anand-s/m_qalm huggingface dataset:
Question: What are the symptoms of Rotor syndrome?
Answer: Rotor syndrome is characterized by conjugated hyperbilirubinemia, coproporphyrinuria, and near-absent hepatic uptake of anionic diagnostics.
Question: What are the targets of pemigatinib?
Answer: Pemigatinib is a small molecule inhibitor of fibroblast growth factor receptor (FGFR) 1, FGFR2 and FGFR3, received accelerated approval  for the treatment of adults with previously treated, unresectable, locally advanced or metastatic cholangiocarcinoma and a FGFR2 fusion or other rearrangement, as detected by a US FDA-approved test.
Question: What kind of bonds are connecting keratin molecules?
Answer: cystine disulfide bonds
amide bonds
hydrogen bonds
Question: Which R packages have been developed for the discovery of mutational signatures in cancer?
Answer: signeR: an empirical Bayesian approach to mutational signature discovery. Mutational signatures can be used to understand cancer origins and provide a unique opportunity to group tumor types that share the same origins and result from similar processes. These signatures have been identified from high throughput sequencing data generated from cancer genomes by using non-negative matrix factorisation (NMF) techniques. The extraction of mutational signatures from high-throughput data still remains a daunting task.RESULTS: Here we present a new method for the statistical estimation of mutational signatures based on an empirical Bayesian treatment of the NMF model.
Question: Which R packages have been developed for the discovery of mutational signatures in cancer?
Answer: SomaticSignatures: inferring mutational signatures from single-nucleotide variants.Mutational signatures are patterns in the occurrence of somatic single-nucleotide variants that can reflect underlying mutational processes.The SomaticSignatures package provides flexible, interoperable and easy-to-use tools that identify such signatures in cancer sequencing data.It facilitates large-scale, cross-dataset estimation of mutational signatures, implements existing methods for pattern decomposition, supports extension through user-defined approaches and integrates with existing Bioconductor workflows.AVAILABILITY AND IMPLEMENTATION: The R package SomaticSignatures is available as part of the Bioconductor project.Its documentation provides additional details on the methods and demonstrates applications to biological datasets.These mutagenic processes often produce characteristic mutational patterns called mutational signatures.The decomposition of a cancer genome's mutation catalog into mutations consistent with such signatures can provide valuable information about cancer etiology.Hence, one needs to be able to not only decompose a patient's mutational profile into signatures but also establish the accuracy of such decomposition.Results: We proposed two complementary ways of measuring confidence and stability of decomposition results and applied them to analyze mutational signatures in breast cancer genomes.
Question: Which R packages have been developed for the discovery of mutational signatures in cancer?
Answer: signeR is an R package for a new method for the statistical estimation of mutational signatures based on an empirical Bayesian treatment of the NMF model.
Question: Which R packages have been developed for the discovery of mutational signatures in cancer?
Answer: signeR: an empirical Bayesian approach to mutational signature discovery. Mutational signatures can be used to understand cancer origins and provide a unique opportunity to group tumor types that share the same origins and result from similar processes. These signatures have been identified from high throughput sequencing data generated from cancer genomes by using non-negative matrix factorisation (NMF) techniques.
Question: Which R packages have been developed for the discovery of mutational signatures in cancer?
Answer: signeR: an empirical Bayesian approach to mutational signature discovery. The extraction of mutational signatures from high-throughput data still remains a daunting task.RESULTS: Here we present a new method for the statistical estimation of mutational signatures based on an empirical Bayesian treatment of the NMF model. Results on real data agree well with current knowledge.AVAILABILITY AND IMPLEMENTATION: signeR is implemented in R and C ++, and is available as a R package at http://bioconductor.org/packages/signeR
Question: Which R packages have been developed for the discovery of mutational signatures in cancer?
Answer: signeR: an empirical Bayesian approach to mutational signature discovery.
