anand-s/m_qalm huggingface dataset:
Question: Which trinucleotide repeat disorders are affecting the nervous system?
Answer: At least six neudegenerative disorders result from trinucleotide repeat expansion: X-linked spinal and bulbar muscular atrophy (SBMA), two fragile X syndromes of mental retardation (FRAXA and FRAXE), Huntington's disease (HD), spinocerebellar ataxia type 1 (SCA1), and dentatorubral-pallidoluysian atrophy (DRPLA).
Question: Global quantitative phosphoproteomic analyses are emerging. List the preferred technologies for the enrichment for phosphorylated peptides?
Answer: There are many different approaches to enrich for phosphorylated peptides: titanium dioxide, IMAC, simple derivatization through phosphoramidate chemistry and antibodies.
Question: Which drugs were investigated in the ALPHEUS trial?
Answer: ALPHEUS study examined if ticagrelor was superior to clopidogrel in reducing periprocedural myocardial necrosis in stable coronary patients undergoing high-risk elective percutaneous coronary intervention (PCI).
Question: List all articles on network meta-analysis for smoking cessation
Answer: Cardiovascular events associated with smoking cessation pharmacotherapies: a network meta-analysis.
Pharmacological interventions for smoking cessation: an overview and network meta-analysis
Effectiveness and cost-effectiveness of computer and other electronic aids for smoking cessation: a systematic review and network meta-analysis.
Smoking cessation interventions in COPD: a network meta-analysis of randomised trials.
Question: Which post-translational histone modifications are characteristic of facultative heterochromatin?
Answer: Nuclear VapB methyltransferase diminishes the establishment of facultative heterochromatin by decreasing histone 3 lysine 9 trimethylation (H3K9me3). Dramatic changes in exposure of a repressive chromatin mark, H3K9me2, indicate that during development linker histone plays a role in establishing the facultative heterochromatin territory and architecture in the nucleus. Histone H3 trimethylation at lysine 36 is associated with constitutive and facultative heterochromatin.
Question: Which are the best treatment options to treat Helicobacter pylori?
Answer: The best treatment options  for eradication of Helicobacter pylori involve triple or quadruple drugs therapy with different types of antibiotics.
Bismuth may be also an additional option. Proton pump inhibitors are also included in treatment.
The more effective drug list includes: amoxicillin, claritromycin, metronidazole rifabutin.
Also chitosan microspheres with Eudragit L100 have been tested.
Question: Which are the available biomedical text mining tools for the detection of protein-protein interactions?
Answer: Protein-protein interactions (PPI) can be extracted from biomedical literature using text mining approaches. These approaches have been classified into two categories, the statistical calculation of the co-occurrence of proteins and the computational linguistic method. Moreover, bioinformatics methods based on sequence, structural, or evolutionary information have been developed to predict protein-protein interactions. The available state-of-the-art biomedical text mining tools are: eFIP (Extracting Functional Impact of Phosphorylation), a system for text mining of protein interaction networks of phosphorylated proteins; GeneView, a suite of state-of-the-art text-mining tools designed for the automated identification of protein–protein interactions; PPI finder, a text mining tool for human protein-protein interactions based on computational linguistic methods. PPI Finder system consists of the Information Retrieval module and Information Extraction module; PreBIND and Textomy are two components of a biomedical literature-mining system optimized to discover protein-protein interactions using a support vector machine; BioMap system is optimized for the identification of protein-protein interactions from large biomedical literature datasets; Protopia searches for and integrates protein-protein interactions and the information about them contained in five different Protein Interaction Web Databases; STRING uses Natural Language Processing to extract a subset of semantically specified known and predicted protein-protein interactions.
Question: Which are the available biomedical text mining tools for the detection of protein-protein interactions?
Answer: Several tools have been developed to detect protein-protein interactions (PPIs) by text mining the biomedical literature. Two main computational approaches used for this task are co-occurrence-based methods and Natural Language Processing methods. Biomedical text mining tools for PPI identification are the following (in alphabetical order): BioCreative Meta Server, BioMap, eFIP, Extracting Functional Impact of Phosphorylation, GeneView, HAPPI, Hidden Vector State model, iHop, LAITOR, OntoGene, OpenDMAP, PIE (Protein interaction information extraction system), PPI finder (Paired-PPI Finder), PPInterFinder, PPIs, PolySearch, PreBind and Textomy, Protopia, STRING, TafTalent.
Question: Intetumumab has been tested in clinical trials for treatment of which cancers?
Answer: Intetumumab has been tested in clinical trials for treatment of prostate cancer, melanoma and angiosarcoma.
Question: List viral vectors used in gene therapy.
