nirantk/geneticsQA-train huggingface dataset:
Question: What are the major clinical Villefranche criteria for classic Ehlers-Danlos syndrome?

Context:
All type V collagen defects were identified within a group of 102 patients fulfilling all major clinical Villefranche criteria, that is, skin hyperextensibility, dystrophic scarring and joint hypermobility
All type V collagen defects were identified within a group of 102 patients fulfilling all major clinical Villefranche criteria, that is, skin hyperextensibility, dystrophic scarring and joint hypermobility

Answer: The major clinical Villefranche criteria for classic Ehlers-Danlos syndrome are skin hyperextensibility, dystrophic scarring, and joint hypermobility.
Exact answer: skin hyperextensibility, dystrophic scarring, joint hypermobility
Question: How many microorganisms are present in human normal gut?

Context:
. A major breakthrough in understanding the etiology of neurological disorders is the recent insight on the role of the gut microbiota (GM). Human GM also referred to as the "forgotten organ" is home to 10(13-14) microorganisms
The gut microbiome comprises the collective genome of the trillions of microorganisms residing in our gastrointestinal ecosystem.
The gut microbiome (i.e. the 100 trillion symbiotic microorganisms which inhabit the mammalian gastrointestinal tract) influences numerous aspects of host metabolism, development and immunity.
The microorganisms inhabiting the human gut are abundant (10(14) cells) and diverse (approximately 500 species per individual).

Answer: Human gut microbiota is home to 10 to 100 trillions microorganisms.
Exact answer: 10 to 100 trillions microorganisms.
Question: To which disease does the loss of CD28 expression by liver-infiltrating T cells contribute?

Context:
Loss of CD28 expression by liver-infiltrating T cells contributes to pathogenesis of primary sclerosing cholangitis.
Loss of CD28 expression by liver-infiltrating T cells contributes to pathogenesis of primary sclerosing cholangitis
Loss of CD28 expression by liver-infiltrating T cells contributes to pathogenesis of primary sclerosing cholangitis.

Answer: Loss of CD28 expression by liver-infiltrating T cells contributes to pathogenesis of primary sclerosing cholangitis.
Loss of CD28 expression by liver-infiltrating T cells contributes to pathogenesis of primary sclerosing cholangitis. 
loss of cd28 expression by liver-infiltrating t cells contributes to pathogenesis of primary sclerosing cholangitis.
Exact answer: Primary sclerosing cholangitis
Question: Has proteomics been used in the study of Pick's disease?

Context:
In Pick's disease, increased AGE, CML, CEL, HNE and MDAL bands of about 50 kDa were observed in the frontal cortex (but not in the occipital cortex) in association with increased density of glial acidic protein bands.
Thus, brain and cerebrospinal fluid (CSF) samples from patients with Alzheimer's disease, Down syndrome, Pick's disease, Parkinson's disease, schizophrenia, and other disorders as well as brain and CSF from animals serving as models of neurological disorders have been analyzed by proteomics. 
The present study is designed to investigate expression of peroxiredoxins (Prxs), the newly characterized family of highly conserved antioxidant enzymes, and other antioxidant enzymes in frontal cortex and cerebellum of DS, AD and PD patients using the technique of proteomics. 
HMT levels were measured in the frontal cortex and cerebellum of brains of patients with AD, DS, and PiD, and normal aged subjects using proteomics techniques. 

Answer: Yes, proteomics has been used in the study of Pick's disease.
Exact answer: yes
Question: Which pipelines are used for analyzing data from ChIP-nexus experiments?

