anand-s/m_qalm huggingface dataset:
Question: Which proteins are the different members of the NF-kappaB family of transcription factors?
Answer: Nuclear factor kappa B (NFκB) is a dimeric transcription factor comprised of five family members RelA (p65), RelB, c-Rel, NF-kB1/p50 and NF-kB2/p52.
Question: Which compounds exist that are thyroid hormone analogs?
Answer: Compoounds such as 3,5-diiodo-L-thyronine, T2, GC-24, CO23, DITPA, 3,5-diiodothyropropionic acid, GC-1, Tetrac, 3,3',5,5'-tetraiodo-thyroacetic acid, KB- 2115, KB - 141, thyronamines, T4-agarose, CGS 23425, D-T3, 3,3',5-triiodo-D-thyronine, 3,5-T2, 3,5-diiodo-L-thyronine, DIT, 3,5-diiodo-L-tyrosine, MIT, 3-monoiodo-L-tyrosine, triac, 3, 3',5-triiodo-thyroacetic acid, 3,5-Diiodo-4-hydroxyphenylpropionic acid, DIHPA, 3,5-Dimethyl-3'-isopropyl-L-thyronine, DIMIT, 3,5-diiodo-3'-isopropylthyroacetic acid and IpTA2 are compounds that are thyroid hormone analogs.
Question: List the four most important interferonopathies
Answer: Aicardi-Goutières syndrome
chilblain lupus
ubiquitin specific peptidase 18 (USP18)-deficiency
Singleton-Merten syndrome
Question: List the four most important interferonopathies
Answer: Inappropriate upregulation of type I IFN signaling and interferon-stimulated gene expression have been linked to several CNS diseases termed "interferonopathies" including Aicardi-Goutieres syndrome, ubiquitin specific peptidase 18 (USP18)-deficiency, haploinsufficiency in A20, otulipenia, familial chiblain lupus.
Question: List proteins that are contained in atherosclerotic plaques?
Answer: extracellular matrix proteins
biglycan
Lumican
Apolipoprotein A-I
Question: List available databases containing information about conserved noncoding elements.
Answer: Ancora and TFCONES.
Question: Which enzymes are responsible for base J creation in Trypanosoma brucei?
Answer: The base is synthesized in a two-step pathway. Initially, a thymidine residue in DNA is hydroxylated by a thymidine hydroxylase (TH). This intermediate (HOMedU) is then glucosylated to form base J. Two proteins involved in J synthesis, JBP1 (J binding protein 1) and JBP2, contain a putative TH domain related to the family of Fe(2+)/2-oxoglutarate-dependent hydroxylases. JBP2 is a chromatin re-modeling protein that induces de novo J-synthesis, allowing JBP1, a J-DNA binding protein, to stimulate additional J-synthesis. A recent computational screen identified a possible candidate for the base J-associated glucosyltransferase (JGT) in trypanosomatid genomes.
Question: Which enzymes are responsible for base J creation in Trypanosoma brucei?
Answer: JBP2 and JBP1
Question: Which enzymes are responsible for base J creation in Trypanosoma brucei?
Answer: The deletion of both alleles of JGT from the genome of Trypanosoma brucei generates a cell line that completely lacks base J. We conclude that JBP2 and JBP1 are the TH enzymes involved in J biosynthesis. -d-glucopyranosyloxymethyluracil . The base is synthesized in a two-step pathway. Synthesis of the modified thymine base, beta-d-glucosyl-hydroxymethyluracil or J, within telomeric DNA of Trypanosoma brucei correlates with the bloodstream form specific epigenetic silencing of telomeric variant surface glycoprotein genes involved in antigenic variation. Two thymidine hydroxylases differentially regulate the formation of glucosylated DNA at regions flanking polymerase II polycistronic transcription units throughout the genome of Trypanosoma brucei. A recent computational screen identified a possible candidate for the base J-associated glucosyltransferase  in trypanosomatid genomes. This intermediate  is then glucosylated to form base J. Here we discuss the regulation of hmU and base J formation in the trypanosome genome by JGT and base J-binding protein. Chromosome-internal J deposition is primarily mediated by JBP1, whereas JBP2-stimulated J deposition at the telomeric regions. Two proteins involved in J synthesis, JBP1 /2-oxoglutarate-dependent hydroxylases. JBP2 and JBP1 are capable of stimulating de novo J-synthesis.
Question: Which enzymes are responsible for base J creation in Trypanosoma brucei?
