nirantk/geneticsQA-train huggingface dataset:
Question: Which is the most known bacterium responsible for botulism (sausage-poisoning)?

Context:
Botulism is a serious foodborne neuroparalytic disease, caused by botulinum neurotoxin (BoNT), produced by the anaerobic bacterium Clostridium botulinum.
Cattle botulism is a fatal intoxication caused by botulinum neurotoxins (BoNTs) produced by Clostridium botulinum serotypes C and D
Botulism in horses in the USA is attributed to Clostridium botulinum types A, B or C.
Clostridium botulinum is the etiological agent of botulism. Due to food-borne poisoning and the potential use of the extremely toxic botulinum neurotoxin (BoNT) from C. botulinum
Botulism is a serious neuroparalytic disease caused by toxins of Clostridium botulinum. Botulinum toxin is produced under anaerobic conditions and is one of the most dangerous toxin in the world.
Botulism is a neuroparalytic disease that can occur in all warm-blooded animals, birds, and fishes. The disease in animals is mainly caused by toxins produced by Clostridium botulinum strains belonging to group III, although outbreaks due to toxins produced by group I and II organisms have been recognized.
Botulism is a severe neuroparalytic disease that affects humans, all warm-blooded animals, and some fishes. The disease is caused by exposure to toxins produced by Clostridium botulinum and other botulinum toxin-producing clostridia.
The botulinum neurotoxins (BoNTs) produced by different strains of the bacterium Clostridium botulinum are responsible for the disease botulism and include a group of immunologically distinct serotypes (A, B, E, and F) that are considered to be the most lethal natural proteins known for humans.
Botulinumtoxin (BTX) is a neurotoxin produced from Clostridium botulinum under anaerobic conditions and is responsible for botulism, a notifiable, bacterial form of food poisoning.
Botulism is a disease characterized by neuromuscular paralysis and is produced from botulinum neurotoxins (BoNTs) found within the Gram positive bacterium Clostridium botulinum.
An epidemiological investigation and laboratory detection studies showed that sausage contaminated by type A Clostridium botulinum caused this outbreak of food poisoning.
Botulism is caused by botulinum neurotoxin produced by the bacterium Clostridium botulinum.
Botulinumtoxin (BTX) is a neurotoxin produced from Clostridium botulinum under anaerobic conditions and is responsible for botulism, a notifiable, bacterial form of food poisoning

Answer: Botulism is a severe neuroparalytic disease caused by botulinum neurotoxin (BoNT), and affects humans, all warm-blooded animals, birds, and some fishes. Botulinum toxin is produced under anaerobic conditions by the bacterium Clostridium botulinum, which is the most known etiological agent of the disease, and some other clostridia, and is one of the most dangerous toxin in the world.
Exact answer: Clostridium botulinum
Question: Explain the concept proteostasis.

Context:
Protein homeostasis, or proteostasis, refers to a proper balance between synthesis, maturation, and degradation of cellular proteins.
Mechanisms that promote the homeostasis of the proteome, or proteostasis, can slow aging and decrease the incidence of age-related diseases.
The eukaryotic cell possesses specialized pathways to turn over and degrade redundant proteins and organelles. Each pathway is unique and responsible for degradation of distinctive cytosolic material. The ubiquitin-proteasome system and autophagy (chaperone-mediated, macro, micro and organelle specific) act synergistically to maintain proteostasis. Defects in this equilibrium can be deleterious at cellular and organism level, giving rise to various disease states.
 protein homeostasis (proteostasis) 
The folding biology common to all three kingdoms of life (Archaea, Bacteria, and Eukarya) is proteostasis. The proteostasis network (PN) functions as a “cloud” to generate, protect, and degrade the proteome.
Maintaining the dynamic proteome of a living cell in the face of an ever-changing environment depends on a fine-tuned balance of protein synthesis and protein degradation. Molecular chaperones exert key functions during protein homeostasis (proteostasis). 
This research highlighted the central importance of protein homeostasis, or proteostasis for short, defined as the cellular state in which the proteome is both stable and functional. It implicates an equilibrium between synthesis, folding, trafficking, aggregation, disaggregation and degradation.
Protein homeostasis, also called proteostasis, is critical for cellular health and its dysregulation is implicated in aging, cancer, metabolic disease, and neurodegenerative disorders.
 protein homeostasis (proteostasis) 
 Disruption of proteostasis is implicated in aging and the pathogenesis of numerous degenerative diseases.
Protein homeostasis, proteostasis, is essential to understand cell function. Protein degradation is a crucial component of the proteostatic mechanisms of the cell.
Maintaining correct cellular function is a fundamental biological process for all forms of life. A critical aspect of this process is the maintenance of protein homeostasis (proteostasis) in the cell, which is largely performed by a group of proteins, referred to as the protein quality control (PQC) network. This network of proteins, comprised of chaperones and proteases, is critical for maintaining proteostasis not only during favourable growth conditions, but also in response to stress. 
All organisms--Bacteria, Archaea and Eukarya--have evolved a protein homeostasis, or proteostasis, network comprising chaperones and folding factors, degradation components, signalling pathways and specialized compartmentalized modules that manage protein folding in response to environmental stimuli and variation. 