Context:
PeakXus: comprehensive transcription factor binding site discovery from ChIP-Nexus and ChIP-Exo experiments.
We describe a peak caller PeakXus that is specifically designed to leverage the increased resolution of ChIP-exo/Nexus and developed with the aim of making as few assumptions of the data as possible to allow discoveries of novel binding patterns. We apply PeakXus to ChIP-Nexus and ChIP-exo experiments performed both in Homo sapiens and in Drosophila melanogaster cell lines.
Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus.
Here, we present a comprehensive software package for ChIP-nexus data that exploits the random barcodes for selective removal of PCR duplicates and for quality control. Furthermore, we developed bespoke methods to estimate the width of the protected region resulting from protein-DNA binding and to infer binding positions from ChIP-nexus data. Finally, we applied our peak calling method as well as the two other methods MACE and MACS2 to the available ChIP-nexus data.
Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus.
PeakXus: comprehensive transcription factor binding site discovery from ChIP-Nexus and ChIP-Exo experiments.

Answer: PeakXus and Q-nexus enable comprehensive transcription factor binding site discovery from ChIP-nexus experiments.
Exact answer: PeakXus, Q-nexus
Question: Does triiodothyronine stimulate red blood cell sodium potassium pump?

Context:
reduction in Na+,K+ATPase activity has been demonstrated in red blood cells (RBCs), as well as an inverse correlation between this enzymatic action and free triiodothyronine (FT3) levels.
The restoration of normal FT3 values also brings about a normalization of Na+,K+ATPase activity in erythrocytes.
at hyperthyroid patients have decreased red cell Na/K-ATPase activity and provide direct evidence that erythrocyte ATPase activity is increased in hypothyroid patients. The change in enzyme activity in patients with nonthyroidal illness and decreased circulating T3 levels was comparable to that in hypothyroidism.
The effect of triiodothyronine (T3) on Na+,K(+)-ATPase activity of K562 human erythroleukemic cell was studied to understand why the erythrocyte sodium pump activity is decreased in hyperthyroidism.
We conclude that T3 stimulates Na+,K(+)-ATPase activity of K562 cells and in the presence of T3 during differentiation, the enzyme activity remains high.

Answer: An inverse correlation between this enzymatic action and free triiodothyronine (FT3) levels.
The effect of triiodothyronine (T3) on Na+,K(+)-ATPase activity in red blood cells may be different in vivo and in vitro.
Exact answer: no
Question: List disorders that have been associated to the polymorphism rs2535629.

Context:
A recent genome-wide analysis indicated that a polymorphism (rs2535629) of ITIH3 showed the strongest association signal with susceptibility to psychiatric disorders in Caucasian populations. 
he aim of the study was to replicate the association of rs2535629 with schizophrenia and major depressive disorder (MDD) in Japanese subjects. 
In the MDD-bipolar cross-disorder analysis, 15 SNPs exceeded genome-wide significance (P<5 × 10(-8)), and all were in a 248 kb interval of high LD on 3p21.1 (chr3:52 425 083-53 822 102, minimum P=5.9 × 10(-9) at rs2535629).
However, there was no preferential transmission at the ITIH3 rs52535629 polymorphism (χ²=0.14, P=0.707).

Answer: schizophrenia and major depressive disorder. 
Exact answer: schizophrenia, major depressive disorder
Question: Which mitochondrial genes are regulated by thyroid hormone?

Context:
We used a polymerase chain reaction (PCR)-based mRNA differential display (DD) analysis to obtain a profile of thyroid hormone-responsive genes in osteoblast-like cells
At the 2-hour time point, 1 true-positive novel clone was identified and shown to be the mitochondrial gene, subunit 6 of ATP synthase (ATPase-6).
We studied the coordination of the two genomes by measuring transcript levels for nuclear (IV, Va, and VIc) and mitochondrial (II and III) subunits of cytochrome-c oxidase after altering the mitochondrial content of rat muscle and liver by altering the thyroid state of the animals. Tissue levels of these mRNAs were generally decreased in hypothyroid animals and were up-regulated again after thyroid hormone (T3) treatment.
Following this procedure, we now report the identification of the mitochondrial NADH dehydrogenase subunit 3 (ND3) gene as target of thyroid hormone.
Sequencing and electrophoretic mobility shift assays confirmed the presence of a thyroid hormone receptor (TR)/c-erbA specific binding site in the mitochondrial ND3 gene.