Question: Which R packages have been developed for the discovery of mutational signatures in cancer?
Answer: It facilitates large-scale, cross-dataset estimation of mutational signatures, implements existing methods for pattern decomposition, supports extension through user-defined approaches and integrates with existing Bioconductor workflows.AVAILABILITY AND IMPLEMENTATION: The R package SomaticSignatures is available as part of the Bioconductor project.
Question: Which R packages have been developed for the discovery of mutational signatures in cancer?
Answer: Cancers arise as the result of somatically acquired changes in the DNA of cancer cells. However, in addition to the mutations that confer a growth advantage, cancer genomes accumulate a large number of somatic mutations resulting from normal DNA damage and repair processes as well as carcinogenic exposures or cancer related aberrations of DNA maintenance machinery. These mutagenic processes often produce characteristic mutational patterns called mutational signatures. The decomposition of a cancer genome's mutation catalog into mutations consistent with such signatures can provide valuable information about cancer etiology. SigneR, SignatureEstimation, pmsignature and SomaticSignatures are R packages that have been developed for the discovery of mutational signatures in cancer.
Question: Which proteins act as factors that promote transcription-coupled repair in bacteria?
Answer: Transcription coupled nucleotide excision repair (TC-NER or TCR) is a cellular process by which UV-induced damage and other road-blocks encountered in the transcribed strand are restored. Bacterial transcription-coupled repair is initiated when RNA polymerase stalled at a DNA lesion is removed by Mfd (Mutation frequency decline), an ATP-dependent DNA translocase. Mfd is the major transcription repair coupling factor in bacteria. Also, the transcription elongation factor NusA, in addition to its role in recruiting translesion synthesis (TLS) DNA polymerases to gaps encountered during transcription,  promotes an alternative class of TCR involved in the identification and removal of a class of lesion, such as the N(2)-f-dG lesion.
Question: Where is X-ray free electron laser used?
Answer: X-ray free electron laser (XFEL) technologies provide coherent and extremely intense photon pulses of short duration. XFELs are particularly useful in structural biology and imaging, in structural studies of single biological macromolecules (e.g. high resolution protein structure determination) and assemblies (e.g. viruses) or nanocrystals, which are not amenable to investigation with traditional crystallographic methods. Moreover, XFELs have the potential to be used for studying enzyme kinetics.
Question: What are the results of loss of the protein Lon1 in the plant Arabidopsis?
Answer: Loss of Lon1 in Arabidopsis changes the mitochondrial proteome leading to altered metabolite profiles and growth retardation. Additionaly, seedling establishment is also impaired.
Question: For the constructions of which organs has 3D printing been tested?
Answer: Nose, ear and meniscus prototypes/constructs have been produced with 3D (3-dimesional) printing.
Question: Which genes were found to be methylated in bladder cancer cells?
Answer: In bladder cancer, hepaCAM (hepatocyte cell adhesion molecule), RARβ(2), APC, TPEF (transmembrane protein containing epidermal growth factor and follistatin domain), RASSF1A, p14(ARF) and p16 genes were found to be methylated. These methylation events were demostrated to associate with downregulation of gene expression.
Question: Mutations in which gene and which protein are associated with Netherton syndrome?
Answer: NS is due to loss-of-function mutations in the SPINK5 gene and to the consequent lack of expression of its encoded protein LEKTI in the skin and all stratified epithelial tissues.
Question: List some ways to reverse Tau hyperphosphorylation in Tauopathies?
Answer: Different ways have been used to try to reverse Tau hyperphosphorylation through administration of inhibitors such as: 7-nitroindazole,  memantine, glycogen synthase kinase-3 inhibitors. 
Other approaches are transplantation of Human umbilical cord blood-derived mesenchymal stem cells and administration of M1 muscarinic agonists.
Question: What tissues have been studied by circadian proteomics?
Answer: Retina
Liver
Question: Which are the clinical characteristics of Tuberous Sclerosis?