Answer: Protein homeostasis, or proteostasis, refers to a proper balance between synthesis, maturation, and degradation of cellular proteins. Disruption of proteostasis is implicated in aging and the pathogenesis of numerous degenerative diseases.
Question: Intact macromolecular assemblies are analysed by advanced mass spectrometry. How large complexes (in molecular weight) have been studied?

Context:
Here we show that the Orbitrap mass analyzer can be used to measure protein assemblies of molecular weights approaching one megadalton with sensitivity down to the detection of single ions.
Using this relationship we show that we can determine masses of both 30S subunits and intact 2.3 MDa 70S ribosomes from Thermus thermophilus.
We confirm the existence of these subpopulations using tandem mass spectrometry of intact 30S subunits. Overall, the results show that, rather than uniform particles, gas-phase ribosomes consist of a number of discrete populations. More generally, the results establish a rigorous procedure for accurate mass measurement and spectral analysis of heterogeneous macromolecular assemblies.

Answer: 2.3 megadalton
Exact answer: 2.3 megadalton
Question: Is paramyxovirus involved in human subacute thyroiditis?

Context:
Most cases of subacute thyroiditis are caused by a variety of viruses, for example, Coxsackie, cytomegalovirus, Epstein-Barr virus, and adenovirus. Influenza immunization or infection may cause subacute thyroiditis.
Coxsackie virus has been reported to be one of the viruses associated with the disease.
The etiology of subacute granulomatous thyroiditis (SAT) is obscure, although it is postulated to be associated with viral infections and genetic factors.
The results suggest that SAT is not usually associated with acute infections
No evidence was obtained to support the proposed role of enteroviruses as an important etiologic agent of SAT.
The viral antibodies evaluated were those of Influenza A and B, Coxsackie A9, B1, B2, B3, B4, B5 and B6, Echo 3, 7, 11 and 12, Parainfluenza 1, 2, 3 and 4, and Adeno 8 virus. The following results were obtained: In class I HLA typing, the frequency of HLA-Bw35 in SAT was 67.4%, which was significantly (p less than 0.0001) higher than that in the control (14.1%). On the other hand, the frequency of Cw1 in SAT (14.6%) was significantly (p less than 0.01) lower than that of the control (32.1%), and that of Cw3 (65.2%) was significantly (p less than 0.01) higher than that of the control (46.5%).

Answer: There is no evidence that paramyxovirus are involved in etiology of subacute thyroiditis.
Exact answer: no
Question: What is the main characteristic of Amyotrophic Lateral Sclerosis?

Context:
Motor neuron diseases (MND), such as amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA), are progressive neurodegenerative diseases that share the common characteristic of upper and/or lower motor neuron degeneration.
Amyotrophic lateral sclerosis (ALS) is a progressive degeneration of upper and lower motor neurons.
There are four main hypotheses about the cause of ALS: excitotoxicity linked to glutamate receptor overactivation; mutation of the superoxide dismutase gene; production of autoantibodies to calcium channels; neurofilament accumulation. The motoneuron degeneration characteristic of ALS could be caused by any one or a combination of these mechanisms.
Amyotrophic lateral sclerosis is the most common adult-onset motor neuron disease and evidence from mice expressing amyotrophic lateral sclerosis-causing SOD1 mutations suggest that neurodegeneration is a non-cell autonomous process where microglial cells influence disease progression

Answer: Amyotrophic lateral sclerosis (ALS) is a progressive degeneration of upper and lower motor neurons. 
Amyotrophic lateral sclerosis (ALS) is a progressive degeneration of upper and lower motor neurons.
Question: What role do septins play in cellular processes?

