anand-s/m_qalm huggingface dataset:
Question: Which proteins participate in the formation of the ryanodine receptor quaternary macromolecular complex?
Answer: Calsequestrin (CSQ) is a Ca(2+) storage protein that interacts with triadin (TRN), the ryanodine receptor (RyR), and junctin (JUN) to form a macromolecular tetrameric Ca(2+) signaling complex in the cardiac junctional sarcoplasmic reticulum (SR). Junctin, calsequestrin, triadin, and the ryanodine receptor form a quaternary complex that may be required for normal operation of Ca2+ release.
Question: What are the different classes of orally administered drugs used to treat diabetes
Answer: There are a number of classes of medications tha are used to treat Type 2 diabetes. These include biguanides like metformin, which decreased hepatic glucose release; sulfonyureas like Glimepride, metglitinides like repaglin and d-phenylalanine derivatives, all of which stimulate pancreatic insulin release; Glitizones or thiazolidinediones which make the body more sensitive to insulin; DPP-4 inhibitors which lower the amount of glucose made in the body; alpha-glucosidase inhibitors which slow the absorbtion of carbohydrate in the blood; and bile acid sequestrants that lower blood glucose
Question: Which are the supplemental antioxidant in athletes?
Answer: There are several antioxidant supplements belonging to different families, i.e. Vitamins, Polyphenols, alpha-lipoic acid, ubiquinones, n-3- polyunsaturated acids (PUFAs), minerals and others. Nonetheless the widespread use of these supplements, it is still debated their true usefulness, and it is not unanimously advised their use in athletes.
Question: Name the three phase 3, randomized, double-blind, placebo-controlled that assessed galcanezumab?
Answer: Galcanezumab has been assessed in the phase 3, randomized, double-blind, placebo-controlled EVOLVE-1, EVOLVE-2 and REGAIN studies.
Question: Which clinical trials for psoriasis involved tofacitinib? (November 2017)
Answer: Four phase 3 clinical trials have been performed to assess tofacitinib in psoriasis patients: OPT Retreatment, OPT Pivotal 1, OPT Pivotal 2, OPT Compare
Question: SPAG5 was implicated in which cancers?
Answer: SPAG5 was implicated in prostate cancer, lung cancer and cervical cancer.
Question: Which factors are considered in the FUNC score for intracerebral hemorrhage?
Answer: FUNC score includes Age, Glasgow Coma Scale, ICH location, volume and pre-ICH cognitive impairment.
Question: List mutations that are implicated in the Gray Platelet Syndrome.
Answer: GFI1B and NBEAL2 mutations are implicated in the Gray Platelet Syndrome.
Question: List autoimmune disorders associated with GAD65 autoantibodies.
Answer: Autoantibodies to the smaller isoform of glutamate decarboxylase (GAD) can be found in patients with type 1 diabetes and a number of neurological disorders, including stiff-person syndrome, cerebellar ataxia and limbic encephalitis.
Question: List features of the Perry syndrome.
Answer: Perry syndrome is a familial parkinsonism associated with central hypoventilation, mental depression, and weight loss.
Question: List the types of defensins expressed in humans.
Answer: Defensins are antimicrobial peptides that participate in the innate immunity of hosts. Humans constitutively and/or inducibly express α- and β-defensins, which are known for their antiviral and antibacterial activities.
Question: What are the computational methods for the prediction of beta-barrel transmembrane proteins?
Answer: Computational tools have been developed for beta-barrel transmembrane protein discrimination, topology prediction and prediction of their structural features.
