nirantk/geneticsQA-train huggingface dataset:
Question: Which fimA genotypes are associated with disease?

Context:
 FimA has been characterized as an important virulence factor for P. gingivalis, and many studies, both animal experiments and clinical investigations, have characterized fimA genotypes II, Ib, and IV to be associated with disease (periodontitis and cardiovascular disease) 
Long fimbriae (FimA) are important virulence factors of Porphyromonas gingivalis. Based on the diversity of the fimA gene, this species is classified into 6 genotypes. 
 In cases of chronic apical periodontitis, P. gingivalis variant type IV was the most prevalent (24%), followed by types I (20%), II (16%), and III (8%). In acute abscess samples, variant type II was the most prevalent (12%), followed by types III and IV (8% of each) and type I (4%).
We show that P. gingivalis strains with genotype I and II of FimA are efficient in interaction with saliva or S. gordonii. 
A strong association between Porphyromonas gingivalis fimA genotypes II and Ib and chronic periodontitis exists in the Spanish population. The most prevalent genotype in periodontal patients is II.
Our results suggest that the presence of P. gingivalis is associated with periodontal diseases, and that the type II, IV and Ib/II combination are the most common among fimA genotypes.
Statistical analysis, however, revealed that a more significant correlation was found between periodontitis and the occurrence of type Ib fimA.
 Type II of fimA was the most prevalent genotype of P. gingivalis in patients with AgP. 
The population of Tregs further decreased in patients with type II FimA compared with the other types. P.gingivlias FimA genotype II was the dominant type associated with decreased Treg population. 
A trend toward a greater frequency of FimA II genotype in patients with moderate and severe periodontitis was determined.
The fimA type Ib genotype of P. gingivalis was found to play a critical role in the destruction of peri-implant tissue, suggesting that it may be a distinct risk factor for peri-implantitis.

Answer: FimA has been characterized as an important virulence factor for P. gingivalis, and many studies, both animal experiments and clinical investigations, have characterized fimA genotypes II, Ib, and IV to be associated with disease (periodontitis and cardiovascular disease)
Exact answer: genotypes II, genotypes Ib, genotypes IV
Question: Which is the largest metabolic gene cluster in yeast?

Context:
The DAL cluster is the largest metabolic gene cluster in yeast and consists of six adjacent genes encoding proteins that enable Saccharomyces cerevisiae to use allantoin as a nitrogen source.
The DAL cluster is the largest metabolic gene cluster in yeast and consists of six adjacent genes encoding proteins that enable Saccharomyces cerevisiae to use allantoin as a nitrogen source.
Birth of a metabolic gene cluster in yeast by adaptive gene relocation.
The DAL cluster is the largest metabolic gene cluster in yeast and consists of six adjacent genes encoding proteins that enable Saccharomyces cerevisiae to use allantoin as a nitrogen source
Birth of a metabolic gene cluster in yeast by adaptive gene relocation
The DAL cluster is the largest metabolic gene cluster in yeast and consists of six adjacent genes encoding proteins that enable Saccharomyces cerevisiae to use allantoin as a nitrogen source. 
For example the DAL metabolic cluster in yeast was assembled in recent evolutionary times in the Hemiascomycetes lineage, through a set of rearrangements that brought together the genes involved in the allantoin degradation pathway. 
For example the DAL metabolic cluster in yeast was assembled in recent evolutionary times in the Hemiascomycetes lineage, through a set of rearrangements that brought together the genes involved in the allantoin degradation pathway.

Answer: The DAL cluster is the largest metabolic gene cluster in yeast and consists of six adjacent genes encoding proteins that enable Saccharomyces cerevisiae to use allantoin as a nitrogen source.
the dal cluster is the largest metabolic gene cluster in yeast and consists of six adjacent genes encoding proteins that enable saccharomyces cerevisiae to use allantoin as a nitrogen source.
The DAL cluster is the largest metabolic gene cluster in yeast and consists of six adjacent genes encoding proteins that enable Saccharomyces cerevisiae to use allantoin as a nitrogen source. The DAL cluster is located in a domain of modified chromatin involving both H2A.Z histone exchange and Hst1-Sum1-mediated histone deacetylation, and it may be a coadapted gene complex formed by epistatic selection.
The DAL cluster is the largest metabolic gene cluster in yeast and consists of six adjacent genes encoding proteins that enable Saccharomyces cerevisiae to use allantoin as a nitrogen source. Six of the eight genes involved in allantoin degradation, which were previously scattered around the genome, became relocated to a single subtelomeric site in an ancestor of S. cerevisiae and Saccharomyces castellii.
Exact answer: The DAL cluster
Question: Global quantitative phosphoproteomic analyses are emerging. List the preferred technologies for the enrichment for phosphorylated peptides?