Answer: subunit 6 of ATP synthase, ATPase-6, mitochondrial II and III subunits of cytochrome-c oxidase, NADH dehydrogenase subunit 3
Exact answer: subunit 6 of ATP synthase, ATPase-6, mitochondrial II and III subunits of cytochrome-c oxidase, NADH dehydrogenase subunit 3, ND3
Question: Which protein is required for Argonaute 2 recruitment to stress granules and P-bodies?

Context:
we examined whether another Hsp90 inhibitor radicicol (RA) affected P-bodies and stress granules. Treatment with RA reduced the level of the Hsp90 client protein Argonaute 2 and the number of P-bodies. Although stress granules still assembled in RA-treated cells upon heat shock, they were smaller and more dispersed in the cytoplasm than those in untreated cells
Hsp90 regulates the function of argonaute 2 and its recruitment to stress granules and P-bodies
Processing bodies (PBs) and stress granules (SGs) are the two main types of ribonucleoprotein complexes with which Argonautes are associated. Targeting of Argonautes to these structures seems to be regulated by different factors. In the present study, we show that heat-shock protein (Hsp) 90 activity is required for efficient targeting of hAgo2 to PBs and SGs
Hsp90 regulates the function of argonaute 2 and its recruitment to stress granules and P-bodies.
Treatment with RA reduced the level of the Hsp90 client protein Argonaute 2 and the number of P-bodies.
Treatment with RA reduced the level of the Hsp90 client protein Argonaute 2 and the number of P-bodies. 
In the present study, we show that heat-shock protein (Hsp) 90 activity is required for efficient targeting of hAgo2 to PBs and SGs. 
To verify these observations, we examined whether another Hsp90 inhibitor radicicol (RA) affected P-bodies and stress granules. Treatment with RA reduced the level of the Hsp90 client protein Argonaute 2 and the number of P-bodies.
Treatment with RA reduced the level of the Hsp90 client protein Argonaute 2 and the number of P-bodies.

Answer: Hsp90 regulates the function of argonaute 2 and its recruitment to stress granules and P-bodies.
Exact answer: Hsp90
Question: Have mutations in the Polycomb group been found in human diseases?

Context:
We identify a novel mutation in PHC1, a human orthologue of the Drosophila polyhomeotic member of polycomb group (PcG), which significantly decreases PHC1 protein expression, increases Geminin protein level and markedly abolishes the capacity to ubiquitinate histone H2A in patient cells.
In clinical specimens of head and neck cancer, we found that coamplification of BMI1 and AURKA correlated with poorer prognosis.
Mutations of EZH2, RUNX1, TP53, and ASXL1 were associated with shorter overall survival independent of the LR-PSS.
In this study, we show the high frequency of spontaneous γδ T-cell leukemia (T-ALL) occurrence in mice with biallelic deletion of enhancer of zeste homolog 2 (Ezh2).
Subsequently, analysis of deletion profiles of other PRC2 members revealed frequent losses of genes such as EZH2, AEBP2, and SUZ12; however, the deletions targeting these genes were large. We also identified two patients with homozygous losses of JARID2 and AEBP2. We observed frequent codeletion of AEBP2 and ETV6, and similarly, SUZ12 and NF1.
A total of 25 different EZH2 mutations were detected in 5.9% of PMF, 1.2% of PPV-MF, and 9.4% of PET-MF patients; most were exonic heterozygous missense changes.
In the present investigation we have focused on the candidate region in 6p23, a region that have been found linked to CL/P in several investigations, in the attempt to find out the susceptibility gene provisionally named OFC1. Gene expression experiments in mice embryo of positional candidate genes revealed that JARID2 was highly and specifically expressed in epithelial cells in merging palatal shelves.
High expression of EZH2 and amplification of EZH2 was found in 54.1% and 12.0% of ESCCs, respectively.
We also observed that HOXA9 levels were significantly inversely correlated with survival and that BMI-1 was overexpressed in cases with 11q23 rearrangements, suggesting that p19(ARF) suppression may be involved in MLL-associated leukemia.
We demonstrate that in multiple experimental models of metastatic prostate cancer both BMI1 and Ezh2 genes are amplified and gene amplification is associated with increased expression of corresponding mRNAs and proteins.
he EZH2 gene amplification was significantly (P < 0.05) associated with increased EZH2 protein expression.
The third tumor showed a t(6p;10q;10p) as the sole karyotypic abnormality, leading to the fusion of PHF1 with another partner, the enhancer of polycomb (EPC1) gene from 10p11; EPC1 has hitherto not been associated with neoplasia.

