nirantk/geneticsQA-train huggingface dataset:
Question: What is MIRA-seq?

Context:
MIRA-seq for DNA methylation analysis of CpG islands.
MIRA-seq is a reliable, genome-scale DNA methylation analysis platform for scoring DNA methylation differences at CpG-rich genomic regions. The method is not limited by primer or probe design and is cost effective.
Using MIRA-seq, we have characterized the DNA methylome of metastatic melanoma and normal melanocytes.
Global gene expression was measured by RNA-Seq, while an epigenetic basis for expression differences was examined by methylated CpG island recovery assay sequencing (MIRA-Seq) analysis.
Global gene expression was measured by RNA-Seq, while an epigenetic basis for expression differences was examined by methylated CpG island recovery assay sequencing (MIRA-Seq) analysis.
MIRA-seq for DNA methylation analysis of CpG islands.
MIRA-seq is a reliable, genome-scale DNA methylation analysis platform for scoring DNA methylation differences at CpG-rich genomic regions.
Despite extensive breed differences in the transcriptome, MIRA-Seq unveiled relatively similar patterns of genome-wide DNA methylation between breeds, with an overall hypomethylation of gene promoters.
Methylated CpG island recovery assay sequencing (MIRA-Seq) revealed numerous methylation peaks spread across the genome, combined with an overall hypomethylation of gene promoter regions, and a remarkable similarity, except for 20 regions along the genome, between the fibroblasts collected at the two ages from the same animals.

Answer: MIRA-seq is a reliable, genome-scale DNA methylation analysis platform for scoring DNA methylation differences at CpG-rich genomic regions. The method is not limited by primer or probe design and is cost effective.
Question: What is the physiological role of LKB1 involved in Peutz-Jeghers syndrome?

Context:
Recent functional genetic studies have pointed out that LKB1 plays a physiological role in controlling the Wnt-signaling pathway and activation of the pathway as a consequence of LKB1 haploinsufficiency might be responsible for the development of harmatomatous polyps.
PJS polyps from all patients showed generalized membrane and cytoplasmic localizations of beta-catenin along the mucosal endothelium.

Answer: LKB1 plays a physiological role in controlling the Wnt-signaling.
Exact answer: LKB1 plays a physiological role in controlling the Wnt-signaling.
Question: Is intense physical activity associated with longevity?

Context:
Our major finding is that repeated very intense exercise prolongs life span in well trained practitioners.
Death rates declined with increased levels of total activity (estimated in kilocalories), and declined also with increased intensity of effort measured as from none, to light, to moderately vigorous or vigorous sports play. Death rates at any given quantity of physical exercise were lower for men playing moderately intense sports than for less vigorous men.
he purpose of this study was to investigate if jogging, which can be very vigorous, is associated with increased all-cause mortality in men and women.
This long-term study of joggers showed that jogging was associated with significantly lower all-cause mortality and a substantial increase in survival for both men and women.
Light activities (<4 multiples of resting metabolic rate (METs)) were not associated with reduced mortality rates, moderate activities (4-<6 METs) appeared somewhat beneficial, and vigorous activities (> or =6 METs) clearly predicted lower mortality rates (p, trend = 0.72, 0.07, and <0.001, respectively).
These data demonstrate a graded inverse relationship between total physical activity and mortality. Furthermore, vigorous activities but not nonvigorous activities were associated with longevity.
The capacity for prolonged and vigorous physical exercise, particularly if the exercise is recreational, is a strong indicator of longevity.

Answer: YES:
Exact answer: yes
Question: Can exosomes be detected in urine?

Context:
Exosomes are nanovesicles secreted into the extracellular environment upon internal vesicle fusion with the plasma membrane. The molecular content of exosomes is a fingerprint of the releasing cell type and of its status. For this reason, and because they are released in easily accessible body fluids such as blood and urine, they represent a precious biomedical tool. 
Exosomes are vesicles that are released from the kidney into urine.
Quantification of human urinary exosomes by nanoparticle tracking analysis.
Urinary extracellular vesicles (uEVs) are released by cells throughout the nephron and contain biomolecules from their cells of origin.
Urinary exosomes have been proposed as potential diagnostic tools.
Urinary exosomes as a source of kidney dysfunction biomarker in renal transplantation
. Here we sought to optimize the methodologies for the isolation and quantification of urinary exosomal microRNA as a prelude to biomarker discovery studies. 
Exosomes are small (30-150 nm) vesicles containing unique RNA and protein cargo, secreted by all cell types in culture. They are also found in abundance in body fluids including blood, saliva, and urine. 
Urinary exosome-like vesicles (ELVs) are a heterogenous mixture (diameter 40-200 nm) containing vesicles shed from all segments of the nephron including glomerular podocytes
Exosomes are cytoplasm containing vesicles released by many cells that can be found in several biological fluids including urine.
Proteomic analysis of urinary exosomes in cardiovascular and associated kidney diseases by two-dimensional electrophoresis and LC-MS/MS

Answer: Yes, urinary exosomes can be detected in urine.
Exact answer: yes
Question: What histone trimethylation has been associated to RNA splicing?