Context:
TiSH--a robust and sensitive global phosphoproteomics strategy employing a combination of TiO2, SIMAC, and HILIC.
An initial TiO(2) phosphopeptide pre-enrichment step is followed by post-fractionation using sequential elution from IMAC (SIMAC) to separate multi- and mono-phosphorylated peptides, and hydrophilic interaction liquid chromatography (HILIC) of the mono-phosphorylated peptides (collectively abbreviated "TiSH").
After enrichment by anti-phosphotyrosine antibodies, we identified 29 potential novel c-Src substrate proteins.
Combining immunoprecipitation with an antiphosphotyrosine antibody, titanium dioxide phosphopeptide enrichment, isobaric tag for the relative and absolute quantitation methodology, and strong cation exchange separation, we were able to identify 2814 phosphopeptides.
Phosphopeptide fractionation by strong cation exchange chromatography combined with immobilized metal affinity chromatography (IMAC) enrichment enabled quantification of more than 8000 distinct phosphorylation sites in Ppt1 wild-type versus Ppt1-deficient yeast cells
By employing titanium dioxide in addition to antiphosphotyrosine antibodies as enrichment methods, we identified 4164 phosphopeptides on 1670 phosphoproteins.
Our method combines the use of strong cation exchange (SCX) and titanium dioxide (TiO(2)) for phosphopeptide enrichment, high-resolution MS for peptide and protein identification, and stable isotope labeling by amino acids in cell culture (SILAC) for quantification.
Phosphopeptides were isolated with high specificity through a simple derivatization procedure based on phosphoramidate chemistry.

Answer: There are many different approaches to enrich for phosphorylated peptides: titanium dioxide, IMAC, simple derivatization through phosphoramidate chemistry and antibodies.
Exact answer: enriched for phosphorylated peptides using titanium dioxide, sequential elution from IMAC, simple derivatization procedure based on phosphoramidate chemistry, antiphosphotyrosine antibodies
Question: Which tool is used for the identification of recurrent variants in noncoding regions?

Context:
LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations.
In cancer research, background models for mutation rates have been extensively calibrated in coding regions, leading to the identification of many driver genes, recurrently mutated more than expected. Noncoding regions are also associated with disease; however, background models for them have not been investigated in as much detail. This is partially due to limited noncoding functional annotation. Also, great mutation heterogeneity and potential correlations between neighboring sites give rise to substantial overdispersion in mutation count, resulting in problematic background rate estimation. Here, we address these issues with a new computational framework called LARVA. It integrates variants with a comprehensive set of noncoding functional elements, modeling the mutation counts of the elements with a β-binomial distribution to handle overdispersion. LARVA, moreover, uses regional genomic features such as replication timing to better estimate local mutation rates and mutational hotspots. We demonstrate LARVA's effectiveness on 760 whole-genome tumor sequences, showing that it identifies well-known noncoding drivers, such as mutations in the TERT promoter. Furthermore, LARVA highlights several novel highly mutated regulatory sites that could potentially be noncoding drivers. We make LARVA available as a software tool and release our highly mutated annotations as an online resource (larva.gersteinlab.org).
LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations
LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations.

Answer: LARVA is an integrative framework for large-scale analysis of recurrent variants in noncoding annotations. It integrates variants with a comprehensive set of noncoding functional elements, modeling the mutation counts of the elements with a β-binomial distribution to handle overdispersion. LARVA, moreover, uses regional genomic features such as replication timing to better estimate local mutation rates and mutational hotspots. Furthermore, LARVA highlights several novel highly mutated regulatory sites that could potentially be noncoding drivers.
Exact answer: LARVA
Question: Which are the main histone modifications associated with enhancers?