Answer: Yes, different members of the Polycomb family have been found mutated in diseases such as primary microcephaly, nonsyndromic cleft lip and several cancers (including hemotopoietic malignancies, esophageal carcinoma, head and neck cancer or prostate cancer).

Exact anser:
Yes
Exact answer: yes
Question: List protein gel staining methods visualizing the entire protein set.

Context:
DIGE requires the labelling of proteins by fluorochromes prior to their separation on 2DE gels. 
Stains-All (ISA) staining method for phosphoproteins in SDS-PAGE was described.
 Pro-Q Diamond stain
Quantitative proteome analyses suggest that the well-established stain colloidal Coomassie Blue, when used as an infrared dye, may provide sensitive, post-electrophoretic in-gel protein detection that can rival even Sypro Ruby.
Several new fast staining protocols for the visualization of proteins separated by SDS-PAGE utilizing Coomassie Blue staining (CBS) have been described in literature. 
The CyDye family of fluorescent dyes is currently the overwhelming choice for applications in proteomic analysis, using two-dimensional difference gel electrophoresis (2D-DIGE)
his enables the co-detection of phosphoproteins as well as total proteins from the same gel and is accomplished by utilizing two different fluorescent stains, the ProQ-Diamond, which stains only phosphorylated proteins, and Sypro Ruby, which stains the entire subset of proteins.
Detection of the resulting protein maps relies on staining (i.e. colloidal coomassie blue (CCB) or SYPRO Ruby (SR), in addition to many others). Fluorescent in-gel protein stains are generally preferred for higher sensitivity, reduced background, and wider dynamic range.
Commonly used staining methods with excellent mass spectrometry compatibility are coomassie brilliant blue (CBB) or fluorescent dyes.
The typical concentration of protein loaded varies from 0.13 to 1.40 μg/μL for a classical silver staining method in 2DE gel
Silver staining is widely used to detect protein in polyacrylamide gels when high sensitivity is required.
Silver staining is used to detect proteins after electrophoretic separation on polyacrylamide gels

Answer: Several staining protocols for the visualization of proteins separated by SDS-PAGE have been described in literature: 
fluorescence
Sypro Ruby
Colloidal Coomassie Blue
Coomassie Blue
Silver staining
Coomassie Brilliant Blue
Exact answer: fluorochromes, fluorescence, Sypro Ruby, Colloidal Coomassie Blue, Coomassie Blue, Silver staining, Coomassie Brilliant Blue
Question: Do RNA:DNA hybrids preferentially form in high or low GC regions?

