anand-s/m_qalm huggingface dataset:
Question: Which method has been developed for mapping of Transcription Start Sites (TSS) starting from nanograms of RNA?
Answer: SLIC-CAGE has been developed as a method to identify transcriptome-wide the binding sites of transcription start sites (TSSs) using a simple two-step protocol with 500-50,000 cells and reveals the interplay between genomic locations of DNA-binding proteins, transcription, individual nucleosomes and transcriptional starting sites.
Cap analysis of gene expression (CAGE) is a methodology for genome-wide quantitative mapping of mRNA 5' ends to precisely capture transcription start sites at a single nucleotide resolution. In combination with high-throughput sequencing, CAGE has revolutionized our understanding of the rules of transcription initiation, led to discovery of new core promoter sequence features, and discovered transcription initiation at enhancers genome-wide. SLIC-CAGE is a Super-Low Input Carrier-CAGE approach to capture 5' ends of RNA polymerase II transcripts from as little as 5-10 ng of total RNA. This dramatic increase in sensitivity is achieved by specially designed, selectively degradable carrier RNA.
SLIC-CAGE has been developed as a method to identify transcriptome-wide the binding sites of transcription start sites (TSSs) using a simple two-step protocol with 500-50,000 cells and reveals the interplay between genomic locations of DNA-binding sites, transcription, mRNA, and nucleosomes.
Question: Which tool has been developed for microRNA-target enrichment and network-based analysis?
Answer: MIENTURNET (MicroRNA ENrichment TURned NETwork) is a web tool that receives in input a list of miRNAs or mRNAs and tackles the problem of prioritizing miRNA-target interactions by performing a statistical analysis followed by a fully featured network-based visualization and analysis. The statistics is used to assess the significance of an over-representation of miRNA-target interactions and then MIENTURNET filters based on the statistical significance associated with each miRNA-target interaction. In addition, the holistic approach of the network theory is used to infer possible evidences of miRNA regulation by capturing emergent properties of the miRNA-target regulatory network that would be not evident through a pairwise analysis of the individual components.
MIENTURNET (MicroRNA ENrichment TURned NETwork) is an interactive web tool for microRNA-target enrichment and network-based analysis.
MIENTURNET is a web tool for microRNA-target enrichment and network-based analysis. MIENTURNET offers the possibility to consistently perform both statistical and network-based analyses.
Question: Which intraflagellar transport (IFT) motor protein has been linked to human skeletal ciliopathies?
Answer: Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliopathies
Intraflagellar transport (IFT) depends on two evolutionarily conserved modules, subcomplexes A (IFT-A) and B (IFT-B), to drive ciliary assembly and maintenance. All six IFT-A components and their motor protein, DYNC2H1, have been linked to human skeletal ciliopathies, including asphyxiating thoracic dystrophy (ATD; also known as Jeune syndrome), Sensenbrenner syndrome, and Mainzer-Saldino syndrome (MZSDS).
Question: Which class of genomic elements was assessed as part of the FANTOM6 project?
Answer: Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, the expression of 285 lncRNAs was systematically knocked down in human dermal fibroblasts. Cellular growth, morphological changes, and transcriptomic responses were quantified using Capped Analysis of Gene Expression (CAGE).
The functional annotation of the mammalian genome 6 (FANTOM6) project aims to systematically map all human long noncoding RNAs (lncRNAs) in a gene-dependent manner through dedicated efforts from national and international teams
Question: Which gene is associated with response to abacavir?
Answer: Large studies established the effectiveness of prospective HLA-B*57:01 screening to prevent HSRs to abacavir.
Question: What pathological condition is MK-1602 used for?
Answer: MK-1602 has been assessed in clinical trials for the acute treatment of migraine.
Question: What is a bacteriocin?
Answer: Bacteriocins, the ribosomally produced antimicrobial peptides of bacteria, represent an untapped source of promising antibiotic alternatives.
One such strategy involves using narrow-spectrum protein antibiotics (so-called bacteriocins), which diverse bacteria use to compete against closely related species.
Question: Which R/Bioconductor package has been developed for the analysis of psychiatric disease genes?