Context:
Using H3K4me2 as a mark for active enhancers
Hyperacetylation of histones H3 and H4, a mark of active chromatin, is established broadly across target loci by enhancers that function over long distances
The enhancer region itself was marked by mono-methylation at K4 and K9, distinguishing it from the methyl marks in the gene coding region
H3K4 methylation to monovalent and bivalent domains

Answer: Histone 3 lysine 4 mono- (H3K4me1) and di-methylation (H3K4me2) are the main post-transcriptional histone modifications related to enhancer activity.
Using H3K4me2 as a mark for active enhancers (PMID: 22270183) Hyperacetylation of histones H3 and H4, a mark of active chromatin, is established broadly across target loci by enhancers that function over long distances (PMID: 19021773) The enhancer region itself was marked by mono-methylation at K4 and K9, distinguishing it from the methyl marks in the gene coding region (PMID: 19021773) H3K4 methylation to monovalent and bivalent domains (PMID: 20621055)
H3K4 methylation to monovalent and bivalent domains. The enhancer region itself was marked by mono-methylation at K4 and K9, distinguishing it from the methyl marks in the gene coding region. Hyperacetylation of histones H3 and H4, a mark of active chromatin, is established broadly across target loci by enhancers that function over long distances. Using H3K4me2 as a mark for active enhancers. 
Exact answer: Histone 3 lysine 4 mono-methylation (H3K4me1)
Histone 3 lysine 4 di-methylation (H3K4me2)
Question: What is known about potential implication of thyroid hormone receptors in arterial hypertension?

Context:
For the first time, our study showed associations between the THRA rs939348 polymorphism and systolic BP and the risk of hypertension but not with CHD, although we admit that the statistical power available to study any relationship with CHD was very limited.
The results of Western blot analyses showed that the levels of the three TR isoforms do not differ significantly between SHRs and control rats of the same age, either in the left or in the right ventricle.

Answer: thyroid hormone receptors are implicated in arterial hypertension
An associations between the THRA rs939348 polymorphism and systolic BP and the risk of hypertension has been observed
The levels of the three thyroid hormone receptors isoforms do not differ significantly between spontaneous hypertensive rats and control rats of the same age, either in the left or in the right ventricle.
The published results are still unconclusive.
Question: Which glands are subject to attack by lymphocytes in Sjogren's syndrome?

Context:
In Sjögren's syndrome the autoimmune response is directed against the exocrine glands, which, as histopathological hallmark of the disease, display persistent and progressive focal mononuclear cell infiltrates.
Sjögren's syndrome (SS) is an autoimmune disease characterized by clonal B cell attack of the exocrine glands and dysregulated expression of B cell-activating factor (BAFF).
Sjögren's syndrome (SjS) is a human autoimmune disease characterized by exocrine dysfunction resulting from chronic autoimmune attack primarily against the lacrimal and/or salivary glands.
Sjögren's syndrome is an autoimmune disease in which immune cells chronically attack the lachrymal and salivary glands.
Sjögren's syndrome (SjS) is a systemic autoimmune disease in which an immunological attack against the salivary and lacrimal glands results, respectively, in severe dry mouth and dry eye diseases.
Sjögren's syndrome (SS) is a chronic autoimmune disease affecting epithelial tissues. Exocrine glands are the primary target and their functional impairment comes as a result of immune attack of epithelial cells of the affected organs (autoimmune epithelitis).
Sjögren's syndrome (SjS) is a human autoimmune disease characterized by the loss of exocrine function as a result of a chronic immune attack directed primarily against the salivary and lacrimal glands leading to xerostomia (dry mouth) and xerophthalmia (dry eyes).
The purpose of this qualitative research was to explore the lived experiences of women with Sjogren's Syndrome (SS), a chronic autoimmune syndrome in which invading lymphocytes attack moisture-producing glands of the body. This syndrome, affecting 4 million Americans, involves extreme dryness of the eyes and mouth and other systemic complications such as fatigue and muscle and joint pain.
NOD mice manifest many features of autoimmune exocrinopathy (Sjögren's syndrome), a disease generally characterized by a chronic, progressive immunological attack against the exocrine tissues of the salivary and lacrimal glands.