Context:
 ", "The human genome codes for 13 members of a family of filament-forming GTP-binding proteins known as septins.", "Septins are evolutionary conserved cytoskeletal GTPases forming heteropolymer complexes involved in cytokinesis and other cellular processes", "Septins comprise a conserved family of GTPases important in cytokinesis.", "Septins are a highly conserved family of GTP-binding cytoskeletal proteins implicated in multiple cellular functions, including membrane transport, apoptosis, cell polarity, cell cycle regulation, cytokinesis, and oncogenesis"]

Answer: Septins play a crucial role in cellular processes such as cytokinesis and other functions. They are evolutionary conserved cytoskeletal GTPases forming heteropolymer complexes involved in various cellular functions like membrane transport, apoptosis, cell polarity, cell cycle regulation, and oncogenesis.
Question: Is there a package in R/bioconductor for classification of alternative splicing?

Context:
spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.
Recent software improvements in full-length transcript deconvolution prompted us to develop spliceR, an R package for classification of alternative splicing and prediction of coding potential.
spliceR uses the full-length transcript output from RNA-seq assemblers to detect single or multiple exon skipping, alternative donor and acceptor sites, intron retention, alternative first or last exon usage, and mutually exclusive exon events. For each of these events spliceR also annotates the genomic coordinates of the differentially spliced elements, facilitating downstream sequence analysis. For each transcript isoform fraction values are calculated to identify transcript switching between conditions. Lastly, spliceR predicts the coding potential, as well as the potential nonsense mediated decay (NMD) sensitivity of each transcript.
Recent software improvements in full-length transcript deconvolution prompted us to develop spliceR, an R package for classification of alternative splicing and prediction of coding potential.
Recent software improvements in full-length transcript deconvolution prompted us to develop spliceR, an R package for classification of alternative splicing and prediction of coding potential. 
Recent software improvements in full-length transcript deconvolution prompted us to develop spliceR, an R package for classification of alternative splicing and prediction of coding potential.

Answer: Yes. SpliceR is an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.
Exact answer: yes
Question: What is the relationship between nucleosomes and exons?

Context:
Nucleosomes preferentially are located at the ends of exons, thus protecting splice junctions, with the N9 positions of guanines of the GT and AG junctions oriented toward the histones.
Nucleosomes were found to be preferentially positioned within constitutive exons and/or constitutive portions of alternative exons, which was not associated with gene expression or states of cells but was based on sequence and positively related with the sequence conservation of splicing sites
Here, we discuss the evidence supporting these ideas, from the first proposal of chromatin affecting alternative splicing, performed 20 years ago, to the latest findings including genome-wide evidence that nucleosomes are preferentially positioned in exons.
Here we show, by analysis of data sets from human sperm and T cells and medaka (Japanese killifish, Oryzias latipes) blastulae, that internal exons of genes are characterized by sharply elevated average nucleosome occupancy in comparison to flanking intronic sequences.
sing public data, we here show that there is a higher nucleosome-positioning signal in internal human exons and that this positioning is independent of expression. We observed a similarly strong nucleosome-positioning signal in internal exons of Caenorhabditis elegans.
we have found stable nucleosome occupancy within human and Caenorhabditis elegans exons that is stronger in exons with weak splice sites.
This confirms previously reported findings about preferential positioning of splice junctions within the nucleosomes.

Answer: Nucleosomes are preferentially located within exons compared to nearby intronic sequences. Preferential positioning within the exons is indepedent of gene expression levels, stronger in exons with weak splice sites and conserved through metazoan evolution.
Question: Which is the relation between sweating and anaerobic threshold?