Answer: The clinical characteristics of Tuberous Sclerosis include epilepsy, subependymal giant cell astrocytomas, lymphangioleiomyomatosis, rhabdomyoma, renal angiomyolipomas, cortical tubers, neurofibromas, angiofibromas, mental retardation, and behavioral disorders.
Question: Which are the mammalian orthologs of Drosophila Yki?
Answer: There are two mammalian orthologs of Yki: YAP and TAZ
Question: In which proteins is the chromodomain present?
Answer: The chromodomain (chromatin organizer modifier domain) is a highly conserved motif, 40-50 amino acids in length, present in a wide range of animal and plant proteins involved in chromatin organization. Chromodomain-containing proteins can be classified into boader families based, particularly, on the presence of other types of domains. Chromodomain is present in: the heterochromatin proteins HP1 alpha and HP1 beta, chromointgrases (e.g. Tf1 integrase) the chromodomain helicase DNA-binding proteins (CHD) and CHD 1-like (CHD1L), CReMM (chromatin-related mesenchymal modulator), dna methyltransferase 3 (cmt3), the chromointegrase of the LTR-retrotransposons, the Polycomb group (PcG) proteins, the mouse Polycomb homologs (Cbx2, Cbx4, Cbx6, Cbx7, Cbx8), the chromodomain Y chromosome (CDY) family of proteins and the CDY-like protein (CDYL), the histone acetyltransferases TgMYST-A and –B, MRG-1 and -15 (MORF4-Related Gene on chromosome 15), ADP/ATP translocase 1, MPP8, MSL3, NlMof, Chp1, Chriz, dMi-2, Corto, cpSRP43, KISMET, PICKLE (PKL), ScoHET1 and ScoHET2.
Question: List inhibtors targeting the mitochondrial permeability transition pore.
Answer: Cyclosporine A
Atractyloside
N-metyl-4-isoleucine-cyclosporine
Sanglifehrin A 
TRO-19622
Question: List inhibtors targeting the mitochondrial permeability transition pore.
Answer: The opening of the mitochondrial permeability transition pore appears to be inhibited by KB-R 7943, diacylglycerol analog 1-oleoyl-2-acetyl-sn-glycerol, cyclosporin A (CsA) and BRL37344.
Question: What are the two types of duplicated genes in the yeast S. cerevisiae?
Answer: Yeast genes are duplicated both via the whole genome duplication and via smaller scale duplications. The genome of the budding yeast contains 50% of protein-coding genes that are paralogs, including 457 pairs of duplicated genes coming probably from an ancient whole genome duplication.
Question: What are the two types of duplicated genes in the yeast S. cerevisiae?
Answer: The mechanism of duplication matters, with whole-genome duplicates being more transcriptionally altered than small-scale duplicates.
Question: Which drugs were tested in the candor trial?
Answer: CANDOR trial investigated carfilzomib, dexamethasone, and daratumumab for patients with relapsed or refractory multiple myeloma.
Question: List kinases that phosphorylates the protein Bora.
Answer: During cell division Bora becomes multiply phosphorylated by a variety of cell cycle kinases, including Aurora A and Plk1, and GSK3β and Cdk1 albeit at distinctive sites.
Question: List all the available databases of super enhancers
Answer: dbSUPER and SEA are the available databases of super enhancers.
Question: List all the available databases of super enhancers
Answer: dbSUPER and SEA are the most well-known and widely used Super-Enhancer Databases.
Question: What are the most common side effects of amantadine ER?
Answer: The most common side effects of amantadine ER are hallucination, dizziness, orthostatic hypotension and pedal edema.
Question: Which malignancies is Keytruda approved for before 2017?
Answer: Before 2017 Keytruda was approved for the treatment of several types of malignancies, such as metastatic melanoma, metastatic non-small-cell lung cancer, recurrent or metastatic head and neck cancer, refractory Hodgkin lymphoma, and urothelial carcinoma.
