification of these proteins resides in their characteristic sugar, the mannose-6-phosphate (M6P), which allows an easy purification by affinity chromatography on immobilized M6P receptor (MPR
ecretions of these cells were affinity purified using an affinity matrix derivatized with MPR46 and MPR300. In the protein fraction bound to the affinity matrix and eluted with mannose 6-phosphate,
Proteins containing mannose 6-phosphate (Man6-P), a carbohydrate modification used for targeting resident soluble lysosomal proteins to the lysosome, were affinity-purified using immobilized Man6-P receptor.
. We purified mannose 6-phosphorylated proteins by affinity chromatography
Since lysosomal soluble proteins are characterized by the presence of mannose-6-phosphate, they were purified on an affinity support bearing mannose-6-phosphate receptor
The most abundant lysosomal substrates of Acp2 and Acp5 were identified by Man6P affinity chromatography and mass spectrometry.
urinary proteins were affinity purified on immobilized Man-6-P receptors,
A number of proteomic studies have focused on lysosomal proteins, exploiting the fact that Man-6-P-containing forms can be purified by affinity chromatography on immobilized MPRs.
In this study, we purified the Man-6-P glycoforms of proteins from human plasma by affinity chromatography on immobilized MPRs

Answer: The rationale for purification of the soluble lysosomal  proteins resides in their characteristic sugar, the mannose-6-phosphate (M6P),  which allows an easy purification by affinity chromatography on immobilized M6P receptors.
Question: What is the CEGA catalog?

Context:
CEGA--a catalog of conserved elements from genomic alignments.
To facilitate the study of such CNCs/UCEs, we present our resource of Conserved Elements from Genomic Alignments (CEGA), accessible from http://cega.ezlab.org. Harnessing the power of multiple species comparisons to detect genomic elements under purifying selection, CEGA provides a comprehensive set of CNCs identified at different radiations along the vertebrate lineage. Evolutionary constraint is identified using threshold-free phylogenetic modeling of unbiased and sensitive global alignments of genomic synteny blocks identified using protein orthology. We identified CNCs independently for five vertebrate clades, each referring to a different last common ancestor and therefore to an overlapping but varying set of CNCs with 24 488 in vertebrates, 241 575 in amniotes, 709 743 in Eutheria, 642 701 in Boreoeutheria and 612 364 in Euarchontoglires, spanning from 6 Mbp in vertebrates to 119 Mbp in Euarchontoglires. The dynamic CEGA web interface displays alignments, genomic locations, as well as biologically relevant data to help prioritize and select CNCs of interest for further functional investigations.
To facilitate the study of such CNCs/UCEs, we present our resource of Conserved Elements from Genomic Alignments (CEGA), accessible from http://cega.ezlab.org.
To facilitate the study of such CNCs/UCEs, we present our resource of Conserved Elements from Genomic Alignments (CEGA), accessible from http://cega.ezlab.org
CEGA--a catalog of conserved elements from genomic alignments
CEGA--a catalog of conserved elements from genomic alignments.
To facilitate the study of such CNCs/UCEs, we present our resource of Conserved Elements from Genomic Alignments (CEGA), accessible from http://cega.ezlab.org.

Answer: CEGA is a catalog of conserved elements from genomic alignments. Harnessing the power of multiple species comparisons to detect genomic elements under purifying selection, CEGA provides a comprehensive set of CNCs identified at different radiations along the vertebrate lineage. Evolutionary constraint is identified using threshold-free phylogenetic modeling of unbiased and sensitive global alignments of genomic synteny blocks identified using protein orthology. The dynamic CEGA web interface displays alignments, genomic locations, as well as biologically relevant data to help prioritize and select CNCs of interest for further functional investigations.
Question: Which are the thyroid hormone analogs utilized in human studies?

Context:
Here, we evaluate the therapeutic potential of the TH analog 3,5,3',5'-tetraiodothyroacetic acid (tetrac) as a replacement for T(4) in brain development. 
This treatment was sufficient to promote TH-dependent neuronal differentiation in the cerebellum, cerebral cortex, and striatum but was ineffective in suppressing hypothalamic TRH expression. 
In the current study, we investigated the effect of a natural thyroid hormone analogue - 3, 3?, 5-triiodo-thyroacetic acid (TRIAC) on regulating proliferation and differentiation and its possible molecular mechanism in normal human epidermal keratinocytes and C57BL/6 mice.
TRIAC was effective and safe in ameliorating the effects of hyperthyroidism and ADHD symptoms in a child with known genetic RTH.

Answer: TRIAC and TETRAC are two different thyroid hormone analogs utilized in human studies
Exact answer: TRIAC, TETRAC
Question: Can aspirin be used in cancer prevention?

Context:
 Evidence for an association between aspirin or other nonsteroidal antiinflammatory drug (NSAID) use and basal cell carcinoma (BCC) has been inconsistent.
 We report for the first time, in a typical risk US clinical population, a lack of protective association of aspirin for polyps among active smokers. Future prospective studies are recommended to confirm this mitigating effect in order to improve the precision of the growing evidence base about the chemopreventive benefit of aspirin in colorectal cancer.
The most serious side effect of prolonged aspirin treatment is haemorrhage, especially from the GI tract. This is likely to be less of a problem with chemoprevention at lower doses. One also needs to consider the impact if aspirin resistance, an increasingly recognised clinical entity.
Overall, our results do support the hypothesis that use of NSAIDs or statins may reduce the odds of developing pancreatic cancer.
Understanding is growing of the possible mechanisms by which aspirin exerts its anticancer effects. 
Long-term aspirin use was associated with a modest but significantly reduced risk for overall cancer, especially gastrointestinal tract tumors. Regular aspirin use may prevent a substantial proportion of colorectal cancers and complement the benefits of screening.

Answer: Long-term aspirin use was associated with a modest but significantly reduced risk for overall cancer, especially gastrointestinal tract tumors. Regular aspirin use may prevent a substantial proportion of colorectal cancers and complement the benefits of screening.