Answer: PsyGeNET is a knowledge resource on psychiatric diseases and their genes, developed by text mining and curated by domain experts. Psygenet2r is an R package that contains a variety of functions for leveraging PsyGeNET database and facilitating its analysis and interpretation. The package offers different types of queries to the database along with variety of analysis and visualization tools, including the study of the anatomical structures in which the genes are expressed and gaining insight of gene's molecular function. Psygenet2r is especially suited for network medicine analysis of psychiatric disorders.
psygenet2r
Question: Which technique led to the elucidation of the role of HOXD10 in regulating lymphatic endothelial responses to VEGF-C?
Answer: DeepCAGE transcriptomics identify HOXD10 as a transcription factor regulating lymphatic endothelial responses to VEGF-C.
DeepCAGE transcriptomics identify HOXD10 as a transcription factor regulating lymphatic endothelial responses to VEGF-C
DeepCAGE transcriptomics identify HOXD10 as a transcription factor regulating lymphatic endothelial responses to VEGF-C.
Question: In which kingdom do microsporidia belong, according to their current classification scheme?
Answer: Traditionally, microsporidia were considered as protozoans, but recently they have been reclassified as the earliest-diverging clade of sequenced fungi. Microsporidia are a diverse group of obligate, intracellular, eukaryotic, spore-forming parasites; they are ubiquitous fungi, with genomes that have undergone a strong reduction.
Question: Givosiran is used for treatment of which disease?
Answer: Givosiran is approved for treatment of porphyria.
Question: Which disease is caused by de novo VPS4A mutations?
Answer: Mutations in the VPS4A gene, which encodes the alpha-subunit of the lysosomal sorting enzyme, beta-N-acetylhexosaminidase 4, are the cause of multisystem disease type 4 or Ferroportin disease.
De novo mutations in the gene encoding for endosomal sorting enzyme VPS4A (Val4A) cause multisystem disease
De νovo VPS4A mutations cause multisystem disease with abnormal neurodevelopment.
Question: Which is the main target of the anti-arrhythmic activity of flecainide?
Answer: Flecainide is a class 1c antiarrhythmic that acts by blocking sodium channels and is used mainly in the treatment of supraventricular arrhythmias.
Question: What percentage of Homo sapiens DNA is of Neanderthal origin?
Answer: We find that the power to reject ancient admixture might be particularly low if the population size of Homo sapiens was comparable to the Neanderthal population size. Our results indicate that 3.6% of the Neanderthal genome is shared with roughly 65.4% of the average European gene pool, which clinally diminishes with distance from Europe.
Approximately 2-4% of genetic material in human populations outside Africa is derived from Neanderthals who interbred with anatomically modern humans. 3.6% of the Neanderthal genome is shared with roughly 65.4% of the average European gene pool, which clinally diminishes with distance from Europe.
Our results indicate that 3.6% of the Neanderthal genome is shared with roughly 65.4% of the average European gene pool, which clinally diminishes with distance from Europe. Here, we present evidence of Neanderthal introgression within the chromosome 3p21.31 region, occurring with a high frequency in East Asians (ranging from 49.4% to 66.5%) and at a low frequency in Europeans.
3.6 % of the neanderthal genome is shared with roughly 65.4 % of the average european gene pool , which clinally diminishes with distance from europe.This work suggests that differences in effective population size may play a far more important role in shaping levels of introgression than previously thought.
Question: What is the target of tanezumab?
Answer: Tanezumab is a humanized monoclonal antibody against nerve growth factor.
Question: What is the prevalence of short QT syndrome?
Answer: The prevalence of short QT syndrome is low and varies between 0.01% and 0.1%
Question: In which phase of clinical trials was sutezolid in 2018?
Answer: By 2018 sutezolid had been evaluated in phase II clinical trials.
Question: What is the genus for the common European honey bee?
Answer: The genus and species of the European honey bee is Apis mellifera.
Question: Where do the Schwann cells and melanocytes originate from?
Answer: Schwann cells and melanocytes originate from the multipotent population of neural crest cells.
Question: Is APOBEC3B protein predominantly cytoplasmic or nuclear?
Answer: Contrary to other APOBEC family members, APOBEC3B was found to predominantly concentrate to the cell nucleus.
Question: Which pathway is activated by ficolin-3?
Answer: Ficolin-3 activates lectin complement pathway.
Question: What is the function of the Eyeless associated gene in Drosophila?
Answer: Eyeless (ey) also known as Pax6, is one of the most critical transcription factors for initiating the entire eye development in Drosophila.
Theeye-associated Pax6 gene controls neuronal navigation in Drosophila.