Question: Which are the different homologs or family members of the hedgehog proteins in mammals?
Answer: Hedgehog (Hh) signaling proteins stimulate cell proliferation, differentiation, and tissue patterning at multiple points in animal development. A single Hh homolog is present in Drosophila, but three Hh homologs, Sonic hedgehog (Shh), Indian hedgehog (Ihh) , and Desert hedgehog (Dhh), are present in mammals.
Question: Which cellular functions are affected by lncRNA H19 in the heart?
Answer: H19 could inhibit autophagy in cardiomyocytes by epigenetically silencing of DIRAS3. Elevated H19 promotes apoptosis through PA2G4. Downregulation of H19 promotes proliferation and inhibits apoptosis. H19 induces mineralization of valve interstitial cells. H19 contributes to cardiac fibroblast proliferation and fibrosis, which act in part through repression of DUSP5/ERK1/2.
Question: Which currently known mitochondrial diseases have been attributed to POLG mutations?
Answer: Mutations in the POLG gene have emerged as one of the most common causes of inherited mitochondrial disease in children and adults. They are responsible for a heterogeneous group of at least 6 major phenotypes of neurodegenerative disease that include: 1) childhood Myocerebrohepatopathy Spectrum disorders (MCHS), 2) Alpers syndrome, 3) Ataxia Neuropathy Spectrum (ANS) disorders, 4) Myoclonus Epilepsy Myopathy Sensory Ataxia (MEMSA), 5) autosomal recessive Progressive External Ophthalmoplegia (arPEO), and 6) autosomal dominant Progressive External Ophthalmoplegia (adPEO).
Question: Which currently known mitochondrial diseases have been attributed to POLG mutations?
Answer: Mutations in the POLG gene have emerged as one of the most common causes of inherited mitochondrial disease in children and adults. They are responsible for a heterogeneous group of at least 6 major phenotypes of neurodegenerative disease that include: 1) childhood Myocerebrohepatopathy Spectrum disorders (MCHS), 2) Alpers syndrome, 3) Ataxia Neuropathy Spectrum (ANS) disorders, 4) Myoclonus Epilepsy Myopathy Sensory Ataxia (MEMSA), 5) autosomal recessive Progressive External Ophthalmoplegia (arPEO), and 6) autosomal dominant Progressive External Ophthalmoplegia (adPEO)
Question: Which are the different isoforms of the mammalian Notch receptor?
Answer: Notch signaling is an evolutionarily conserved mechanism, used to regulate cell fate decisions. Four Notch receptors have been identified in man: Notch-1, Notch-2, Notch-3 and Notch-4.
Question: Which drugs are included in the FEC-75 regimen?
Answer: Fluorouracil, epirubicin, and cyclophosphamide are included in the FEC-75 regimen. This chemotherapy regiment is used for breast cancer treatment.
Question: List 3 conventional synthetic DMARDs.
Answer: Three conventional synthetic (cs) DMARDs include methotrexate (MTX), leflunomide, and sulfasalazine.
Question: List symptoms of Allgrove syndrome.
Answer: The classical clinical triad of the Allgrove syndrome includes alacrima, achalasia and adrenal insufficiency. It can be also associated with progressive peripheral neuropathy.
Question: Which proteins compose the error prevention GO (8-oxo-G) system in Pseudomonas putida?
Answer: In P. putida (Pseudomonas putida) the error prevention GO (8-oxo-G) system is composed of MutY, MutM, and MutT enzymes.
Question: Which are the bioinformatics tools for gene structure prediction?

Answer: The in silico prediction of the complete structure of genes is one of the main challenges of bioinformatics. A critical part in the gene structure prediction is to identify the boundaries between exons and introns (i.e. splice sites) in the coding region. Several advanced bioinformatics tools have been developed for the precise delineation of a given gene structure: WPSS, SCGPred, TICO, GLIMMER, MetWAMer, WebScipio, GeneSeqer,  SplicePredictor, DGSplicer, Transcript Assembly Program (TAP), GeneBuilder, SeqHelp, HSPL, RNASPL, HEXON, CDSB, HBR, FGENE and FGENEH for human genes.