Answer: We have previously characterized two thymidine-hydroxylases (TH), JBP1 and JBP2, which regulate J-biosynthesis.JBP2 is a chromatin re-modeling protein that induces de novo J-synthesis, allowing JBP1, a J-DNA binding protein, to stimulate additional J-synthesis.Chromosome-internal J deposition is primarily mediated by JBP1, whereas JBP2-stimulated J deposition at the telomeric regions.Here we show that mutation of key residues in the TH domain of JBP2 ablate its ability to induce de novo J synthesis.JBP1 and JBP2 are two distinct thymidine hydroxylases involved in J biosynthesis in genomic DNA of African trypanosomes.Here we discuss the regulation of hmU and base J formation in the trypanosome genome by JGT and base J-binding protein.The deletion of both alleles of JGT from the genome of Trypanosoma brucei generates a cell line that completely lacks base JWe have recently proposed a model in which chromatin remodeling by a SWI2/SNF2-like protein (JBP2) regulates the developmental and de novo site-specific localization of J synthesis within bloodstream form trypanosome DNA.
Question: List updates for JASPAR 2020
Answer: JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) for TFs across multiple species in six taxonomic groups. In this 8th release of JASPAR, the CORE collection has been expanded with 245 new PFMs (169 for vertebrates, 42 for plants, 17 for nematodes, 10 for insects, and 7 for fungi), and 156 PFMs were updated (125 for vertebrates, 28 for plants and 3 for insects). This collection has a dedicated web form to engage the community in the curation of unvalidated TF-binding profiles.
Question: List updates for JASPAR 2020
Answer: JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) for TFs across multiple species in six taxonomic groups. In this 8th release of JASPAR, the CORE collection has been expanded with 245 new PFMs (169 for vertebrates, 42 for plants, 17 for nematodes, 10 for insects, and 7 for fungi), and 156 PFMs were updated (125 for vertebrates, 28 for plants and 3 for insects). These new profiles represent an 18% expansion compared to the previous release. JASPAR 2020 comes with a novel collection of unvalidated TF-binding profiles for which curators did not find orthogonal supporting evidence in the literature. This collection has a dedicated web form to engage the community in the curation of unvalidated TF-binding profiles. Moreover, a Q&A forum was created to ease the communication between the user community and JASPAR curators. Finally, the genomic tracks, inference tool, and TF-binding profile similarity clusters were updated.
Question: List updates for JASPAR 2020
Answer: JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) for TFs across multiple species in six taxonomic groups. In this 8th release of JASPAR, the CORE collection has been expanded with 245 new PFMs (169 for vertebrates, 42 for plants, 17 for nematodes, 10 for insects, and 7 for fungi), and 156 PFMs were updated (125 for vertebrates, 28 for plants and 3 for insects). These new profiles represent an 18% expansion compared to the previous release. This collection has a dedicated web form to engage the community in the curation of unvalidated TF-binding profiles.
Question: List updates for JASPAR 2020
Answer: JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) for TFs across multiple species in six taxonomic groups. In this 8th release of JASPAR, the CORE collection has been expanded with 245 new PFMs (169 for vertebrates, 42 for plants, 17 for nematodes, 10 for insects, and 7 for fungi), and 156 PFMs were updated (125 for vertebrates, 28 for plants and 3 for insects). These new profiles represent an 18% expansion compared to the previous release.
Question: List updates for JASPAR 2020
Answer: JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) for TFs across multiple species in six taxonomic groups. In this 8th release of JASPAR, the CORE collection has been expanded with 245 new PFMs (169 for vertebrates, 42 for plants, 17 for nematodes, 10 for insects, and 7 for fungi), and 156 PFMs were updated (125 for vertebrates, 28 for plants and 3 for insects). JASPAR 2020 comes with a novel collection of unvalidated TF-binding profiles for which our curators did not find orthogonal supporting evidence in the literature.
Question: Which type of variants can be called by the VarDict algorithm?
Answer: VarDict is a novel and versatile variant caller for both DNA- and RNA-sequencing data. It simultaneously calls SNV, MNV, InDels, complex and structural variants, expanding the detected genetic driver landscape of tumors. It performs local realignments on the fly for more accurate allele frequency estimation.
Question: Which type of variants can be called by the VarDict algorithm?
Answer: VarDict simultaneously calls SNV, MNV, InDels, complex and structural variants, expanding the detected genetic driver landscape of tumors. It performs local realignments on the fly for more accurate allele frequency estimation. VarDict performance scales linearly to sequencing depth, enabling ultra-deep sequencing used to explore tumor evolution or detect tumor DNA circulating in blood.