Eyeless (ey) is one of the most critical transcription factors for initiating the entire eye development in Drosophila. Two Pax6 genes are in Drosophila: eyeless (ey) and twin of eyeless (toy)
Eyeless (ey) is one of the most critical transcription factors for initiating the entire eye development in Drosophila.
Question: In which process Src, Cortactin and MT1-MMP are playing an essential role?
Answer: Src was shown to be required for invadopodia formation and function, whereas Cortactin was found to regulate cofilin and N-WASp activities to control the stages of invadopodium assembly and maturation. Finally, membrane type 1 matrix metalloproteinase (MT1-MMP) was demostrated as the key invadopodial enzyme responsible for gelatin matrix degradation in cancer cells.
Question: Angelman syndrome is associated with deletion of a part of Chromosome 15 but if the deletion occurs in the paternally inherited chromosome 15, what is the disease?
Answer: Prader-Willi syndrome (PWS) results from a deletion of the paternal genes in the region of chromosome 15q11-q13.
 prader-willi syndrome (pws) results from a deletion of the paternal genes in the region of chromosome 15q11-q13.
Prader-Willi syndrome (PWS) results from a deletion of the paternal genes in the region of chromosome 15q11-q13. 
 Prader-Willi syndrome (PWS) results from a deletion of the paternal genes in the region of chromosome 15q11-q13.
Question: What does bDMARD stand for?
Answer: bDMARDs are biologic disease-modifying antirheumatic drugs.
Question: Are male or female persons more prone to autoimmunity?
Answer: Sex hormones have long been implicated in autoimmune diseases because women account for 80% of cases. Examples of this autoimmune dimorphism include (but are not limited to) lupus, rheumatoid arthritis and multiple sclerosis with the two former more prevalent in females than males and the latter more severe during pregnancy. Most recently, sex chromosome abnormalities and skewed X chromosome inactivation have been suggested as novel players, particularly in later-onset diseases.
Sex hormones have long been implicated in autoimmune diseases because women account for 80% of cases. Most recently, sex chromosome abnormalities and skewed X chromosome inactivation have been suggested as novel players, particularly in later-onset diseases.
Sex hormones have long been implicated in autoimmune diseases because women account for 80% of cases.
females
Sex hormones have long been implicated in autoimmune diseases because women account for 80% of cases. Sex hormone expression is altered among patients with autoimmune disease, and this variation of expression contributes to immune dysregulation.
Question: What is evaluated with the SAD PERSONS scale?
Answer: SAD PERSONS scale was developed to evaluate suicide risk.
Question: Which molecule is targeted by Teprotumumab?
Answer: Teprotumumab is a human monoclonal antibody that targets IGF-1R. It can be used for treatment of thyroid eye disease.
Question: How many clinical trials for off-label drugs in neonates are cited in the literature.
Answer: There are no reports on clinical trials of off-label drugs in neonates. An analysis of Pediatric Investigation Plans submitted between 2007 and 2010 shows that neonates were included in the study of 4 products, but it is unknown if the trial drugs are off-label and if the trials are being conducted at all.
Question: What is  Achondroplasia?
Answer: Achondrogenesis type II also known as  Achondroplasia  is an autosomal-dominant disease leading to severe micromelic dwarfism
Achondrogenesis type II is an autosomal-dominant disease leading to severe micromelic dwarfism. 
Achondrogenesis type II is an autosomal-dominant disease leading to severe micromelic dwarfism.
achondrogenesis type ii is an autosomal-dominant disease leading to severe micromelic dwarfism.
achondrogenesis type ii is an autosomal-dominant disease to severe micromelic dwarfism. .
Question: How many pseudogenes are contained in the C. elegans genome?
Answer: Evidence suggests that a fifth of annotated Caenorhabditis elegans genes may be pseudogenes.  At least 4% of the annotated C. elegans genes can be recognized as pseudogenes simply from closer inspection of the sequence data. Thus out of 18000 transcripts, around 3500 are expected to be pseudogenes.
Evidence suggesting that a fifth of annotated Caenorhabditis elegans genes may be pseudogenes The remaining explanation is that most of the annotated genes in the recently duplicated category are pseudogenes, a proportion corresponding to 20% of all of the annotated C. elegans genes  At least 4% of the annotated C. elegans genes can be recognized as pseudogenes simply from closer inspection of the sequence data
Evidence suggesting that a fifth of annotated Caenorhabditis elegans genes may be pseudogenes
Question: Which gene is associated with the Mitchell-Riley syndrome?