Context:
Intrinsic termination signals for multisubunit bacterial RNA polymerases (RNAPs) encode a GC-rich stem-loop structure followed by a polyuridine [poly(U)] tract, and it has been proposed that steric clash of the stem-loop with the exit pore of the RNAP imposes a shearing force on the RNA in the downstream RNA:DNA hybrid, resulting in misalignment of the active site
We have observed that transcription through the GC-rich FMR1 5'UTR region favors R-loop formation, with the nascent (G-rich) RNA forming a stable RNA:DNA hybrid with the template DNA strand, thereby displacing the non-template DNA strand.
Transcription termination by bacterial RNA polymerase (RNAP) occurs at sequences coding for a GC-rich RNA hairpin followed by a U-rich tract. We used single-molecule techniques to investigate the mechanism by which three representative terminators (his, t500, and tR2) destabilize the elongation complex (EC).
In the 5' flanking region, nucleotides -234 to -213 encompass a GC-rich region which exhibits high homology (greater than 70%) to the 5' flanking regions of the genes of all the apolipoproteins published to date, namely, apo-A-II (-497 to -471), apo-A-I (approximately -196 to -179), apo-E (-409 to -391), and apo-C-III (approximately -116 to -103).
Recently, we demonstrated that cotranscriptional RNA•DNA hybrids are preferentially formed at GC-rich trinucleotide and tetranucleotide repeat sequences in vitro as well as in human genomic DNA.
Considering the extent of transcription through the human genome as well as the abundance of GC-rich and/or non-canonical DNA structure forming tandem repeats, RNA•DNA hybrids may represent a common mutagenic conformation.
Recently, we demonstrated that cotranscriptional RNA•DNA hybrids are preferentially formed at GC-rich trinucleotide and tetranucleotide repeat sequences in vitro as well as in human genomic DNA. 

Answer: Transcription through a GC-rich region favors R-loop formation, with the nascent (G-rich) RNA forming a stable RNA:DNA hybrid with the template DNA strand.
Exact answer: yes
Question: List Genes associated with adolescent idiopathic scoliosis

Context:
Exome Sequencing Identifies a Rare HSPG2 Variant Associated with Familial Idiopathic Scoliosis.
Overall, these findings demonstrate a novel role for kif6 in spinal development and identify a new candidate gene for human idiopathic scoliosis.
HL1 is of interest, as it encodes an axon guidance protein related to Robo3. Mutations in the Robo3 protein cause horizontal gaze palsy with progressive scoliosis (HGPPS), a rare disease marked by severe scoliosis. Other top associations in our GWAS were with SNPs in the DSCAM gene encoding an axon guidance protein in the same structural class with Chl1 and Robo3.

Answer: Exome Sequencing Identifies a Rare HSPG2 Variant Associated with Familial Idiopathic Scoliosis.Overall, these findings demonstrate a novel role for kif6 in spinal development and identify a new candidate gene for human idiopathic scoliosis.
No genetic associations have yet been found to adolescent idiopathic scoliosis.
Exact answer: no associations found yet
Question: What is the reason for the narcolepsy cases developed after H1N1 influenza vaccination?

Context:
The proposed mechanism for postvaccination narcolepsy is one in which an environmental trigger causes or enhances an antibody-mediated autoimmune response in patients with a preexisting genetic susceptibility. 
The loss of hypothalamic hypocretin/orexin (hcrt) producing neurons causes narcolepsy with cataplexy. An autoimmune basis for the disease has long been suspected and recent results have greatly strengthened this hypothesis. 
pointing towards processes such as molecular mimicry or bystander activation as crucial for disease development. 
Although no formal link can be established, the unusual characteristics of the reported cases and the striking temporal relationship suggests that narcolepsy may be the result of an autoimmune reaction triggered by H1N1 vaccination in susceptible individuals.
Pandemrix vaccination is a precipitating factor for narcolepsy, especially in combination with HLA-DQB1*0602. 
Recently identified autoantibodies to Tribbles homologue 2 in some patients, as well as cases associated with H1N1 vaccination, support an autoimmune mechanism. 
n China, narcolepsy onset is highly correlated with seasonal and annual patterns of upper airway infections, including H1N1 influenza. In 2010, the peak seasonal onset of narcolepsy was phase delayed by 6 months relative to winter H1N1 infections, and the correlation was independent of H1N1 vaccination in the majority of the sample.
H1N1 vaccination was strongly associated with an increased risk of narcolepsy-cataplexy in both children and adults in France

Answer: The proposed mechanism for postvaccination narcolepsy is one in which an environmental trigger causes or enhances an antibody-mediated autoimmune response in patients with a preexisting genetic susceptibility.
Question: Is there any evidence of dysregulated long non coding RNAs and Alzheimer's disease?