Context:
histone H3 lysine 36 tri-methylation (H3K36Me3), exhibits different patterns around the cleavage sites of genes using multiple polyadenylation sites from those of genes using a single polyadenylation site.
ChIP-sequencing data mapped onto skipped exon events reveal a correlation between histone H3K36 trimethylation peaks and skipped exons, suggesting epigenetic marks being part of alternative splicing regulation.
Vezf1 interacts with Mrg15/Mrgbp, a protein that recognizes H3K36 trimethylation, consistent with the role of histone modifications at alternatively spliced sites
H2BK123ub1 is also a feature of introns in the yeast genome, and the disruption of this modification alters the intragenic distribution of H3 trimethylation on lysine 36 (H3K36me3), which functionally correlates with alternative RNA splicing in humans
We investigated whether a causal relationship exists between splicing and chromatin modification by asking whether splice-site mutations affect the methylation of histone H3K36
 splicing can also contribute to histone modification,
Genome-wide analysis of histone methylation in human cell lines and mouse primary T cells reveals that intron-containing genes are preferentially marked with histone H3 Lys36 trimethylation (H3K36me3) 
 transcription and splicing are functionally intertwined, and that modified nucleosomes with trimethylation of lysine 36 in histone subunit 3 (H3K36me3) are enriched at internal exons and the downstream flanking intronic regions of highly expressed genes
methylated H3K4 serves to facilitate the competency of pre-mRNA maturation 

Answer: Mostly H3K36me3 but there is some evidence that H3K4me3 may also play a role in splicing
Exact answer: H3K36me3
Question: How was quantitative proteomic analysis used in isolating and studying the pseudopodium from migratory cells?

Context:
we developed an approach to biochemically isolate the pseudopodium from the cell body using 3.0-micrometer porous filters for large-scale quantitative proteomic and phosphoproteomic analysis.
Recent work using unique subcellular fractionation methodologies combined with spatial genomic, proteomic, and phosphoproteomic profiling has provided insight into the invadopodiome and pseudopodiome signaling networks 
ere, we purified the pseudopodial proteomes
tumor cells were placed on a fibronectin-coated porous membrane to form pseudopodia. According to the motile potentials of the cells, the cells formed pseudopodial microprocesses in the pores. An excimer laser, which was used for ophthalmic refractive surgeries, horizontally ablated cells at the membrane surface to remove the cell body. 
we describe methods for the immunoaffinity purification of phosphotyrosine proteins (pY) from pseudopodia that have been isolated from migratory cells. These methods are compatible with current mass spectrometry-based protein identification technologies and can be utilized for the large-scale identification of the pseudopodium pY proteome in various migratory cell lines, including primary and cancer cells.

Answer: An approach was developed to biochemically isolate the pseudopodium from the cell body using 3.0-micrometer porous filters for large-scale quantitative proteomic and phosphoproteomic analysis.
Question: Is oxalate renal excretion increased after bariatric surgery?

Context:
Despite the fact that bariatric surgery-induced weight loss is associated with a significant decrease in morbidity and mortality and improvement in renal function, bariatric surgery has recently been shown to be associated with a significant risk of nephrolithiasis. The main risk factor for nephrolithiasis is increased excretion of urinary oxalate.
Enteric hyperoxaluria, nephrolithiasis, and oxalate nephropathy must be considered with the other risks of RYGBP.
The urinary excretion of oxalate was high: 1.112 mumol/24 h (normal range: 55-400 mumol/24 h), and citrate excretion was low: 1.48 mmol/24 h (normal range: 2-5 mmol/24 h). 
Hyperoxaluria in patients with JIB was found to be a result of hyperabsorption of oxalate, and these patients displayed altered oxalate kinetics with continued urinary excretion of orally administered 14C-oxalate for more than 48 hours. 
Malabsorption of calcium and low fasting urinary calcium excretion in the JIB patients were associated with high tubular reabsorption of calcium, the latter presumably attributable to a compensatory increase in circulating parathyroid hormone (PTH). In most recurrent renal stone formers the urinary calcium concentration was increased, with an inverse relationship to serum PTH, indicating intestinal hyperabsorption of calcium. A

Answer: Bariatric surgery is associated with a significant risk of nephrolithiasis.
Enteric hyperoxaluria, nephrolithiasis, and oxalate nephropathy must be considered with the other risks of bariatric surgery
Hyperoxaluria in patients treated with bariatric surgery was found to be a result of hyperabsorption of oxalate
Urinary oxalate increases after bariatric surgery
Exact answer: yes
Question: Which is the prevalence of cystic fibrosis in the human population?