Initial methods developed for the prediction of the transmembrane beta strands were based on hydrophobicity analysis, using sliding windows along the sequence, in order to capture the alternating patterns of hydrophobic-hydrophilic residues of the transmembrane strands, or using generalized secondary structure prediction methods. Other approaches included the construction of special empirical rules using amino-acid propensities and prior knowledge of the structural nature of the proteins, and the development of Neural Network-based predictors to predict the location of alpha-carbon atoms with respect to the membrane. During the last few years, other more refined methods, appeared, including: Neural Networks, Hidden Markov Models, Support Vector Machines, k-Nearest Neighbors, Radial Basis Functions, Bayesian Networks, Genetic Algorithms, Mahalanobis Discriminant Functions, Cellular Automata, N-to-1 Extreme Learning Machines. Hidden Markov Model-based methods are among the most successful in topology prediction, being able to capture the unique architecture of beta-barrel transmembrane proteins. Consensus methods, as well as pipelines of several related tools (e.g. subcellular localization prediciton, alpha-helical transmembrane protein prediction, signal-peptide/lipoprotein prediction) have also used for discriminating beta-barrel transmembrane proteins. Recently, a number of methods for predicting more detailed structural features (e.g. surface accessibility, residue contacts, even detailed atomic 3D models) tailored to beta-barrel transmembrane proteins have been developed, based on knowledge-based potential functions, graph theoretic models, physical models and multi-tape S-attribute grammars. Methods/tools falling in the aforementioned classes are (listed in alphabetical order): BBF (beta-barrel finder), BETAWARE, BOCTOPUS, BOMP, BTMX (Beta barrel TransMembrane eXposure), HHomp, HMM-B2TMR, OMBBpred, PROFtmb, PRED-TMBB, TMB-Hunt, TBBPred, TMBETAPRED-RBF, TMBHMM, TransFold, TMBpro, TMBKNN, Wimley
Question: What is the treatment of triiodothyronine toxicosis?
Answer: Treatment of T3 toxicosis is a complex medical problem because not well responsive to the various options. Usual treatment includes antithyroid drugs such as propyltiouracil, radioactive iodine or beta blockers like propanol; surgery may be also necessary in some cases.
Question: Which are the plant DNA (cytosine-5) methyltransferase families?
Answer: The plant DNA (cytosine-5)methyltransferases are classified into the families: MET, CMT, and the de novo DRM.
Question: Which databases can exchange data using Matchmaker Exchange's API?
Answer: Matchmaker Exchange (MME) was created to establish a federated network connecting databases of genomic and phenotypic data using a common application programming interface (API). To date, seven databases can exchange data using the API: GeneMatcher, PhenomeCentral, DECIPHER, MyGene2, matchbox, Australian Genomics Health Alliance Patient Archive, and Monarch Initiative; the latter included for model organism matching.
Question: For which indications has midostaurin received FDA and EMA approval?
Answer: Midostaurin was approved by the Food and Drug Administration (FDA) and the European Medical Agency (EMA) for acute myeloid leukemia with activating FLT3 mutations in combination with intensive induction and consolidation therapy as well as aggressive systemic mastocytosis (ASM), systemic mastocytosis with associated hematological neoplasm (SM-AHN) or mast cell leukemia (MCL).
Question: What are the effects of STEF depletion?
Answer: The mechanisms regulating the actin cap are currently poorly understood. STEF/TIAM2, a Rac1 selective guanine nucleotide exchange factor, localises at the nuclear envelope, co-localising with the key perinuclear proteins Nesprin-2G and Non-muscle myosin IIB (NMMIIB), where it regulates perinuclear Rac1 activity. STEF depletion reduces apical perinuclear actin cables (a phenotype rescued by targeting active Rac1 to the nuclear envelope), decreases nuclear stiffness and reduces expression of TAZ-regulated genes, indicating an alteration in mechanosensing pathways as a consequence of disruption of the actin cap.
Question: List the three most abundant bacterial phyla present in mouse feces.
Answer: Firmicutes
Proteobacteria 
Bacteroidetes
Question: List inflammatory caspase proteins?
Answer: caspase-1
caspase-4
caspase-5
Question: List phagosomal markers.