Context:
It is concluded that the sweating response during upright recovery is significantly modified by exercise intensity and may likely be influenced by the nonthermal baroreceptor reflex adjustments postexercise.
 The purpose of this paper is to delineate the effects of training status, heat acclimation, environmental conditions and host factors on the sweating response to exercise.
These results would suggest that at a given exercise intensity in subjects with a higher aerobic capacity body temperature is maintained with a lower sweating rate than that in subjects with a lower aerobic capacity.

Answer: There is no clear evidence of the relationship between sweating and anaerobic threshold
Exact answer: There is no clear evidence of the relationship between sweating and anaerobic threshold
Question: Why do we use "N-terminal proteomics"?

Context:
ChaFRADIC is a powerful and practicable tool for protease and peptidase research,
systematic identification of protease cleavage events by quantitative N-terminal proteomics,
 identifying the largest set of protein protease substrates ever reported and gaining novel insight into substrate specificity differences of these cathepsins.
new insights into the structure-function relationship of protease targets and their validation from large-scale approaches.
revealed unknown cleavage specificities, uncharacterized extended specificity profiles, and macromolecular determinants in substrate selection that were confirmed by molecular modeling. 

Answer: N-terminal proteomics allows the systematic identification of protease/peptidase cleavage events revealing substrate cleavage specificities.
Question: What is the function of gasdermin D?

Context:
gasdermin D (GSDMD) protein to trigger pyroptosis, a lytic form of cell death that is crucial for immune defences and diseases. 
Here we show that the gasdermin-N domains of the gasdermin proteins GSDMD, GSDMA3 and GSDMA can bind membrane lipids, phosphoinositides and cardiolipin, and exhibit membrane-disrupting cytotoxicity in mammalian cells and artificially transformed bacteria.

Answer: The gasdermin-N domains of the gasdermin proteins can bind membrane lipids, phosphoinositides and cardiolipin to produce membrane-disrupting cytotoxicity.
Question: What is the most probable defect underlying triple negative breast cancer?

Context:
We have previously reported an array comparative genomic hybridization profile that identifies triple-negative breast cancers (TNBC), with BRCA1 dysfunction
BRCA1-like status was assessed in 101 patients with early-stage TNBC receiving adjuvant cyclophosphamide-based chemotherapy.
Sixty-six tumors (65%) had a BRCA1-like profile.

Answer: The most probable defect underlying triple negative breast cancer is BRCA1 dysfunction.
Exact answer: BRCA1 dysfunction
Question: Has small pox been eradicated from the world?

Context:
small pox has been eradicated.
smallpox is now eradicated
In May 1980 the World Health Assembly in Geneva announced in solemn form the world-wide eradication of the small-pox and gave recommendations to the member countries for concluding measures concerning the small-pox vaccination, the foundation of vaccine reserves and the control of the epidemiological situation in the world.
As a result of vaccination, diseases such as polio and measles have been controlled and small pox has been eradicated
Small pox eradication from the world is the perfect example of the role of mass vaccination of the entire community of the universe. 
The French owe a lot to this Central Committee of Vaccine, which greatly contributed to fighting small pox and eradicating the disease finally.
Small pox eradication from the world is the perfect example of the role of mass vaccination of the entire community of the universe.
Also, the vaccine that Jenner used, which decreased the prevalence of Small Pox worldwide in his own time, and later was used to eradicate Small Pox altogether, is discussed in light of recent data..
the only known cases of smallpox happened from an outbreak in Birmingham, England caused by a laboratory accident in the year of 1979. On May the 8 th 1980 the disease was declared as eliminated from the world by the WHO (WHO-Resolution 33.33).

Answer: smallpox is now eradicated., Yes, small pox has been eradicated., smallpox is now eradicated, small pox has been eradicated.
Exact answer: yes
Question: What is the role of cohesins at the IFNG locus?