Context:
The allelic frequency of this variant was calculated to be 0.7% for this population
The results of literature reviews, surveys, and registry analyses revealed a mean prevalence of 0.737/10,000 in the 27 EU countries, which is similar to the value of 0.797 in the United States, and only one outlier, namely the Republic of Ireland at 2.98
The age related prevalence of CF among the South Asian and general populations was: 0-14 years, 1:9200 versus 1:6600; 15-24 years, 1:13,200 versus 1:7600; older than 25 years, 1:56,600 versus 1:12,400.
A theoretical estimate of the prevalence of cystic fibrosis based on anthropological data suggested a frequency of 25 affected individuals/100,000 inhabitants. However, our data indicated that the true prevalence in the population was considerably lower (6.9 cases/100,000 inhabitants)
CF mutations were identified in 374 (4.0%) individuals.
The aim of this study was to evaluate the screening policies of cystic fibrosis (CF) in the Jewish population.

Answer: Prevalence of Cystic Fibrosis varies according to the population. A theoretical estimate of the prevalence of cystic fibrosis based on anthropological data suggested a frequency of 25 affected individuals/100,000 inhabitants. However, real data indicated that the true prevalence in the population was considerably lower (6.9 cases/100,000 inhabitants). Results of literature reviews, surveys, and registry analyses revealed a mean prevalence of 0.737/10,000 in the 27 EU countries, which is similar to the value of 0.797 in the United States, and only one outlier, namely the Republic of Ireland at 2.98.
The results of literature reviews, surveys, and registry analyses revealed a mean prevalence of 0.737/10,000 in the 27 EU countries, which is similar to the value of 0.797 in the United States, and only one outlier, namely the Republic of Ireland at 2.98 (PMID: 18442953) The allelic frequency of this variant was calculated to be 0.7% for this population (PMID: 22627569) CF mutations were identified in 374 (4.0%) individuals. (PMID: 11336401)
Exact answer: 0.7–7/100000 inhabitants
Question: Which is the histone residue methylated by MLL1?

Context:
lack of interaction with the histone methyltransferase, MLL1, resulting in decreased histone H3K4me3 and gene transcription
histone H3K4me3 methylase MLL1 complex
MEN1 encodes menin, a subunit of MLL1/MLL2-containing histone methyltransferase complexes that trimethylate histone H3 at lysine 4 (H3K4me3
MLL1, MLL5, Set1 and ASH1 to be highly up-regulated during transdifferentiation of HSCs. All of these histone methyltransferases regulate methylation of lysine 4 of histone H3, which is a signature of actively transcribed genes
MLL1 (Mixed Lineage Leukemia 1), a histone methyltransferase that methylates H3K4 residues
H3K4) in Saccharomyces cerevisiae is implemented by Set1/COMPASS, which was originally purified based on the similarity of yeast Set1 to human MLL1 and Drosophila melanogaster Trithorax (Trx)
istone H3 lysine 4 (K4) methylation is a prevalent mark associated with transcription activation and is mainly catalyzed by the MLL/SET1 family histone methyltransferase
Mutations in the MLL1 SET domain that fail to support overall H3 K4 methylation
MLL1, a mammalian homolog of Drosophila trithorax, is an H3K4-specific methyltransferase implicated in transcriptional control
We show that the mixed lineage leukemia 1 (MLL1) protein, a histone methyltransferase specific for H3K4
MLL1 histone H3 Lys4 methyltransferase complexes
MLL1 histone methyltransferase (H3K4me3) complex
In the human MLL1 (mixed-lineage leukemia-1) HMT complex, DPY-30L binds to the BRE2 homolog ASH2L in order to regulate histone 3-lysine 4 trimethylation.
MLL1 and MLL2 H3K4 methyltransferase complexes are tethered by p52 on the MMP9 but not on the IkappaBalpha promoter, and the H3K4 trimethyltransferase activity r
The biological function of MLL1 is mediated by the histone H3K4 methyltransferase activity of the carboxyl-terminal SET domain.
Set1/COMPASS is capable of methylating H3K4, a posttranslational modification associated with actively transcribed genes. There is only one Set1 in yeast; yet in mammalian cells there are multiple H3K4 methylases, including Set1A/B, forming human COMPASS complexes, and MLL1-4
 trimethylated H3K4 histones and histone methyltransferase MLL1
 lacZ knock-in allele of mixed-lineage leukemia 1 (Mll1), a histone methyltransferase expressed in GABAergic and other cortical neurons, resulted in decreased H3K4 methylation
effectors of H3K4 methylation is mixed-lineage leukemia 1 (MLL1)
MLL1/MLL2 histone methyltransferase complexes specific for Lys4 of histone H3 (H3K4)
H3 K4 methyltransferase MLL1
purified complex has a robust MLL1-mediated histone methyltransferase activity that can effect mono-, di-, and trimethylation of H3 K4
MLL1 localizes with RNA polymerase II (Pol II) to the 5' end of actively transcribed genes, where histone H3 lysine 4 trimethylation occurs