Answer: Rab7
LAMP1
Cathepsin D
Rab9
V-ATPase 
CD63
Question: Which receptor(s) recognize lysosomal hydrolases in trans-Golgi network (TGN)?
Answer: The majority of lysosomal hydrolases in trans-Golgi network (TGN) are specifically recognized by mannose 6-phosphate (M6P) receptors (MPRs), which ensure their transport to the endosomal/lysosomal system. Other receptors can also carry lysosomal hydrolases from the trans-Golgi network (TGN) to the endosomal system. These M6P alternative receptors are the lysosomal integral membrane protein (LIMP-2) and the multi-ligand receptor sortilin. These reseptors enable a mannose-6-phosphate-independent pathway from TGN to lysosomes.
Question: Which genes code for the alpha subunit of the DNA polymerase III in most Firmicutes?
Answer: Bacterial DNA polymerase III is the primary complex of DNA replication. In most Firmicutes, which are low-GC, gram-positive bacteria, the alpha subunit of their DNA polymerase III is encoded by polC and dnaE. DnaE is widely conserved in most bacteria, while PolC is present mainly in Firmicutes clade.
Question: Which genes are more frequently affected by somatic mutations in Chronic Lymphocytic Leukemia
Answer: TP53, ATM, NOTCH1, XPO1, MYD88, KLHL6, SF3B1, ZMYM3, MAPK1, FBXW7 and DDX3X
Question: List ribosomal biogenesis proteins.
Answer: FGF13
p53
TGFβ/Activin
PTEN
Nucleostemin
HEATR1
Question: List omics technologies comprised in system biology.
Answer: System biology combines various omics technologies such as genomics, transcriptomics, proteomics, metabolomics, epigenomics, glucomics, degradomics and fluxomics.
Question: Which disease phenotypes are associated to PRPS1 mutations?
Answer: X-linked Charcot-Marie-Tooth disease type 5 (CMTX5), Arts syndrome, and non-syndromic sensorineural deafness (DFN2) are allelic syndromes, caused by reduced activity of phosphoribosylpyrophosphate synthetase 1 (PRS-I) due to loss-of-function mutations in PRPS1.
Question: Which are the methods for in silico prediction of the origin of replication (ori) among bacteria?
Answer: Several in silico methods have been applied for prediction of the origin of replication (ori). DNA base composition asymmetry, such as GC skew, is the basis of numerous in silico methods used to detect the ori in prokaryotes. The Z curve analysis is also used for ori identification. Comparative genomics, by BLAST analyses of the intergenic sequences compared to related species have been applied in ori prediction. The finding of the dnaA gene and its binding sites, DnaA boxes, as well as the finding of the binding sites of other proteins, such as CtrA and IHF, are fundamental characteristics used for in silico prediction of the ori. Also, the localization of boundary genes, such as cell division cycle (cdc6) gene, and consensus origin recognition box (ORB) sequences have been employed for ori detection. The study of the gene order around the origin sequence and the distribution of the genes encoded in the leading versus the lagging strand are also used for in silico detection of the ori.
Question: Which two catechol-O-methyl transferase (COMT) inhibitors can be used for treatment of Parkinson disease?
Answer: Tolcapone (central and peripheral) and entacapone (peripheral) are catechol-O-methyl transferase inhibitors that are used for treatment of Parkinson disease.
Question: List drugs included in the DHAP-R chemotherapy regiment.
Answer: Dexamethasone (a steroid hormone), cytarabine (ara-C), cisplatin (platinum agent) and rituximab are included in the DHAP-R chemotherapy protocol.
Question: Which are the families of mammalian DNA-(cytosine-5)-methyltransferases?