Answer: adeno-associated viruses
lentiviruses
herpes simplex viral vector
Question: Which are the consequences of the hyperphosphorylated tau in Alzheimers' Disease?
Answer: The consequences of the hyperphosphorylated tau in Alzheimers' Disease is:
1) The formation of neurofibrillary tangles (NFTs)
2) Impaired glutamate metabolism
3) Decreased tau affinity for microtubules binding
4) Dendritic and axonal instability
5) Synaptic degeneration
6) Neuronal loss.
Question: List places in the body where somatostatin is produced.
Answer: Somatostatin is a cyclic peptide well known for its strong regulatory effects throughout the body. Also known by the name of growth hormone inhibiting hormone, it is produced in many locations, which include the olfactory bulb, hair follicles, pancreas, retina, and central nervous system (CNS).
Question: List Parkin binding partners
Answer: HSP90
CDC37
GRP75
HSP60
LRPPRC
TUFM
PICK1
PSMA7
Pael receptor
Question: Which NGS alignment software implement the Burrows-Wheeler Transform?
Answer: The most widely used software belong to the family of the Burrows-Wheeler Aligner (BWA) and its variants for local alignment BWASW, map reduce BWASW-PMR and multi-threaded implementation BWA-MT. Other approaches include Bowtie, SOAP2, BWBBLE, SOAP2 and FANSe2.
Question: Which two cotransporters are inhibited by sotagliflozin?
Answer: Sotagliflozin works by inhibiting sodium-glucose cotransporter 1 (SGLT1) and sodium-glucose cotransporter 2 (SGLT2). It is used for treatment of diabetes.
Question: What is the inheritance of hypophosphatemic rickets?
Answer: Hypophosphatemic rickets are transmitted with:
1) autosomal recessive
2) autosomal dominant
3) X-linked recessive and
4) X-linked dominant inheritance.
Question: What are the main benefits of pharmacophore models?
Answer: As researchers continue to search for new targets of therapeutic interest, transmembrane and G-protein coupled receptors are of ever-increasing importance. However, crystal structures for these targets may be impossible to resolve, posing great challenges in rational drug design. Structure-based virtual screening is not an option when the active site geometry is unknown, but assaying an entire library for hits is an inefficient and expensive proposition.
Pharmacophore modeling solves this problem by determining the spatial arrangement of chemical features that confer drug activity toward a target receptor. Having established the chemical space occupied by active ligands, pharmacophore modeling software allows researchers to create 3-D structure-activity relationships, screen databases, and generate hits without the benefit of a receptor structure.
Question: Which genes are implicated in short QT syndrome?
Answer: The genes that are implicated in short QT syndrome are KCNJ2, KCNH2, CACNA2D1 and KCNQ1.
Question: Which eukaryote genomes contain operons?
Answer: Genes in nematode and ascidian genomes frequently occur in operons such genes comprise 15-20% of the coding genome for Caenorhabditis elegans and Ciona intestinalis We find that birth-death models of operon evolution reasonably describe the relative abundance of operons of different sizes in the C. elegans and Ciona genomes and generate predictions about the number of monocistronic, nonoperon genes that likely participate in the birth-death process
Question: Which eukaryote genomes contain operons?
Answer: The eukaryote genomes contain operons, which can be classified into boader families based, particularly, on the presence of other types of genes. Operons have been found to be present in the following genomes: caenorhabditis elegans, ciona, c. elegans, trichinella spiralis, trichuris muris and ciona intestinalis. Operons have also been reported to exist in the non-coding regions of the human and plant genomes.
Question: Which eukaryote genomes contain operons?
Answer: Genes in nematode and ascidian genomes frequently occur in operons. Such genes comprise 15-20% of the coding genome for Caenorhabditis elegans and Ciona intestinalis.  The organization of genes into operons, clusters of genes that are co-transcribed to produce polycistronic pre-mRNAs, is a trait found in a wide range of eukaryotic groups, including multiple animal phyla.
Question: Which eukaryote genomes contain operons?
Answer: Operons are widespread in prokaryotes, but are uncommon in eukaryotes, except nematode worms, where approximately 15% of genes reside in over 1100 operons in the model organism Caenorhabditis elegans
Question: Which eukaryote genomes contain operons?
Answer: Operons are widespread in prokaryotes, but are uncommon in eukaryotes, except nematode worms, where approximately 15% of genes reside in over 1100 operons in the model organism Caenorhabditis elegans. Birth-death models of operon evolution reasonably describe the relative abundance of operons of different sizes in the C. elegans and Ciona genomes
Question: Which are the predominant rotavirus genotypes around the world?