Context:
lncRNAs in central nervous system (CNS) development and neurodegenerative diseases, including Alzheimer's disease (AD)
(lncRNA) within mRNA sequences of Alzheimer's disease genes, namely, APP, APOE, PSEN1, and PSEN2
sortilin-related receptor 1 (SORL1) is a risk gene for late-onset Alzheimer's disease (AD)
non-coding (nc) RNA (hereafter referred to as 51A) that maps in antisense configuration to intron 1 of the SORL1 gene
novel GDNF isoforms and cis-antisense GDNFOS gene and their regulation in human middle temporal gyrus of Alzheimer disease
GDNFOS gene has four exons that are spliced into different isoforms. GDNFOS1 and GDNFOS2 are long noncoding RNA
In the MTG of AD patients, the mature GDNF peptide was down-regulated; however, the transcript of GDNF isoform from human exon 2 was up-regulated
The findings of novel GDNF and GDNFOS isoforms and differences in tissue expression patterns dysregulated in AD brains 
novel non-coding (nc) RNA (named 17A) RNA polymerase (pol) III-dependent embedded in the human G-protein-coupled receptor 51 gene (GPR51, GABA B2 receptor)
17A is expressed in human brain, and we report that it is upregulated in cerebral tissues derived from Alzheimer disease patients
Here we identify a conserved noncoding antisense transcript for beta-secretase-1 (BACE1), a crucial enzyme in Alzheimer's disease pathophysiology.
the genotype of this SNP shows different distribution in normal elders, mild cognitive impairment, and Alzheimer disease subjects, suggesting that this lincRNA may have a role in physiology and pathophysiology of human brain

Answer: It is becoming increasingly evident that long non coding RNAs (lncRNAs) play a role on neurodegenerative diseases such as Alzheimer (AD).  BACE1-AS, GDNFOS and 17A are examples of these lncRNAs. In some instances those lncRNAs are embedded or transcribed from the opposite strand of coding genes.
Question: List FDA approved treatments for androgenetic allopecia

Context:
Topical minoxidil 2%-5% 1 mL twice daily or finasteride 1 mg daily are recommended as first line treatments, followed by the use of Food and Drug Administration-cleared HairMax LaserComb® in patients who do not respond to first line modalities.
Recently, in addition to the two currently approved U.S. Food and Drug Administration (FDA) medications (minoxidil and finasteride), a novel device was FDA-approved for the treatment of hair loss, the laser hair comb.
In addition, low-level light therapy (LLLT) has recently been approved by the United States Food and Drug Administration (FDA) for the treatment of hair loss. 
Currently there are two U.S. Food and Drug Administration (FDA)-approved agents that promote hair regrowth: over-the-counter topical minoxidil solution for men and women and prescription oral finasteride tablets for men. 
Topical monoxidil and oral finasteride are commonly in use and have FDA approval for the treatment of male androgenetic alopecia; dutasteride, a type I and II 5-alpha-reductase inhibitor, is on hold in Phase III trials.
The only FDA-approved dermatological indication of finasteride is androgenetic alopecia.
Finasteride (Propecia) was approved by the FDA in 1998 for treating men with androgenetic alopecia.

Answer: Recently, in addition to the two currently approved U.S. Food and Drug Administration (FDA) medications (minoxidil and finasteride), a novel device was FDA-approved for the treatment of hair loss, the laser hair comb.
Exact answer: Minoxidil, Finasteride, Laser hair comb