Answer: DNA (cytosine-5)-methyltransferases catalyze the specific transfer of a methyl group  to the C5 position of cytosine residues in DNA. Three families of DNA (cytosine-5)-methyltransferases have been identified in mammals: DNMT1, DNMT2 and DNMT3 (including DNMT3a, DNMT3b and DNMT3L isoforms). All of them share homologous catalytic domains. DNMT1 is the ���maintenance” methyltransferase family. DNMT1 is specific for hemi-methylated DNA and ensures the faithful transmission of DNA methylation patterns in every replication cycle. DNMT3 is required for de novo methylation of DNA. DNMT3 targets unmethylated DNA and is responsible for the establishment of new methylation patterns. Dnmt2, in contrast to all other mammalian DNA (cytosine-5)-methyltransferases, does not possess a large N-terminal regulatory domain. The DNA methylation activity of DNMT2 is still controversial.
Question: List adipokines.
Answer: adiponectin
leptin
resistin
Question: List clinical symptoms of the MECOM-associated syndrome
Answer: Heterozygous mutations in MECOM (MDS1 and EVI1 complex locus) have been reported to be causative of a rare association of congenital amegakaryocytic thrombocytopenia and radioulnar synostosis. The clinical picture included radioulnar synostosis, bone marrow failure, clinodactyly, cardiac and renal malformations, B-cell deficiency, and presenile hearing loss. No single clinical manifestation was detected in all patients affected by MECOM mutations. Radioulnar synostosis and B-cell deficiency were observed only in patients with mutations affecting a short region in the C-terminal zinc finger domain of EVI1.
Question: What are the symptoms of abacavir hypersensitivity?
Answer: Patients receiving abacavir develop an idiosyncratic hypersensitivity reaction that can include a wide range of symptoms. The most common are: fever, enathema, skin rash, nausea, vomiting, diarrhoea, cough, gastrointestinal disorders, anaphylactic shock, respiratory symptoms.
Question: List types of DNA lesions caused by UV light.
Answer: cyclobutane pyrimidine dimers
pyrimidine pyrimidone photoproducts
8-oxo-7,8-dihydroguanine
Question: In which isochores are Alu elements enriched?
Answer: Alu elements are enriched in high GC% isochores due to reduced Alu loss by recombination in these regions. The frequency of Alu sequences increases with increasing GC, but attains a maximum in H2 isochores.
Question: Which genes have been found mutated in Gray platelet syndrome patients?
Answer: The genetic defects responsible for gray platelet syndrome are mutations in the genes NBEAL2, GATA1 and GFI1B.
Question: Which genes have been found mutated in Gray platelet syndrome patients?
Answer: The genetic defect responsible for gray platelet syndrome was recently identified in biallelic mutations in the NBEAL2 gene.
A nonsense mutation in the gene encoding the transcription factor GFI1B (growth factor independent 1B) that causes autosomal dominant gray platelet syndrome.
X-linked gray platelet syndrome due to a GATA1 Arg216Gln mutation.
Question: Which drugs are included in TAS-102?
Answer: TAS-102 is a novel oral nucleoside antitumor agent consisting of trifluridine and tipiracil hydrochloride at a molar ratio of 1:0.5.
Question: List human proteins that are subject to a dimer-to-tetramer transition.
Answer: GAC
SHMT2
AMPAR
Orai1
Orai3
Question: What are the indications for alteplase?
Answer: Intravenous alteplase (recombinant tissue plasminogen activator) is the only approved thrombolytic agent at present indicated for acute ischaemic stoke.
Food and Drug Administration approval of alteplase for central venous catheter (CVC) occlusions. 
Alteplase is now firmly established as a treatment of choice in the management of acute myocardial infarction. The efficacy of intravenous alteplase in the treatment of pulmonary thromboembolism has also been established and appears to be similar to that of streptokinase and urokinase in this indication and in arterial thrombotic occlusion. However, its use in this latter indication and in other vascular disorders has not been as extensively documented. 
Preliminary data suggest efficacy of alteplase of deep vein thrombosis and arterial thrombotic occlusion.
Question: Which computational methods are used for the definition of synteny?