Answer: The predominant RV genotypes circulating all over the world are G1P[8], G2P[4], G3P[8], G4P[8], and G9P[8], while G12[P6] and G12[P8] are emerging genotypes.
Question: Name the factors required for selenoprotein synthesis in eukaryotes
Answer: eFSec, SBP2, SECp43, PSTK, Sec synthase (Sec S, SLA/LP), SPS2 (SelD), tRNASec, SECIS element, (L30), SPS1
Question: Which are the main methods for pharmacophore modelling?
Answer: A pharmacophore describes the arrangement of molecular features a ligand must contain to efficaciously bind a receptor. Pharmacophore models are developed to improve molecular understanding of ligand–protein interactions, and can be used as a tool to identify novel compounds that fulfil the pharmacophore requirements and have a high probability of being biologically active. Protein structure-based pharmacophores (SBPs) derive these molecular features by conversion of protein properties to reciprocal ligand space. Unlike ligand-based pharmacophore models, which require templates of ligands in their bioactive conformation, SBPs do not depend on ligand information.
Question: List the off-label use of SSRIs
Answer: depression during childhood and adolescence
Premature ejaculation (PE)
erectile dysfunction
Insomnia
postprostatectomy established stress urinary incontinence.
mood and anxiety disorders during pregnancy and breast feeding
symptoms of vasomotor dysregulation (hot flashes) associated with the menopausal transition and sex hormone deprivation
..off-label uses include the treatment of bulimia, benzodiazepine/alcohol dependence, fibromyalgia, central nervous system degenerative diseases (behavioral disorders in dementia and other organic disorders), schizophrenia, chronic pain disease and diabetic neuropathy, sexual dysfunction.
Question: What are the advantages of the top down mass spectrometric analysis of histones?
Answer: Top down mass spectrometry is a way to analyze intact proteins thus enabling: isoform characteriztion and analysis of post-translational modifications.
Question: List clinical features of EEM syndrome.
Answer: EEM syndrome is characterized by ectodermal dysplasia, ectrodactyly and macular dystrophy.
Question: Which mitochondrial genes are regulated by thyroid hormone?
Answer: subunit 6 of ATP synthase, ATPase-6, mitochondrial II and III subunits of cytochrome-c oxidase, NADH dehydrogenase subunit 3
Question: List available tools for genomic visualisation in comparative genomics
Answer: Insyght, Genomicus and Sockeye.
Question: Which components of the stress granules are known to be related to motor neuron degeneration in Amyotrophic Lateral Sclerosis?
Answer: Of note, both ALS and FTD are characterized by pathological inclusions, where some well-known SG markers localize with the ALS related proteins TDP-43 and FUS.
Question: Which components of the stress granules are known to be related to motor neuron degeneration in Amyotrophic Lateral Sclerosis?
Answer: TDP-43 and FUS have been identified as key proteins in the pathogenesis of some cases of ALS. Although their role in motor neuron degeneration is not yet known, TDP-43 and FUS have been shown to accumulate in RNA stress granules (SGs) in cell models and in spinal cord tissue from Amyotrophic Lateral Sclerosis (ALS) patients.
Question: Which proteins in the cerebro-spinal fluid can be used for early diagnosis of Alzheimer's disease?
Answer: CSF is a clear fluid that bathes and cushions the brain and spinal cord. Adults have about 1 pint of CSF, which physicians can sample through a minimally invasive procedure called a lumbar puncture, or spinal tap. Research suggests that Alzheimer's disease in its earliest stages may cause changes in CSF levels of tau and beta-amyloid, two proteins that form abnormal brain deposits strongly linked to the disease.
Question: Which drugs may interfere thyroxine absorption?
Answer: bile acid sequestrants, ferrous sulphate, sucralfate, calcium carbonate, aluminium-containing antacids, phosphate binders, raloxifene and proton-pump inhibitors, have also been shown to interfere with the absorption of levothyroxine
sevelamer hydrochloride or chromium picolinate should be advised to separate the time of ingestion of these drugs from their thyroid hormone preparation by several hours
Question: Which bacteria are enriched in the gut microbiome of infants following exposure to fury pets?
Answer: Pre- and postnatal pet exposure enriched the abundance of Oscillospira and/or Ruminococcus in infants.
Question: Which protein complexes contain mitofilin?
Answer: mitochondrial inter-membrane space bridging (MIB) complex 
mitochondrial inner membrane organizing system (MINOS)
MitOS for mitochondrial organizing structure
Question: Which are the human glutamate transporters?