Answer: Histone H3 at lysine 4 (H3K4)
Exact answer: H3K4
Question: List clinical trials for prevention of sarcopenia

Context:
several clinical trials with androgen replacement therapy have failed to show clinical benefit.
Clinical trials are needed to find better interventions for this syndrome.
emergence of many promising interventions towards this age-related condition (e.g., physical exercise [in particular, resistance training], testosterone, antioxidant supplementations), the need for Phase II trial designs is high. 
The objective of this study was to evaluate the effect of omega-3 fatty acid supplementation on the rate of muscle protein synthesis in older adults.
This trial was registered at clinical trials.gov as NCT00794079.
The extreme paucity of clinical trials on sarcopenia in literature is mainly due to difficulties in designing studies able to isolate the aging process from its multiple and interconnected consequences.

Answer: Several clinical trials with androgen replacement therapy. 
Study was to evaluate the effect of omega-3 fatty acid supplementation on the rate of muscle protein synthesis. This trial was registered at clinical trials.gov as NCT00794079
Exact answer: androgen replacement trials, omega-3 fatty acid supplementation, NCT00794079
Question: Which are the musculoskeletal manifestations of Marfan syndrome?

Context:
Musculoskeletal manifestations include scoliosis, dural ectasia, protrusio acetabuli, and ligamentous laxity.
Scoliosis, pectus excavatum and carinatum, arachnodactyly, and acetabular protrusion are common musculoskeletal manifestations.
Two cases are described in which protrusio acetabuli was a major problem. Otto pelvis should be considered as one of the musculoskeletal manifestations of Marfan's syndrome.
The following musculoskeletal abnormalities were found: pectus in 3 patients (11%), pectus and scoliosis in 19 (73%), dolichostenomelia in 11 (42%) and arachnodactyly in 21 (80%).
Musculoskeletal clinicians should be aware of the diagnostic features of Marfan syndrome. Patients with three to four physically evident features, or two highly specific features (e.g., thumb and wrist signs, craniofacial features, dural ectasia, or protrusio), should be carefully reexamined and possibly referred for an echocardiogram or a genetics consultation.

Answer: Musculoskeletal manifestations of Marfan syndrome include scoliosis, dural ectasia, pectus excavatum and carinatum, arachnodactyly, otto pelvis (protrusio acetabuli), dolichostenomelia and ligamentous laxity.
Exact answer: scoliosis, dural ectasia, pectus excavatum and carinatum, arachnodactyly, otto pelvis, protrusio acetabuli, dolichostenomelia, ligamentous laxity
Question: Are alterations in ultraconserved elements associated with colorectal adenocarcinoma?

Context:
Genetic variants within ultraconserved elements and susceptibility to right- and left-sided colorectal adenocarcinoma
Our results strongly suggest that several genetic variants in the UCEs may contribute to CRC susceptibility, individually and jointly, and that different genetic etiology may be involved in RCRC and LCRC
Identification of polymorphisms in ultraconserved elements associated with clinical outcomes in locally advanced colorectal adenocarcinoma
To the authors' knowledge, this is the first study to evaluate the association between SNPs within UCEs and clinical outcome in patients with CRC. The results suggested that SNPs within UCEs may be valuable prognostic biomarkers for patients with locally advanced CRC who receive 5-fluorouracil-based chemotherapy
Identification of polymorphisms in ultraconserved elements associated with clinical outcomes in locally advanced colorectal adenocarcinoma.
Genetic variants within ultraconserved elements and susceptibility to right- and left-sided colorectal adenocarcinoma.
We investigated whether single nucleotide polymorphisms within ultraconserved elements (UCEs) are associated with susceptibility to overall colorectal cancer (CRC) and susceptibility to tumor site-specific CRC.
We investigated whether single nucleotide polymorphisms within ultraconserved elements (UCEs) are associated with susceptibility to overall colorectal cancer (CRC) and susceptibility to tumor site-specific CRC
Identification of polymorphisms in ultraconserved elements associated with clinical outcomes in locally advanced colorectal adenocarcinoma.
Genetic variants within ultraconserved elements and susceptibility to right- and left-sided colorectal adenocarcinoma.
Expression levels of transcribed ultraconserved regions uc.73 and uc.388 are altered in colorectal cancer.