Answer: The computational methods which are used for the definition of synteny are:1) multisyn, 2) poff, 3) orthocluster, 4) phyldiag, 5) synblast, 6) cinteny, 7) domain team, 8)mcscanx and 9) run Orthoclusterdb and 10) view synteny.
Question: Which computational methods are used for the definition of synteny?
Answer: Computational methods used for the definition of synteny include multisyn, poff, orthocluster, phyldiag, synblast, cinteny, domainmanagement, domainweekly, domainScanx, run orthocluster, orthClusterdb and view synteny.
Question: Which computational methods are used for the definition of synteny?
Answer: Computational methods used for the definition of synteny include multisyn, poff, orthocluster, phyldiag, synblast, cinteny, domainmanagement, domainScanx, run orthoclustereddb, view synteny and others.
Question: Which computational methods are used for the definition of synteny?
Answer: The automated and fast detection of syntenic domain teams is implemented in the DomainTeam software. Here we present the SynBlast pipeline that is designed to construct and evaluate local synteny information. Cinteny allows one to automatically compare multiple genomes and perform sensitivity analysis for synteny block detection and for the subsequent computation of reversal distances. OrthoClusterDB is a new online platform for the identification and visualization of synteny blocks. OrthoClusterDB consists of two key web pages: Run OrthoCluster and View Synteny. MCScan is an algorithm able to scan multiple genomes or subgenomes in order to identify putative homologous chromosomal regions, and align these regions using genes as anchors. PoFF is an extension for the standalone tool Proteinortho, which enhances orthology detection by combining clustering, sequence similarity, and synteny.  MultiSyn: A Webtool for Multiple Synteny Detection and Visualization of User's Sequence of Interest Compared to Public Plant Species.
Question: Which computational methods are used for the definition of synteny?
Answer: Cinteny allows one to automatically compare multiple genomes and perform sensitivity analysis for synteny block detection. Here we present the SynBlast pipeline that is designed to construct and evaluate local synteny information. PoFF is an extension for the standalone tool Proteinortho, which enhances orthology detection by combining clustering, sequence similarity, and synteny.
Question: Which computational methods are used for the definition of synteny?
Answer: Computational methods used for the definition of synteny include multisyn, poff, orthocluster, phyldiag, synblast, cinteny, domainmanagement, electrophobicity, run orthoclustereddb, mcScan and view synteny.
Question: Which computational methods are used for the definition of synteny?
Answer: The computational methods that are used for the definition of synteny are: multisyn, poff, orthocluster, phyldiag, synblast, cinteny, domainteam, mcscanx and run orthoclustersdb.
Question: List processes which are under the control of the YAP protein.
Answer: Yes-associated protein (YAP), a transcription coactivator, is the major downstream effector of the Hippo pathway, which plays a critical role in organ size control, cell poliferation and cancer development and tissue homeostasis and differentiation.
Question: List 4 targeted synthetic DMARDs that are JAK inhibitors.
Answer: Targeted synthetic (ts) DMARDs that are Janus kinase (JAK) inhibitors include tofacitinib, baricitinib, filgotinib, upadacitinib.
Question: List features of the DEND syndrome.
Answer: Clinical features of the DEND syndrome include developmental delay, epilepsy and neonatal diabetes.
Question: A common problem in proteomics is the contamination of samples with exogenous proteins (often from other species). These proteins can be found in specific databases. List some contaminants.
Answer: Some common contaminants in proteomics are proteases (used for the digestion of the proteins), keratins (usually from the skin),  proteins originated from the serum of the culture media and antibodies if used in the experiment.
Question: Which drugs are included in the Lonsurf pill?
Answer: Lunsurf pill includes trifluridine and tipiracil. It is a novel form of chemotherapy for metastatic colorectal cancer.
Question: List clinical features of the IMAGe syndrome.
Answer: Clinical features of IMAGe syndrome include intra-uterine growth restriction, metaphyseal dysplasia, adrenal hypoplasia congenita and genital abnormalities. It is s caused by gain-of-function mutations of maternally expressed gene CDKN1C on chromosome 11p15.5.