Context:
Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus.
Here we show that cohesin forms the topological and mechanistic basis for cell-type-specific long-range chromosomal interactions in cis at the developmentally regulated cytokine locus IFNG. Hence, the ability of cohesin to constrain chromosome topology is used not only for the purpose of sister chromatid cohesion, but also to dynamically define the spatial conformation of specific loci. This new aspect of cohesin function is probably important for normal development and disease
Here we show that cohesin forms the topological and mechanistic basis for cell-type-specific long-range chromosomal interactions in cis at the developmentally regulated cytokine locus IFNG.
Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus
Here we show that cohesin forms the topological and mechanistic basis for cell-type-specific long-range chromosomal interactions in cis at the developmentally regulated cytokine locus IFNG
Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus.
Here we show that cohesin forms the topological and mechanistic basis for cell-type-specific long-range chromosomal interactions in cis at the developmentally regulated cytokine locus IFNG.

Answer: Cohesins form cell-type-specific long-range chromosomal cis-interactions at the developmentally regulated IFNG locus. Hence, the ability of cohesin to constrain chromosome topology is used not only for the purpose of sister chromatid cohesion, but also to dynamically define the spatial conformation of specific loci. This new aspect of cohesin function is probably important for normal development and disease.
Question: What are the characteristics of the "Universal Proteomics Standard 2" (UPS2)?

Context:
the UPS2 proteomic dynamic range standard introduced by The Association of Biomolecular Resource Facilities Proteomics Standards Research Group in 2006)
Universal Proteomics Standard sample with a dynamic range of 5 orders of magnitude (UPS2).

Answer: The UPS2 proteomic dynamic range standard was introduced by the Association of Biomolecular Resource Facilities Proteomics Standards Research Group in 2006 and it has a dynamic range of 5 orders of magnitude.
Question: What is the main application of SWATH-MS in proteomics?

Context:
it is a valuable resource for the selection of candidate proteotypic peptides for targeted proteomic experiments via Selected Reaction Monitoring (SRM) or SWATH-MS
SWATH-MS is a data-independent acquisition method that generates, in a single measurement, a complete recording of the fragment ion spectra of all the analytes in a biological sample for which the precursor ions are within a predetermined m/z versus retention time window.
ew strategies, such as SWATH™ MS, which allows us to systematically characterize and quantify query sample sets of 'any protein of interest' in complex biological samples,
Here we present a new strategy that systematically queries sample sets for the presence and quantity of essentially any protein of interest. 

Answer: Using the method called SWATH-MS one might ask sample sets for the presence and quantity of essentially any protein of interest.
Exact answer: The identification and quantification of any protein.
Question: is there an increase in ultrasound comets after intense exercise?

Context:
Healthy athletes developed subclinical increase in pulmonary water content immediately after an Ironman race at sea level, as shown by the increased number of ULCs related to cardiac changes occurring during exercise.
Increased EVLW is associated with estimated PCWP and indices of left ventricular systolic and diastolic dysfunction. The additional exercise-induced increase of PCWP, the worsening of left ventricular diastolic function, and extensive wall-motion abnormalities correlate with variations of EVLW.
 Among them chest ultrasonography can detect and quantify the extravascular lung water, creating "comet-tail" ultrasound artefacts (ULCs) from water-thickened pulmonary interlobular septa.
 In top-level breath-hold divers, chest sonography frequently reveals an increased number of ULCs after immersion, indicating a relatively high prevalence of (often subclinical) reversible extravascular lung water accumulation.

Answer: Strenuous exercise and exercise perfomed in extreme conditions provoke increase in interstitial pulmonary water content as shown by the increased number of ultrasuond comets
Exact answer: yes
Question: Which is the "bonding hormone"?

Context:
The neurohypophysial hormone oxytocin (OXT) and its receptor (OXTR) have critical roles in the regulation of pro-social behaviors, including social recognition, pair bonding, parental behavior, and stress-related responses.
Neuropeptide hormone oxytocin has roles in social bonding, energy metabolism, and wound healing contributing to good physical, mental and social health. 
Oxytocin is known as the 'love hormone' due its role in promoting mother-child and pair bonding.
The oxytocin (OT) hormone pathway is involved in numerous physiological processes, and one of its receptor genes (OXTR) has been implicated in pair bonding behavior in mammalian lineages.
oxytocin, a hormone involved in parent-offspring bonding

Answer: Oxytocin is known as the 'bonding hormone' due its role in promoting mother-child and pair bonding.
Exact answer: Oxytocin