question:You will be presented with the abstract, introduction, and discussion section from a biomedical research article. Your task is to create a summary that a layperson can understand, capturing the essence of the research article. Keep essential scientific terms, but ensure that the language remains clear and the concepts are explained in an uncomplicated manner.Title: Cotranslational microRNA mediated messenger RNA destabilization}Article:Abstract:MicroRNAs are small( 22 nucleotide) regulatory molecules that play important roles in a wide variety of biological processes. These RNAs, which bind to targeted mRNAs via limited base pairing interactions, act to reduce protein production from those mRNAs. Considerable evidence indicates that miRNAs destabilize targeted mRNAs by recruiting enzymes that function in normal mRNA decay and mRNA degradation is widely thought to occur when mRNAs are in a ribosome free state. Nevertheless, when examined, miRNA targeted mRNAs are invariably found to be polysome associated; observations that appear to be at face value incompatible with a simple decay model. Here, we provide evidence that turnover of miRNA-targeted mRNAs occurs while they are being translated. Cotranslational mRNA degradation is initiated by decapping and proceeds 5’ to 3’ behind the last translating ribosome. These results provide an explanation for a long standing mystery in the miRNA field.Introduction:microRNAs, a large family of regulatory molecules discovered over twenty years ago, have been shown to exert pervasive effects on a wide array of biological processes( reviewed in Ameres and Zamore, 2013; Ebert and Sharp, 2012). It has become clear that a majority of mRNAs are targeted by miRNAs via limited base pairing interactions between the miRNAs and miRNA responsive elements( MREs)( Bartel, 2009). Although there are exceptions, most MREs are located in 3’ UTRs( Bartel, 2009). The current consensus view of miRNA-mediated gene regulation is that it involves post-transcriptional down regulation of protein production from targeted mRNAs. Repression by miRNAs is largely attributable to mRNA destabilization and several lines of evidence indicate that this destabilization involves recruitment of factors which participate in normal mRNA decay pathways( Bagga et al., 2005; Guo et al., 2010; Eichhorn et al., 2014; Behm-Ansmant et al., 2006a; 2006b; Eulalio et al., 2008b; Jonas and Izaurralde, 2015). These factors include deadenylases and decapping enzymes( e. g. Braun et al., 2011; Chekulaeva et al., 2011; Rehwinkel et al., 2005). Although much has been learned regarding the biological functions of mRNAs and their mechanism( s) of action, there is one aspect that has largely eluded explanation; i. e. the interplay between the translation machinery and miRNA-mediated repression. In very early studies, the first miRNA targeted mRNAs were found to be fully associated with polysomes( Olsen and Ambros, 1999; Seggerson et al., 2002; Wightman et al., 1993). These observations have been reproduced numerous times over the years; whenever the subcellular localization of mRNA targets has been examined, those mRNAs are found to be exclusively on polysomes and unambiguous evidence has indicated that these polysomes are engaged in active translation( Gu et al., 2009; Nottrott et al., 2006; Petersen et al., 2006). Complementing these studies are several studies indicating that a substantive fraction of miRNAs themselves is also associated with actively translating ribosomes( Maroney et al., 2006; Nelson et al., 2004; Kim et al., 2004). Other observations, including the fact that MREs are less effective when present in open reading frames and the presence of a so-called ribosome shadow( absence of MREs in the 3’ UTR just downstream of stop codons) are consistent with an interaction between miRNA-effector complexes and translating ribosomes( Bartel, 2009). In sum, this body of evidence has led to the development of the hypothesis, which still persists in the literature, that miRNAs regulate translation in some way during the elongation phase but this hypothesis has been recalcitrant to mechanistic proof. It is difficult to reconcile the large body of evidence that shows that miRNA targeted mRNAs are associated with translating ribosomes with the equally compelling body of evidence that indicates that most miRNA-mediated downregulation occurs through mRNA destabilization. The conundrum is that the prevalent view of mRNA decay holds that decay occurs when mRNAs are in a ribosome free state, perhaps in subcellular aggregates known as P bodies, sites of concentrated RNA degradative activities( reviewed in Valencia-Sanchez et al., 2006). Here, we provide a solution to this longstanding puzzle by demonstrating that miRNA-mediated mRNA decay occurs cotranslationlly. Decay is initiated by mRNA decapping while targeted mRNAs are polysome bound and proceeds 5’ to 3’ following the last translating ribosome. These observations provide a unifying explanation for a large amount of what has been thought to be disparate experimental data.Discussion:We have provided evidence that miRNAs promote enhanced mRNA decay while the mRNA targets are engaged with actively translating ribosomes. While we have analyzed only two miRNA targets, we think it likely that these observations will be broadly relevant. In cases where the subcellular localization of miRNA targets have been studied, they have invariably been found to be polysome associated( Olsen and Ambros, 1999; Gu et al., 2009; Seggerson et al., 2002; Wightman et al., 1993; Nottrott et al., 2006; Petersen et al., 2006). Moreover, miRNAs themselves have been shown to be polysome associated( Maroney et al., 2006; Nelson et al., 2004; Kim et al., 2004). Our observations are also consistent with a large body of transcriptome wide analyses obtained from studies primarily in mammalial systems that have shown that mRNA