Answer: Mutations in the gene coding for the transcription factor RFX6 (regulatory factor X,6) have been described as the cause of the Mitchell-Riley syndrome.
Question: What is  Exencephaly?
Answer: Exencephaly is a type of cephalic disorder wherein the brain is located outside of the skull
exencephaly, a failure of the cranial neural folds to close which leads to degeneration of the exposed brain tissue termed anencephaly. .
exencephaly, a failure of the cranial neural folds to close which leads to degeneration of the exposed brain tissue termed anencephaly.
Question: Which company produces ORMD-0801?
Answer: ORMD-0801 is produced by Oramed Pharmaceuticals.
Question: To the ligand of which receptors does Denosumab (Prolia) bind?
Answer: Denosumab is a monoclonal antibody against the RANKL
Question: Which brain tumors does neuroligin-3 promote?
Answer: Neuroligin-3 promotes the growth of high-grade gliomas.
Question: Is the transcriptional regulator BACH1 an activator or a repressor?
Answer: BACH1, a basic leucine zipper mammalian transcriptional repressor, negatively regulates heme oxygenase 1 (HMOX1), a key cytoprotective enzyme that has antioxidant and anti-inflammatory activities. In the absence of elevated intracellular heme or oxidative stress, BACH1 functions as a repressor of the enhancers of heme oxygenase-1 (HO-1) gene (Hmox-1) by forming heterodimers with the small Maf proteins such as MafK. Bach1 is recruited to a subset of p53 target genes and contributes to impeding p53 action by promoting histone deacetylation.
BACH1 is, in most contexts, a transcriptional repressor
Question: What is the drug forxiga used for?
Answer: Dapagliflozin (Forxiga®) is the first in a novel class of glucose-lowering agents known as sodium-glucose co-transporter-2 (SGLT2) inhibitors and is used in the treatment of patients with type 2 diabetes.
Question: For which type of diabetes can empagliflozin be used?
Answer: The oral antidiabetes agent, empagliflozin, can be used as monotherapy or alongside other glucose-lowering treatments, including insulin, to treat T2DM.
Question: Which SWI/SNF protein complex subunit has been demonstrated to interact with the FANCA gene product?
Answer: The Fanconi anemia protein FANCA has been shown to interact with the brm-related gene 1 (BRG1) product. BRG1 is a subunit of the SWI/SNF complex, which remodels chromatin structure through a DNA-dependent ATPase activity.
FANCA was demonstrated to associate with the endogenous SWI/SNF complexFANCA may recruit the SWI/SNF complex to target genes, thereby enabling coupled nuclear functions such as transcription and DNA repair
Question: In which breast cancer patients can palbociclib be used?
Answer: Palbociclib is useful for women with hormone receptor-positive, human epidermal growth factor receptor 2-negative breast cancer.
Question: What is PNPPP?
Answer: personally normalized plasma protein profiles (PNPPP)
Question: What is the content of the METLIN database?
Answer: METLIN is a metabolite database containing tandem mass spectrometry data for each metabolite.
Question: Which calcium/calmodulin dependent protein phosphatase is involved in the activation of the family of NFAT transcription factors (Nuclear Factors of Activated T cells)?
Answer: The activity of NFAT proteins is tightly regulated by the Ca(2+)/calmodulin-dependent protein phosphatase 2B/calcineurin (CaN).Dephosphorylation of NFAT by CaN is required for NFAT nuclear localization.
Question: Which clotting factor is inhibited by betrixaban?
Answer: Betrixaban is an orally administered direct clotting factor Xa inhibitor.
Question: What is the effect of Satb1 knock-out in mice?
Answer: inhibited cell viability and migration
While T cell growth in vitro, Satb1 knockdown was found to be effective in vivo by inhibiting T cell proliferation and activating apoptosis in a subset of T cells
knock-out of Satb1 significantly inhibited cell viability and migration, and promoted Schwann cells apoptosis.
SATB1 is essential for maintaining TCR responsiveness during the induction and effector phases and may provide a novel therapeutic target for T cell-mediated autoimmune diseases. knock-out of Satb1 significantly inhibited cell viability and migration, and promoted Schwann cells apoptosis.
Knock-out of Satb1 significantly inhibited cell viability and migration, and promoted Schwann cells apoptosis.