Answer: Sjögren's syndrome (SjS) is a human autoimmune disease characterized by exocrine dysfunction resulting from chronic autoimmune attack primarily against the lacrimal and/or salivary glands.
Exact answer: The lacrimal and/or salivary glands
Question: Which method is used for prediction of novel microRNA genes in cancer-associated genomic regions?

Context:
 In this work we present a new computational tool (SSCprofiler) utilizing a probabilistic method based on Profile Hidden Markov Models to predict novel miRNA precursors. Via the simultaneous integration of biological features such as sequence, structure and conservation, SSCprofiler achieves a performance accuracy of 88.95% sensitivity and 84.16% specificity on a large set of human miRNA genes. The trained classifier is used to identify novel miRNA gene candidates located within cancer-associated genomic regions and rank the resulting predictions using expression information from a full genome tiling array. Finally, four of the top scoring predictions are verified experimentally using northern blot analysis. Our work combines both analytical and experimental techniques to show that SSCprofiler is a highly accurate tool which can be used to identify novel miRNA gene candidates in the human genome. SSCprofiler is freely available as a web service at http://www.imbb.forth.gr/SSCprofiler.html.
In this work we present a new computational tool (SSCprofiler) utilizing a probabilistic method based on Profile Hidden Markov Models to predict novel miRNA precursors.
Our work combines both analytical and experimental techniques to show that SSCprofiler is a highly accurate tool which can be used to identify novel miRNA gene candidates in the human genome.

Answer: SSCprofiler is a computational tool utilizing a probabilistic method based on Profile Hidden Markov Models to predict novel miRNA precursors. Via the simultaneous integration of biological features such as sequence, structure and conservation, SSCprofiler achieves a performance accuracy of 88.95% sensitivity and 84.16% specificity on a large set of human miRNA genes. The trained classifier is used to identify novel miRNA gene candidates located within cancer-associated genomic regions and rank the resulting predictions using expression information from a full genome tiling array. SSCprofiler is freely available as a web service at http://www.imbb.forth.gr/SSCprofiler.html.
Exact answer: SSCprofiler
Question: Are shadow enhancers associated with development?

Context:
Critical developmental control genes sometimes contain "shadow" enhancers that can be located in remote positions, including the introns of neighboring genes
These results suggest that shadow enhancers represent a novel mechanism of canalization whereby complex developmental processes "bring about one definite end-result regardless of minor variations in conditions"
Shadow enhancers flanking the HoxB cluster direct dynamic Hox expression in early heart and endoderm development.
 This suggests that they function as shadow enhancers to modulate the expression of genes from the HoxB complex during cardiac development. Regulatory analysis of the HoxA complex reveals that it also has enhancers in the 3' flanking region which contain RAREs and have the potential to modulate expression in endoderm and heart tissues
This suggests that they function as shadow enhancers to modulate the expression of genes from the HoxB complex during cardiac development.
Recent reports have shown that developmental genes often possess multiple discrete enhancer modules that drive transcription in similar spatio-temporal patterns: primary enhancers located near the basal promoter and secondary, or 'shadow', enhancers located at more remote positions.
Together, the similarities in their location, enhancer output, and dependence on retinoid signaling suggest that a conserved cis-regulatory cassette located in the 3' proximal regions adjacent to the HoxA and HoxB complexes evolved to modulate Hox gene expression during mammalian cardiac and endoderm development. 
This suggests that they function as shadow enhancers to modulate the expression of genes from the HoxB complex during cardiac development.

Answer: Yes. Critical developmental control genes sometimes contain shadow enhancers that can be located in remote positions, including the introns of neighboring genes
Exact answer: yes
Question: What is the Orco protein in mosquitos?