destabilization is the primary if not sole effect of miRNA-mediated down regulation of protein production from targeted mRNAs( Guo et al., 2010; Eichhorn et al, 2014). They are also consistent with studies in Drosophila S2 cells that have shown that miRNA effector complexes as well as general decay enzymes including deadenylases and decapping factors are ribosome associated( Antic et al., 2015). While cotranslational miRNA-mediated mRNA decay rationalizes a very large body of published results, there are some observations that are difficult to reconcile with this unifying model of miRNA-mediated action. For example one study in a C. elegans cell free system showed that miRNA-targeted mRNAs were deadenylated and translationally repressed but not degraded( Wu et al., 2010). Another example, also from C. elegans, used ribosome profiling in vivo to show that miRNA mediated regulation in some cases correlated with mRNA abundance but in other cases did not( Stadler et al., 2012). Finally, there are also examples of Drosophila miRNA targeted mRNAs which appear to be regulated at the level of translation and not stability( e. g. Huntzinger and Izaurralde, 2011 and Behm-Ansmant et al., 2006a; 2006b). These examples might indicate that some specific mRNPs are subject to distinct regulatory pathways. Future studies may elucidate mRNP specific factors that mediate these effects. Cotranslational mRNA decay was shown several years ago for a selected group of mRNAs in budding yeast( Hu et al., 2009). More recently, studies have shown that such decay is the dominant if not sole pathway for normal mRNA decay in yeast( Pelechano et al., 2015). Our findings extend these observations to higher eukaryotes and suggest that cotranslational decay may be a widespread phenomenon. Our results do not speak specifically to how mRNA decay is triggered. In that regard there has been a longstanding debate in the field as to whether inhibition of translation initiation is a prerequisite for miRNA-mediated enhanced decay( Bazzini et al., 2012; Djuranovic et al., 2012; Eichhorn et al., 2014; Subtelny et al., 2014). Indeed over the years a large variety of different inhibition scenarios have been proposed including mRNA sequestration from the translation apparatus and inactivation of an array of initiation factors( e. g. Valencia-Sanchez et al., 2006; Mathonnet et al., 2007; Chendrimada et al., 2007; Kiriakidou et al., 2007; Wang et al., 2008; Fukaya et al., 2014), the latest being eIF4AI and II( Fukao et al., 2014; Meijer et al., 2013). Unfortunately none of these mechanisms including eIF4AI and II( see Galicia-Vázquez et al., 2015) has received sustained experimental support and it is currently unclear how or if initiation of translation is truly impaired in a microRNA-mediated fashion. Independent of miRNA-mediated mRNA decapping, mRNAs decap in general( Coller and Parker, 2004). For general mRNA decapping, translational initiation is also believed to be in competition with the DCP2/1 holoenzyme. Importantly, despite this well accepted notion that initiation and decapping compete, it remains to be established how, when, or even if dissolution of the translational initiation complex occurs prior to DCP2/1-mediated cleavage. Thus the events triggering decapping are still murky but may include recruitment of the RNA helicase DDX6( Chen et al., 2014; Mathys et al., 2014; Rouya et al., 2014). Importantly, however, since eIF-4F requires a cap to stimulate translation, decapping itself clearly and dramatically limits any further ribosome association and thus can itself be thought of as a potent and irreversible inhibitor of translation initiation. The first report of inhibition of initiation of translation came from polysome analysis where it was shown that an miRNA targeted mRNA migrated on lighter polysomes than a control mRNA( Pillai et al., 2005). Notably, however, all of the targeted mRNA was associated with ribosomes; there was no mRNA sedimenting in the RNP region of the gradient( Pillai et al., 2005). These results were interpreted to mean that miRNAs repressed translation initiation. We too observe that targeted mRNAs migrate on lighter polysomes than untargeted mRNAs( Figure 2—figure supplement 4). However, we suggest an alternative explanation for this phenomenon. It seems possible that the act of decapping itself could account for the altered sedimentation of targeted mRNAs. If decapping is a prerequisite for but not rate limiting for mRNA decay, decapped but not degraded mRNAs could persist. Because already engaged ribosomes would continue to elongate and eventually terminate, decapped but intact mRNAs would shift to lighter polysomes as elongating ribosomes clear the mRNA. We note that this notion is not entirely speculative. We have observed decapped mRNAs with 5’ termini that map both near the start site of the mRNA and near the translational initiation codon. Importantly, these RNAs, which would appear to be full length, are detected throughout polysomes of different sizes both large and small( Figure 5D). These observations indicate that 5’ to 3’ exonucleolytic decay is not obligatorily coupled to decapping because if such coupling existed we would not observe full length decapped mRNA. It seems possible the concentration of degradation fragments near the initiation AUG could result from the buildup of ribosomes near the beginning of the open reading frame as observed in ribosome profiling studies( e. g. Ingolia et al., 2011). Collectively, these observations suggest that decapping while a prerequisite for mRNA decay is not likely to be rate limiting for decay itself; exonucleolytic digestion by XRN1 is likely to be rate limiting. In sum, we have provided an explanation for a longstanding mystery in the miRNA field and have suggested a plausible model for miRNA action that is consistent with a large body of experimental results obtained in numerous laboratories.