Question: Which are the main functions of the annexin family?
Answer: Annexins are required for membrane organization and membrane transport events required for the establishment/maintenance of epithelial polarity. 
An association of annexins with ion channels, as membrane-guiding auxiliary proteins or modulators of channel activity. 
Last but not least, some annexins seem to work as extracellular autocrine modulators of receptor function under different physiological conditions.
Question: Which neuroendocrine tumors are associated with specific tumor syndromes?
Answer: Neuroendocrine tumors are a heterogeneous group of benign and malignant neoplasias, detectable in the context of hereditary tumor syndromes in up to 30% of cases. Neuroendocrine tumors include medullary thyroid carcinoma, gastroenteropancreatic tumors, pheochromocytoma, and paraganglioma.
Question: List drugs that are included in the Vosevi polypill.
Answer: Vosevi pill includes sofosbuvir, velpatasvir and voxilaprevir. It is approved by the US Food and Drug Administration (FDA) for adult patients with chronic hepatitis C virus (HCV) infection without cirrhosis or with compensated cirrhosis (Child-Pugh A) who have: genotype 1, 2, 3, 4, 5, or 6 infection and have previously been treated with an HCV regimen containing an NS5A inhibitor; and genotype 1a or 3 infection and have previously been treated with an HCV regimen containing sofosbuvir without an NS5A inhibitor.
Question: List fish anti-freeze proteins.
Answer: AFP-I
AFP-II
AFP-III
Anti-freeze glycoprotein
Thermal hysteresis protein
Question: PH motifs in which genes endow breast cancer growth?
Answer: Although emerging roles of protease-activated receptor1&2 (PAR1&2) in cancer are recognized, their underlying signalling events are poorly understood. Signal-binding motifs in PAR1&2 are critical for breast cancer growth. This occurs via the association of the pleckstrin homology (PH) domain with Akt/PKB as a key signalling event of PARs. Other PH-domain signal-proteins such as Etk/Bmx and Vav3 also associate with PAR1 and PAR2 through their PH domains. PAR1 and PAR2 bind with priority to Etk/Bmx. A point mutation in PAR2, H349A, but not in R352A, abrogates PH-protein association and is sufficient to markedly reduce PAR2-instigated breast tumour growth in vivo and placental extravillous trophoblast (EVT) invasion in vitro. Similarly, the PAR1 mutant hPar1-7A, which is unable to bind the PH domain, reduces mammary tumours and EVT invasion, endowing these motifs with physiological significance and underscoring the importance of these previously unknown PAR1 and PAR2 PH-domain-binding motifs in both pathological and physiological invasion processes.
Question: List proteins interacting with Star-PAP
Answer: Phosphorylation regulates the Star-PAP-PIPKIα interaction and directs specificity toward mRNA targets.
Star-PAP directly associated with cleavage and polyadenylation specificity factor (CPSF) 160 and 73 subunits and also the targeted pre-mRNA.
we show that Larp7 interacts with a poly(A) polymerase Star-PAP to maintain Lin28 mRNA stability.
Question: Which deiodinases are best known to be present in brain?
Answer: All the 3 deiodinases (Type 1, Type 2 and Type 3 deiodinase) are present in the "brain" but Type 1 deiodinase  is only found in neurohypophysis that cannot be actually considered true "brain tissue".
Question: List human diseases involving genomic imprinting.
Answer: Prader Willi Syndrome
Angelman syndrome
Beckwith-Wiedemann syndrome
Hydatidiform mole
Cancer
Silver-Russell syndrome
Diabetes
Question: List proteins that promotes calcification.
Answer: tissue nonspecific alkaline phosphatase (TNAP)
matrix Gla protein (MGP)
fibroblast growth factor-23 (FGF-23)
matrix metalloproteinases