Question: Which are the bioinformatics tools for gene structure prediction?

Answer: SCGPred: a score-based method for gene structure prediction by combining multiple sources of evidence. MetWAMer.gthXML is a special-purpose variant of the software, specifically tailored to refine gene structure predictions generated by the GenomeThreader [30] and GeneSeqer [31] programs for spliced alignment-based gene structure annotation. WebScipio: an online tool for the determination of gene structures using protein sequences.
Question: Which proteins form the nuclear pore basket in human cells?
Answer: Nup133 Is Required for Proper Nuclear Pore Basket Assembly and Dynamics in Embryonic Stem Cells. Moreover, the association of TREX-2 with the NPC requires the basket nucleoporins NUP153 and TPR, but is independent of transcription. The nucleoporin Nup153 is required for nuclear pore basket formation, nuclear pore complex anchoring and import of a subset of nuclear proteins
Question: Which proteins form the nuclear pore basket in human cells?
Answer: Nup133 Is Required for Proper Nuclear Pore Basket Assembly and Dynamics in Embryonic Stem Cells. Here we show that the NPC basket proteins Nup1 and Nup60 directly induce membrane curvature by amphipathic helix insertion into the lipid bilayer Moreover, the association of TREX-2 with the NPC requires the basket nucleoporins NUP153 and TPR, but is independent of transcription.
Question: Which proteins form the nuclear pore basket in human cells?
Answer: Nup133 Is Required for Proper Nuclear Pore Basket Assembly and Dynamics in Embryonic Stem Cells. The nuclear pore complex basket proteins Nup1 and Nup60 directly induce membrane curvature by amphipathic helix insertion into the lipid bilayer. The nucleoporin Nup153 is required for nuclear pore basket formation, nuclear pore complex anchoring and import of a subset of nuclear proteins.
Question: Which proteins form the nuclear pore basket in human cells?
Answer: Nup133 Is Required for Proper Nuclear Pore Basket Assembly and Dynamics in Embryonic Stem Cells. Here we show that the NPC basket proteins Nup1 and Nup60 directly induce membrane curvature by amphipathic helix insertion into the lipid bilayer The nucleoporin Nup153 is required for nuclear pore basket formation, nuclear pore complex anchoring and import of a subset of nuclear proteins
Question: List bacteria that may be useful in uranium bioremediation.
Answer: The main bacteria studied in uranium bioremediation are Geobacteraceae. Other bacteria are: 
Firmicutes, 
Shewanella oneidensis
Pseudomonas aeruginosa
Anaeromyxobacter dehalogenans  
strain Rf4T
Question: What personality traits can be evaluated with the Ten Item Personality Inventory.
Answer: The Ten Item Personality Inventory measures each of the five major facets of personality: openness, extroversion, conscientiousness, agreeableness and neuroticism.
Question: Which drugs were tested in the CheckMate 227 clinical trial?
Answer: CheckMate-227 clinical trial tested ipilimumab plus nivolumab for the treatment of non-small cell lung cancer.
Question: For which diseases members of the 2-aminobenzamide class of histone deacetylase (HDAC) inhibitors show promise as therapeutics?
Answer: Members of the 2-aminobenzamide class of histone deacetylase (HDAC) inhibitors show promise as therapeutics for the neurodegenerative diseases Friedreich's ataxia (FRDA) and Huntington's disease (HD).
Question: For which diseases members of the 2-aminobenzamide class of histone deacetylase (HDAC) inhibitors show promise as therapeutics?