Question: Mutation of which gene is associated with McLeod syndrome?
Answer: Mutation of XK gene  is associated with McLeod syndrome. The XK gene is an X-chromosomal gene. The McLeod phenotype is derived from various forms of XK gene defects that result in the absence of XK protein, and is defined hematologically by the absence of Kx antigen, weakening of Kell system antigens, and red cell acanthocytosis.
Question: How many topological associated domains are contained in the human Hox cluster?
Answer: transcriptional activation is associated with a dynamic bi-modal 3d organization, whereby the genes switch autonomously from an inactive to an active compartment.
Initially, Hox clusters are organized as single chromatin compartments containing all genes and bivalent chromatin marks. Transcriptional activation is associated with a dynamic bi-modal 3D organization, whereby the genes switch autonomously from an inactive to an active compartment. 
, hox clusters are organized as single chromatin compartments containing all genes and bivalent chromatin marks. . activation is associated with a dynamic bi-modal 3d organization , whereby the genes switch autonomously from an inactive to an active compartment. . 
Initially, Hox clusters are organized as single chromatin compartments containing all genes and bivalent chromatin marks. Transcriptional activation is associated with a dynamic bi-modal 3D organization, whereby the genes switch autonomously from an inactive to an active compartment.
Question: Which conditions is caused by mutations in HFE?
Answer: Mutations in the HFE gene, encoding the syntaxin binding protein HFE1, are the cause of hereditary hemochromatosis.
Hereditary hemochromatosis is an autosomal recessive disorder characterized by systemic iron overload with consequent tissue damage . The vast majority of HH patients are homozygous for the C282Y HFE mutation in HFE . The study was to establish a reliable, cost-effective molecular diagnostic service for this potentially lethal disorder in South Africa . The authors suggest lymphocytes from HH patients may have an increased capacity to respond to DEB-induced chromosome breakage .
Hereditary hemochromatosis (HH) is a common autosomal recessive disorder characterized by systemic iron overload with consequent tissue damage. The vast majority of HH patients are homozygous for the C282Y mutation in HFE.
Mutations in the HFE gene cause hereditary hemochromatosis, an iron overload disorder that is hallmarked by excessive accumulation of iron in parenchymal organs.
Hereditary hemochromatosis (HH) is common among Caucasians. Hereditary hemochromatosis patients homozygous for the C282Y HFE mutation.
Hereditary hemochromatosis (HH) is a common autosomal recessive disorder characterized by systemic iron overload with consequent tissue damage. The vast majority of HH patients are homozygous for the C282Y mutation in HFE. HFE mutation can possess the risk of AD in transferrin-, APOE- and APP-normal patients.
Mutations in HFE, a gene encoding a putative lysosomal trafficking protein, cause hereditary hemochromatosis.
The mechanisms by which the hereditary hemochromatosis protein, HFE, decreases transferrin-mediated iron uptake were examined Hereditary hemochromatosis: HFE mutation analysis in Greeks reveals genetic heterogeneity Hereditary hemochromatosis (HH) is common among Caucasians; reported disease frequencies vary from 0.3 to 0.8%.
Mutations in HFE, a gene encoding a putative lysosomal trafficking protein, are the cause of hereditary hemochromatosis.
HFE, a gene encoding a putative lysosomal trafficking protein, is involved in the pathogenesis of hereditary hemochromatosis.
Question: Viliuisk encephalomyelitis is diagnosed in which geographical area?
Answer: Viliuisk encephalomyelitis (VE) is an endemic neurological disease in Northeast Siberia and generally considered to be a chronic encephalomyelitis of unknown origin actually spreading in the Sakha (Yakutian) Republic.
Question: Which tool has been developed for GPU-accelerated alignment of bisulfite-treated DNA sequences?
Answer: The alignment of bisulfite-treated DNA sequences (BS-seq reads) to a large genome involves a significant computational burden beyond that required to align non-bisulfite-treated reads. In the analysis of BS-seq data, this can present an important performance bottleneck that can be mitigated by appropriate algorithmic and software-engineering improvements. One strategy is to modify the read-alignment algorithms by integrating the logic related to BS-seq alignment, with the goal of making the software implementation amenable to optimizations that lead to higher speed and greater sensitivity than might otherwise be attainable. This strategy was evaluated using Arioc, a short-read aligner that uses GPU (general-purpose graphics processing unit) hardware to accelerate computationally-expensive programming logic.