Answer: Glutamate/aspartate transporter (GLAST) and glutamate transporter-1 (GLT-1) are the most abundant subtypes and are essential for the functioning of the mammalian CNS, but the contribution of the EAAC1 subtype in the clearance of synaptic glutamate has remained controversial, because the density of this transporter in different tissues has not been determined. Using immunofluorescence and postembedding immunogold labeling, we investigated the distributions of the glutamate-aspartate transporter (GLAST or excitatory amino acid transporter 1), vesicular glutamate transporter (VGLUT1), and the AMPA receptor glutamate receptor 4 (GluR4) along the spiral.
Question: Which are the human glutamate transporters?
Answer: To date, five distinct mammalian glutamate transporters have been cloned. The extracellular levels of excitatory amino acids are kept low by the action of the glutamate transporters. Glutamate/aspartate transporter (GLAST) and glutamate transporter-1 (GLT-1) are the most abundant subtypes and are essential for the functioning of the mammalian CNS, but the contribution of the EAAC1 subtype in the clearance of synaptic glutamate has remained controversial, because the density of this transporter in different tissues has not been determined. Expression of short interfering RNA-mediated knockdown of RTN2B decreases the EAAC1 protein level in neurons.
Question: Which driver mutations have been identified for Diffuse Intrinsic Pontine Glioma (DIPG)?
Answer: We found conservation of heterozygous K27M mutations in H3F3A (n = 4) or HIST1H3B (n = 3) across all primary, contiguous, and metastatic tumor sites in all DIPGs
Question: Which driver mutations have been identified for Diffuse Intrinsic Pontine Glioma (DIPG)?
Answer: found conservation of heterozygous k27m mutations in h3f3a (n = 4) or hist1h3b (n = 3) across all primary , contiguous , and metastatic tumor sites in all dipgs . h3k27m ubiquitously-associated mutations involve alterations in tp53 cell-cycle (tp53/ppm1d) or specific growth factor pathways (acvr1/pik3r1) . reconstruction indicates histone 3 (h3) k27m--including h3.2k27m--mutations potentially arise first and are invariably associated with specific , high-fidelity obligate partners throughout the tumour and its spread , from diagnosis to end-stage disease , suggesting mutual need for tumorigenesis. . aberrations (n = 3 patients) varied by type and location between primary and metastatic tumors sites but were intra-tumorally conserved. .
Question: Which driver mutations have been identified for Diffuse Intrinsic Pontine Glioma (DIPG)?
Answer: We found conservation of heterozygous K27M mutations in H3F3A (nâ=â4) or HIST1H3B (nâ=â3) across all primary, contiguous, and metastatic tumor sites in all DIPGs. Evolutionary reconstruction indicates histone 3 (H3) K27M--including H3.2K27M--mutations potentially arise first and are invariably associated with specific, high-fidelity obligate partners throughout the tumour and its spread, from diagnosis to end-stage disease, suggesting mutual need for tumorigenesis. These H3K27M ubiquitously-associated mutations involve alterations in TP53 cell-cycle (TP53/PPM1D) or specific growth factor pathways (ACVR1/PIK3R1).
Question: Which driver mutations have been identified for Diffuse Intrinsic Pontine Glioma (DIPG)?
Answer: We found conservation of heterozygous K27M mutations in H3F3A (n=4) or HIST1H3B (n=3) across all primary, contiguous, and metastatic tumor sites in all DIPGs. ACVR1 (n=2), PIK3CA (n=2), FGFR1 (n=2), and MET (n=1) were also intra-tumorally conserved. TP53 aberrations (n=3 patients) varied by type and location between primary and metastatic tumors sites but were intra-tumorally conserved. Evolutionary reconstruction indicates histone 3 (H3) K27M--including H3.2K27M--mutations potentially arise first and are invariably associated with specific, high-fidelity obligate partners throughout the tumour and its spread, from diagnosis to end-stage disease, suggesting mutual need for tumorigenesis. These H3K27M ubiquitously-associated mutations involve alterations in TP53 cell-cycle (TP53/PPM1D) or specific growth factor pathways (ACVR1/PIK3R1).
Question: Which driver mutations have been identified for Diffuse Intrinsic Pontine Glioma (DIPG)?