Question: Which type of variants can be called by the VarDict algorithm?
Answer: VarDict is a novel and versatile variant caller for both DNA- and RNA-sequencing data. It calls SNV, MNV, InDels, complex and structural variants, expanding the detected genetic driver landscape of tumors.
Question: Which type of variants can be called by the VarDict algorithm?
Answer: VarDict simultaneously calls SNV, MNV, InDels, complex and structural variants, expanding the detected genetic driver landscape of tumors.
Question: Please list 2 treatments for a torn rotator cuff
Answer: to compare clinical outcomes between conventional en masse repair and separate double-layer double-row repair for the treatment of delaminated rotator cuff tears.
Question: Please list 2 treatments for a torn rotator cuff
Answer: Surgical repair earlier or later than 3 months after injury may result in similar outcomes and patient satisfaction.
Question: Which diseases are treated with netarsudil?
Answer: In 2 large, randomized, double-masked trials, once-daily dosing of netarsudil 0.02% was found to be effective and well tolerated for the treatment of patients with ocular hypertension and open-angle glaucoma.
Question: Which enzymes are involved in global genome nucleotide excision repair (GG-NER) in bacteria?
Answer: Nucleotide excision repair (NER) is universally used to recognize and remove many types of DNA damage. In eubacteria, the NER system typically consists of UvrA, UvrB, UvrC, the UvrD helicase, DNA polymerase I, and ligase.  Damage recognition during bacterial NER depends upon UvrA, which binds to the damage and loads UvrB onto the DNA. Subsequently, UvrA, UvrB and UvrC form the excinuclease protein UvrABC endonuclease, a multi-enzymatic complex which carries out repair of damaged DNA in sequential manner. In some cases, Cho may be the effective nuclease for NER, rather than UvrC. UvrC nuclease and the short oligonucleotide that contains the DNA lesion are removed from the post-incision complex by UvrD, a superfamily 1A helicase. In gram-positive organisms, PcrA helicase can also displace UvrC and the excised oligonucleotide from a post-incision NER complex.
Question: List all approved indications for Glivec
Answer: CML - blast crisis, in accelerated phase, and in chronic phase after interferon failure or intolerance.  Glivec received orphan drug status from the U.S. Food and Drug Administration (FDA) Office of Orphan Products Development on January 31, 2001, and accelerated approval from the FDA for the above three indications on May 10, 2001.

Gastrointestinal stromal tumor (GIST
Treatment with adjuvant imatinib following surgical resection of localized Kit-positive GIST
 In locally advanced inoperable patients and metastatic patients, Imatinib is the standard treatment.
Question: List all approved indications for Glivec
Answer: Dermatofibrosarcoma protuberans (DFSP) is an uncommon cutaneous neoplasm.
Question: Which two drugs are included in the Harvoni pill?
Answer: Harvoni contains 400 mg sofosbuvir and 90 mg ledipasvir. It used for treatment of hepatitis C virus infection.
Question: List example genes that SWIM tool has identified and which are down-regulated in glioblastoma
Answer: SWIM is a software able to unveil a small pool of genes - called switch genes - critically associated with drastic changes in cell phenotype. Applying SWIM to the expression profiling of glioblastoma stem-like cells and conventional glioma cell lines identifies switch genes related to stem-like phenotype. SWIM identifies 171 switch genes that are all down-regulated in glioblastoma stem-like cells. This list encompasses genes like CAV1, COL5A1, COL6A3, FLNB, HMMR, ITGA3, ITGA5, MET, SDC1, THBS1, and VEGFC, involved in "ECM-receptor interaction" and "focal adhesion" pathways.
Question: List example genes that SWIM tool has identified and which are down-regulated in glioblastoma
Answer: This list encompasses genes like CAV1, COL5A1, COL6A3, FLNB, HMMR, ITGA3, ITGA5, MET, SDC1, THBS1, and VEGFC, involved in "ECM-receptor interaction" and "focal adhesion" pathways.
Question: List example genes that SWIM tool has identified and which are down-regulated in glioblastoma
Answer: SWIM tool has identified and which genes are down-regulated in glioblastoma. These include the genes: itga3, hmmr, sox2, cav1, itga5, thbs1, sdc1, col6a3, col5a1 and sall2.
Question: List example genes that SWIM tool has identified and which are down-regulated in glioblastoma
Answer: SWIM tool has identified and which genes are down-regulated in glioblastoma and which are important for tumorigenesis: met, vegfc, flnb, itga3, hmmr, sox2, cav1, itGA5, thbs1, sdc1, col6a3, col5a1 and sall2.