Context:
Insect odorant receptors function as heteromeric odorant-gated cation channels comprising a conventional odorant-sensitive tuning receptor, and a conserved co-receptor (Orco)
Insects sense odours via several chemosensory receptor families, including the odorant receptors (ORs), membrane proteins that form heteromeric odour-gated ion channels comprising a variable ligand-selective subunit and an obligate co-receptor called Orco
Surprisingly, mutation of the obligate olfactory coreceptor (Orco) does not abolish CO(2) aversion during walking yet eliminates CO(2) tracking in flight. 
 Most odors are detected via a family of odorant receptors (ORs), which form heteromeric complexes consisting of a well-conserved OR co-receptor (Orco) ion channel and a non-conserved tuning OR that provides coding specificity to each complex. Orco functions as a non-selective cation channel and is expressed in the majority of olfactory receptor neurons (ORNs). 
a novel OR co-receptor (Orco)
In insects, odor cues are discriminated through a divergent family of odorant receptors (ORs). A functional OR complex consists of both a conventional odorant-binding OR and a nonconventional coreceptor (Orco) that is highly conserved across insect taxa. 
Insect odorant receptors (ORs) function as odorant-gated ion channels consisting of a conventional, odorant-binding OR and the Orco coreceptor. 

Answer: Odorant co-receptor.
Question: List fish anti-freeze proteins.

Context:
the anti-freeze glycoprotein of Antarctic and Arctic notothenoids, 
pe III anti-freeze protein (AFP)
AFP I or AFP III
type III anti-freeze proteins 
wild type III thermal hysteresis protein
Thermal hysteresis proteins (THPs) have been found in vertebrates, invertebrates, plants, bacteria and fungi and are able to depress the freezing point of water (in the presence of ice crystals) in a non-colligative manner by binding to the surface of nascent ice crystals
skin-type anti-freeze protein-3

Answer: AFP-I
AFP-II
AFP-III
Anti-freeze glycoprotein
Thermal hysteresis protein
Exact answer: anti-freeze protein-3, AFP-III, anti-freeze glycoprotein, Thermal hysteresis protein, AFP-I, AFP-II
Question: What is the role of probiotics in gastrointestinal disease?

Context:
The overall response rate was 80.5%, of which 69.5% of respondents said they recommended or prescribed probiotic food supplements to their patients, including 53.4% of surgeons and 80.8% of gastroenterologists (P = 0.00013). The most popular probiotic supplements among surgeons were probiotic-containing yoghurt and drinks (79.5% and 71.8%, respectively), whereas VSL#3 was more popular with gastroenterologists (83.3%). The most popular indications were irritable bowel syndrome (70.7% of prescribers) and pouchitis (67.5% of prescribers). Many respondents prescribed long-term probiotics.
Current evidence indicates that probiotic effects are strain-specific, they do not act through the same mechanisms, and nor are all probiotics indicated for the same health conditions. However, they do share several common features in that they exert anti-inflammatory effects, they employ different strategies to antagonize competing microorganisms, and they induce cytoprotective changes in the host either through enhancement of barrier function, or through the upregulation of cytoprotective host proteins.
Most surveyed physicians recommended probiotics for irritable bowel syndrome, antibiotic, and Clostridium difficile-associated diarrhea because they believed that the literature supports their usage for these conditions.
This study suggests most gastrointestinal disease specialists recognize a role for and have used probiotics as part of their therapeutic armamentarium
probiotics for these patients with small bowel bacterial overgrowth, inflammatory bowel disease, and radiation enteritis.
These results provide some evidence that viable Bifidobacterium lactis strain Bb 12, added to an acidified infant formula, has some protective effect against acute diarrhea in healthy children.
Probiotics are live, microbial food supplements that benefit the host animal by improving intestinal microbial balance. Their major role in preventing and treating gastrointestinal disease appears to be from their effect on the immune process, protection against abnormal invasive bacteria, and in the production of short-chain fatty acids from starch and non-starch polysaccharides.

Answer: Probiotics are live, microbial food supplements that benefit the host animal by improving intestinal microbial balance. Across all 11 probiotic species and eight different gastrointestinal diseases   - Irritable Bowel Syndrome (IBS), Helicobacter pylori infection (HPP), Necrotizing Enterocolitis (NEC), Pouchitis (Pouch), Antibiotic Associated diarrhea (AAD), Clostridium difficile Disease (CDD), Infectious diarrhea (ID), and Travellers diarrhea (TD) -  probiotics have been shown to have effect on prevention and treatment of gastrointestinal disease through enhancing the immune response, protection against abnormal invasive bacteria. Probiotics have a role in all age groups, incl. infants.