Answer: Members of the 2-aminobenzamide class of histone deacetylase (HDAC) inhibitors show promise as therapeutics for the neurodegenerative diseases Friedreich's ataxia (FRDA) and Huntington's disease (HD)
Question: Which drugs are included in the VAC regiment for Ewing's sarcoma?
Answer: VAC regiment for Ewing's sarcoma includes vincristine, actinomycin, cyclophosphamide.
Question: List adenosine A2A receptor antagonists that are used for Parkinson's disease treatment.
Answer: Istradefylline and preladenant are adenosine A2A receptor antagonists that are used for Parkinson's disease treatment.
Question: Which drugs are utilized to treat eosinophilic esophagitis?
Answer: Therapeutic options of eosinophilic esophagitis include use of proton-pump inhibitors, immunosuppressive drugs, elimination diets, and esophageal dilatation.
Oral viscous budesonide (OVB) is an effective treatment of pan-esophageal disease in children with EoE. OVB improves symptoms and endoscopic and histologic features.
Question: Name siRNA drugs that have entered phase 2-3 clinical trials (by 2019).
Answer: siRNAs that have entered phase 2-3 clinical trials by 2019 include PF-04523655, TKM-080301, Atu027, SYL040012, SYL1001, siG12D-LODER (phase 2), QPI-1002, QPI-1007, and patisiran (phase 3).
Question: Which are the subunits of the IkB protein kinase (IKK)?
Answer: Proinflammatory NF-kappaB activation requires the IkappaB (inhibitor of NF-kappaB) kinase (IKK) complex that contains two catalytic subunits named IKKalpha and IKKbeta and a regulatory subunit named NF-kappaB essential modulator (NEMO).Additional components may exist, transiently or permanently, but their characterization is still unsure.
Question: Which are the subunits of the IkB protein kinase (IKK)?
Answer: The IKK kinase complex is the core element of the NF-kappaB cascade. It is essentially made of two kinases (IKKalpha and IKKbeta) and a regulatory subunit, NEMO (NF-kB Essential Modulator)/IKKgamma. Additional components may exist, transiently or permanently, but their characterization is still unsure.
Question: Which are the subunits of the IkB protein kinase (IKK)?
Answer:  The IKK protein complex is comprised of IKKα, IKKβ and NEMO subunits, with IKKβ thought to play the dominant role in modulating NF-κB activity.   The IkappaB-Kinase (IKK) complex is a multisubunit protein complex crucial for signal-induced phosphorylation of the IkappaB proteins and thus controls the activity of the transcription factor NF-kappaB. Besides the two kinases IKKalpha and IKKbeta, the IKK complex contains NEMO/IKKgamma, an additional subunit with regulatory and adaptor functions.
Question: List 4 drugs used to treat opioid addiction or overdose
Answer: Suboxone (buprenorphine/naloxone) and  methadone are used to assist in opioid withdrawal and Naloxone is used to treat overdoses
Question: Which post-translational histone modifications are characteristic of constitutive heterochromatin?
Answer: H3K9me3 is the major marker of constitutive heterochromatin. Other histone methylation marks usually found in constitutive heterochromatin, are H4K20me3 and H3K79me3. Classical histone modifications associated with heterochromatin include H3K9me2, H3K27me1 and H3K27me2. Histone H3 trimethylation at lysine 36 is associated with constitutive and facultative heterochromatin. H3S10 phosphorylation marks constitutive heterochromatin during interphase in early mouse embryos until the 4-cell stage
Question: What is the drug chloroquine or hydroxychloroquine used for?
Answer: Chloroquine (CQ) has been used for decades as the primary chemotherapeutic drug for the treatment of malaria.
Hydroxychloroquine (HCQ), a 4-aminoquinolone antimalarial, is regarded as the oral therapy of choice for cutaneous and systemic lupus erythematosus (SLE). It is also licensed for rheumatoid arthritis (RA).
Chloroquine is a potent inhibitor of SARS coronavirus infection and spread.