Question: List example genes that SWIM tool has identified and which are down-regulated in glioblastoma
Answer: SWIM identifies 171 switch genes that are all down-regulated in glioblastoma stem-like cells. This list encompasses genes like CAV1, COL5A1, COL6A3, FLNB, HMMR, ITGA3, ITGA5, MET, SDC1, THBS1, and VEGFC, involved in "ECM-receptor interaction" and "focal adhesion" pathways
Question: Signaling of which pathways is inhibited by Dupilumab?
Answer: Dupilumab, a fully human anti-interleukin-4 receptor α monoclonal antibody, inhibits interleukin-4 and interleukin-13 signalling. It is used for treatment of atopic or allergic diseases.
Question: Which are the clinical characteristics of Diamond-Blackfan anemia?
Answer: Diamond-Blackfan anemia (DBA) is a rare congenital erythroid hypoplastic anemia that usually presents early in infancy and is characterized by red cell aplasia, congenital anomalies, and a predisposition to cancer.
Question: Which molecules are inhibited by anticancer drug Dovitinib?
Answer: Dovitinib (TKI-258/CHIR-258) is a pan receptor tyrosine kinase (RTK) inhibitor that targets VEGFR, FGFR, PDGFR, and KIT. It is being widely tested for treatment of various cancers.
Question: List search engines used in proteomics.
Answer: Mascot
X!Tandem
MS-GF
MS Amanda 
MyriMatch
Comet
Tide
Andromeda
OMSSA
Question: List programs suitable for pharmacophore modelling
Answer: A pharmacophore is an abstract description of molecular features which are necessary for molecular recognition of a ligand by a biological macromolecule. The IUPAC defines a pharmacophore to be "an ensemble of steric and electronic features that is necessary to ensure the optimal supramolecular interactions with a specific biological target and to trigger (or block) its biological response". A pharmacophore model explains how structurally diverse ligands can bind to a common receptor site. Furthermore pharmacophore models can be used to identify through denovo design or virtual screening novel ligands that will bind to the same receptor. Nowadays there are many programs suitable for pharmacophore modelling such as LigandScout, Discovery Studio, Catalyst, PharmaGist, Genetic Algorithm Similarity and Molecular Operating Environment.
Question: What are the 4 types of holoprosencephaly?
Answer: Holoprosencephaly is a rare congenital disorder which results from failure of cleavage or incomplete differentiation of the forebrain structures at various levels or to various degrees . Depending on the degree of involvement, it is classified into 4 types: Alobar, Semilobar, Lobar, and Middle interhemispheric fusion variant .
Question: What are the 4 types of holoprosencephaly?
Answer: Holoprosencephaly is a rare congenital disorder which results from failure of cleavage or incomplete differentiation of the forebrain structures at various levels or to various degrees. Depending on the degree of involvement, it is classified into 4 types: Alobar, Semilobar, Lobar and Middle interhemispheric fusion variant.
Question: What are the 4 types of holoprosencephaly?
Answer: The 4 types of holoprosencephaly is a rare congenital disorder which results from failure of cleavage or incomplete differentiation of the foremost structures at various levels or to varying degrees. Depending on the degree of involvement, it is divided into 4 types: Alobar, Halilobar, Lobar and Middle interhemispheric fusion variant.
Question: What are the 4 types of holoprosencephaly?
Answer: 4 types of holoprosencephaly have been described: lobar, alobar, interhemispheric, sacral, and cerebellar.
Question: What are the 4 types of holoprosencephaly?
Answer: The 4 types of holoprosencephaly is a rare congenital disorder which results from failure of cleavage or incomplete differentiation of the foremost structures at various levels or to varying degrees. Depending on the degree of involvement, it is broken down into 4 types: Alobar, Halilobar, Lobar and Middle interhemispheric fusion variant.
Question: What are the 4 types of holoprosencephaly?
Answer: Four types of holoprosencephaly have been described: lobar, alobar, interhemispheric, and sacral. (PMID: 22990134)
Question: Which histone mutations have been associated with pediatric gliomas?