question:You have to answer a biomedical question in binary format, i.e. only yes and no are the only acceptable answer formats. A list of paragraphs is provided as context to help you answer the question.Question: Is erythropoietin effective for treatment of amyotrophic lateral sclerosis?Context: This study was performed to validate the ALS-MITOS as a 6-month proxy of survival in 200 ALS patients followed up to 18 months.METHODS: Analyses were performed on data from the recombinant human erythropoietin RCT that failed to demonstrate differences between groups for both primary and secondary outcomes.CONCLUSIONS: RhEPO 40,000 IU fortnightly did not change the course of ALS.At 12 months, the annualised rate of death (rhEPO 0.11, 95% CI 0.06 to 0.20; placebo: 0.08, CI 0.04 to 0.17), tracheotomy or >23 h NIV (rhEPO 0.16, CI 0.10 to 0.27; placebo 0.18, CI 0.11 to 0.30) did not differ between groups, also after stratification by onset and ALSFRS-R at baseline.

question:You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: ["Protein", "Chemical"].Please return the output as a JSON object of the format: {"Chemical" : ["Dexamethasone", ...], "Protein" : ["BRCA-1", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].Only output the JSON object and do not include any additional text.Abstract:The CYP2B6*6 Allele Significantly Alters the N-demethylation of Ketamine Enantiomers In Vitro.Ketamine is primarily metabolized to norketamine by hepatic cytochrome P450 (CYP) 2B6 and CYP3A4-mediated N-demethylation. However, the relative contribution from each enzyme remains controversial. The CYP2B6*6 allele is associated with reduced enzyme expression and activity that may lead to interindividual variability in ketamine metabolism. We examined the N-demethylation of individual ketamine enantiomers using human liver microsomes (HLMs) genotyped for the CYP2B6*6 allele, insect cell expressed recombinant CYP2B6 and CYP3A4 enzymes and COS-1 cell expressed recombinant CYP2B6.1 and CYP2B6.6 protein variant. Effects of CYP-selective inhibitors on norketamine formation were also determined in HLMs. The two-enzyme Michaelis-Menten model best fitted the HLM kinetic data. The Km value for the high affinity enzyme and the low affinity enzyme were similar to those for the expressed CYP2B6 and CYP3A4, respectively. The intrinsic clearance for both ketamine enantiomers by the high affinity enzyme in HLMs with CYP2B6*1/*1 genotype were at least 2-fold and 6-fold higher, respectively, than those for CYP2B6*1/*6 genotype and CYP2B6*6/*6 genotype. The Vmax and Km values for CYP2B6.1 were approximately 160% and 70% of those for CYP2B6.6, respectively. ThioTEPA (CYP2B6 inhibitor, 25 μM) and the monoclonal antibody against CYP2B6 but not troleandomycin (CYP3A4 inhibitor, 25 μM) or the monoclonal antibody against CYP3A4 inhibited ketamine N-demethylation at clinically relevant concentrations. The degree of inhibition was significantly reduced in HLMs with the CYP2B6*6 allele (gene-dose P<0.05). These results indicate a major role of CYP2B6 in ketamine N-demethylation in vitro and a significant impact of the CYP2B6*6 allele on enzyme-ketamine binding and catalytic activity.

question:You will be presented with a citation segment from the section of a research paper. Classify the intent behind this citation by choosing from one of the following categories:- Method: Cites the paper for its methodology or procedure.- Background: Cites the paper to provide background information.- Result: Cites the paper for its findings or results.Your answer should be a single word from the following list of options: ["Method", "Background", "Result"]. Do not include any other text in your response.Citation sentence:chlorophenolicus T99, a mutant with a transposon insertion in a gene encoding a hydroxyquinol dioxygenase, resulting in an inability to grow on or degrade 4-CP (Nordin et al. 2005).

question:Devise a proper regular expression paradigm out of the following stipulation. The code should specifically envelop the textual components “start”, “end”, and “here”, necessitating a multi-step reasoning approach.

question:Can you elaborate on why JavaScript is acknowledged as a multi-paradigm programming language, encompassing aspects of procedural, object-oriented, and functional programming? Additionally, provide code samples for each paradigm carried out by JavaScript and discuss the advantages and drawbacks of every style. You should also compare and contrast JavaScript with other multi-paradigm languages, like Python and Ruby, in terms of performance, scalability, and ease of use in diverse programming contexts.