Answer: yes
Yes. SNPs within ultraconserved elements (UCEs) may be valuable prognostic biomarkers for patients with locally advanced CRC who receive 5-fluorouracil-based chemotherapy.
Exact answer: yes
Question: What is Mondor's disease?

Context:
INTRODUCTION: Mondor's disease is a rare superficial thrombophlebitis, historically involving the thoracic venous system of women. 
Mondor's disease is a rare benign and self-limiting condition characterized by thrombophlebitis of the superficial veins of the anterolateral thoracoabdominal wall.
Mondor's disease is a rare condition characterized by a superficial thrombophlebitis that can occur in the thoracoabdominal and genital areas. 
CONCLUSION: Penile Mondor disease is a rare complication that can be successfully treated with medical therapy and conservative approach. Our series showed that penile Mondor's disease does not lead to permanent deformation of the penis or erectile dysfunction.
Thrombophlebitis of the thoracoepigastric system of veins is a benign disease and, despite its localized involvement and presentation, the condition is known as Mondor disease (MD).
Though penile Mondor's disease involving the dorsal vein of the penis has been reported by many authors, we report a peculiar case of penile Mondor's disease in a 26-year-old sexually active man with thrombophlebitis of the circumflex vein of the penis with sparing of the dorsal vein.
Mondor's disease of the penis is an uncommon condition, which usually involves the superficial dorsal veins, it was first described by Braun-Falco in 1955.
Penile Mondor's disease is rare disease that's characterized by thrombosis in the dorsal vein of the penis.

Answer: Mondor's disease is a rare benign and self-limiting condition characterized by thrombophlebitis of the superficial veins of the anterolateral thoracoabdominal wall and genital area.
Question: What DNA methylation patterns are common in high-grade thalamic gliomas in young adults with the H3F3A K27M mutation?

Context:
 transgenes are sufficient to reduce the amounts of H3K27me3 in vitro and in vivo.", "In contrast, thalamic gliomas with wild-type H3F3A had DNA methylation profiles similar to those of hemispheric glioblastomas.CONCLUSION: We found that high-grade thalamic gliomas from young adults, like those from children and adolescents, frequently had H3F3A K27M.", "Gliomas with H3F3A K27M from pediatric or young adult patients had similar, characteristic DNA methylation profiles.", "Although the K27M mutation was frequently observed in adult brainstem and thalamic gliomas, this mutation tended to be associated with a poorer prognosis in brainstem gliomas but not in thalamic gliomas.", "Diffuse Midline Gliomas with Histone H3-K27M Mutation: A Series of 47 Cases Assessing the Spectrum of Morphologic Variation and Associated Genetic Alterations.", "In this series, histone H3-K27M mutation was mutually exclusive with IDH1 mutation and EGFR amplification, rarely co-occurred with BRAF-V600E mutation, and was commonly associated with p53 overexpression, ATRX loss (except in pontine gliomas), and monosomy 10.", "The H3.3 K27M mutation results in a poorer prognosis in brainstem gliomas than thalamic gliomas in adults.", "K27M mutation in histone H3.3 defines clinically and biologically distinct subgroups of pediatric diffuse intrinsic pontine gliomas.", "Recently, sequencing of tumor cells revealed that histone H3 is frequently mutated in pediatric HGG, with up to 78\u00a0% of diffuse intrinsic pontine gliomas (DIPGs) carrying K27M and 36\u00a0% of non-brainstem gliomas carrying either K27M or G34R/V mutations.", "Interestingly, the G34 mutations, the K36M mutations, and the majority of K27M mutations occur in genes encoding the replacement histone H3.3."]

Answer: High-grade thalamic gliomas in young adults with the H3F3A K27M mutation commonly have DNA methylation profiles similar to those of hemispheric glioblastomas.