Answer: About 80% of Diffuse intrinsic pontine glioma (DIPG) cases and 70% of midline glioblastomas contain a mutation at one allele of the H3F3A gene (encoding histone H3 variant H3.3), replacing the lysine 27 with methionine (K27M). Moreover, approximately 30% of pediatric high grade gliomas (pedHGG) including GBM and DIPG harbor a lysine 27 mutation (K27M) in histone 3.3 (H3.3) which is correlated with poor outcome. Recent studies on high-grade pediatric GBM have identified two recurrent mutations (K27M and G34R/V) in genes encoding histone H3 (H3F3A for H3.3 and HIST1H3B for H3.1)
Question: Which histone mutations have been associated with pediatric gliomas?
Answer: Moreover, approximately 30% of pediatric high grade gliomas (pedHGG) including GBM and DIPG harbor a lysine 27 mutation (K27M) in histone 3.3 (H3.3) which is correlated with poor outcome and was shown to influence EZH2 function Recent studies on high-grade pediatric GBM have identified two recurrent mutations (K27M and G34R/V) in genes encoding histone H3 (H3F3A for H3.3 and HIST1H3B for H3.1) Recent studies have identified a Lys 27-to-methionine (K27M) mutation at one allele of H3F3A, one of the two genes encoding histone H3 variant H3.3, in 60% of high-grade pediatric glioma cases.
Question: Which histone mutations have been associated with pediatric gliomas?
Answer: Recent studies on high-grade pediatric GBM have identified two recurrent mutations (K27M and G34R/V) in genes encoding histone H3 (H3F3A for H3.3 and HIST1H3B for H3.1). Two new studies show that the known histone H3 alteration p.Lys27Met in pediatric glioma leads to globally diminished trimethylation at histone H3 lysine 27. These results indicate that H3.3K27M mutation reprograms epigenetic landscape and gene expression, which may drive tumorigenesis.
Question: Which histone mutations have been associated with pediatric gliomas?
Answer: , approximately 30% of pediatric high grade gliomas (pedhgg) including gbm and dipg harbor a lysine 27 mutation (k27m) in histone 3.3 (h3.3) which is correlated with poor outcome and was shown to influence ezh2 function . the h3f3a mutant allele found in high-grade pediatric glioma by real-time pcr . studies on high-grade pediatric gbm have identified two recurrent mutations (k27m and g34r/v) in genes encoding histone h3 (h3f3a for h3.3 and hist1h3b for h3.1) . has been reported recently that about 80% of dipg cases and 70% of midline glioblastomas contain a mutation at one allele of the h3f3a gene (encoding histone h3 variant h3.3) , replacing the lysine 27 with methionine (k27m). . , discuss vaccine treatment for children diagnosed with malignant glioma , through targeting epha2 , il-13rα2 and/or histone h3 k27m , while in adults , treatments with rintega , prophage series g-100 and dendritic cells are explored. . studies have identified a lys 27-to-methionine (k27m) mutation at one allele of h3f3a , one of the two genes encoding histone h3 variant h3.3 , in 60% of high-grade pediatric glioma cases. . new studies show that the known histone h3 alteration p.lys27met in pediatric glioma leads to globally diminished trimethylation at histone h3 lysine 27 . were able to discern the h3f3a k27m mutation in a newly obtained pediatric brainstem glioblastoma sample whose h3.3 status was not known previously , and in three other dipg samples as well as paraffin embedded samples these results demonstrate that have developed a new reliable procedure for detecting the h3f3a k27m mutation in pediatric glioblastoma patient samples. .
Question: Which two drugs are included in the Entresto pill?
Answer: Entresto includes Sacubitril and Valsartan.
Question: List the main proteins found in human saliva.
Answer: Amylases
Cystatins
Immunoglobulins
Mucins
Question: Which DNA sequences are more prone for the formation of R-loops?
Answer: R-loops, transcriptionally-induced RNA:DNA hybrids, occurring at repeat tracts (CTG)n, (CAG)n, (CGG)n, (CCG)n and (GAA)n, are associated with diseases including myotonic dystrophy, Huntington's disease, fragile X and Friedreich's ataxia.  Physiological R-loop formation at CpG island promoters can contribute to DNA replication origin specification at these regions, the most efficient replication initiation sites in mammalian cells. R-loops may also possess beneficial effects, as their widespread formation has been detected over CpG island promoters in human genes. R-loops are particularly enriched over G-rich terminator elements.
Question: Which deep learning-based algorithms are used for enhancer prediction?
Answer: EP-DNN and DEEP.
Question: List 3 apoE mimetics.
Answer: COG133, COG112 and Ac-hE18A-NH(2) are apoE mimetics.
Question: What are the advantages of liquid biopsy in NSCLC?
Answer: Liquid biopsy reflected spatial and temporal heterogeneity of the tumor under treatment pressure.