Answer: Recurrent mutations within the histone H3 genes H3F3A and HIST1H3B that convert K27 to methionine (H3K27M) and disrupt the global H3K27 methylation landscape and PRC2-dependent silencing, have recently been identified in pediatric high-grade gliomas including Diffuse Intrinsic Pontine Glioma (DIPG) and Glioblastoma multiforme (GBM; Type IV glioma). The spatial and temporal homogeneity of main driver mutations in DIPG implies they will be captured by limited biopsies and emphasizes the need to develop therapies specifically targeting obligate oncohistone partnerships. TP53 aberrations (n = 3 patients) varied by type and location between primary and metastatic tumors sites but were intra-tumorally conserved.Spatial conservation of prognostically-relevant and therapeutically-targetable somatic mutations in DIPG and mHGG contrasts the significant heterogeneity of driver mutations seen in adult HGG and supports uniform implementation of diagnostic biopsy in DIPG and mHGG to classify molecular risk groups and guide therapeutic strategy. Recently, a subset of these same mutations of ACVR1 have been identified in diffuse intrinsic pontine glioma (DIPG) tumors. Sequencing analysis showed c.83A>T mutations in the H3F3A or HIST1H3B gene in 77 % of our DIPG cohort. Protein profiling identified 2,305 unique proteins indicating distinct DIPG protein expression patterns compared to other pediatric brain tumors. Two distinct subgroups of DIPG were identified.
Question: Which driver mutations have been identified for Diffuse Intrinsic Pontine Glioma (DIPG)?
Answer: We found conservation of heterozygous K27M mutations in H3F3A (n = 4) or HIST1H3B (n = 3) across all primary, contiguous, and metastatic tumor sites in all DIPGs ACVR1 (n = 2), PIK3CA (n = 2), FGFR1 (n = 2), and MET (n = 1) were also intra-tumorally conserved  TP53 aberrations (n = 3 patients) varied by type and location between primary and metastatic tumors sites but were intra-tumorally conserved.
Question: Which driver mutations have been identified for Diffuse Intrinsic Pontine Glioma (DIPG)?
Answer: Evolutionary reconstruction indicates histone 3 (H3) K27M--including H3.2K27M--mutations potentially arise first and are invariably associated with specific, high-fidelity obligate partners throughout the tumour and its spread, from diagnosis to end-stage disease, suggesting mutual need for tumorigenesis. Conservation of heterozygous K27M mutations in H3F3A (n = 4) or HIST1H3B (n = 3) was observed across all primary, contiguous, and metastatic tumor sites in all DIPGs. ACVR1 (n = 2), PIK3CA (n = 2), FGFR1 (n = 2), and MET (n = 1) were also intra-tumorally conserved.  TP53 aberrations (n = 3 patients) varied by type and location between primary and metastatic tumors sites but were intra-tumorally conserved.
Question: Which driver mutations have been identified for Diffuse Intrinsic Pontine Glioma (DIPG)?
Answer: We found conservation of heterozygous K27M mutations in H3F3A (n = 4) or HIST1H3B (n = 3) across all primary, contiguous, and metastatic tumor sites in all DIPGs  TP53 aberrations (n = 3 patients) varied by type and location between primary and metastatic tumors sites but were intra-tumorally conserved. These H3K27M ubiquitously-associated mutations involve alterations in TP53 cell-cycle (TP53/PPM1D) or specific growth factor pathways (ACVR1/PIK3R1).
Question: Which driver mutations have been identified for Diffuse Intrinsic Pontine Glioma (DIPG)?
Answer: We found conservation of heterozygous K27M mutations in H3F3A (n=4) or HIST1H3B (n=3) across all primary, contiguous, and metastatic tumor sites in all DIPGs. Evolutionary reconstruction indicates histone 3 (H3) K27M--including H3.2K27M--mutations potentially arise first and are invariably associated with specific, high-fidelity obligate partners throughout the tumour and its spread, from diagnosis to end-stage disease, suggesting mutual need for tumorigenesis. These H3K27M ubiquitously-associated mutations involve alterations in TP53 cell-cycle (TP53/PPM1D) or specific growth factor pathways (ACVR1/PIK3R1). TP53 aberrations (n=3 patients) varied by type and location between primary and metastatic tumors sites but were intra-tumorally conserved. ACVR1 (n=2), PIK3CA (n=2), FGFR1 (n=2), and MET (n=1) were also intra-tumorally conserved.
Question: Which driver mutations have been identified for Diffuse Intrinsic Pontine Glioma (DIPG)?
Answer: We found conservation of heterozygous K27M mutations in H3F3A (n = 4) or HIST1H3B (n = 3) across all primary, contiguous, and metastatic tumor sites in all DIPGs These H3K27M ubiquitously-associated mutations involve alterations in TP53 cell-cycle (TP53/PPM1D) or specific growth factor pathways (ACVR1/PIK3R1).
Question: Which proteins participate in the formation of the ryanodine receptor quaternary macromolecular complex?
Answer: Junctin is a major transmembrane protein in cardiac junctional sarcoplasmic reticulum, which forms a quaternary complex with the ryanodine receptor (Ca(2+) release channel), triadin, and calsequestrin.