On the Convergence in Probability of Random Sets (Measurable Multifunctions)

Abstract Alu repeats contribute to phylogenetic novelties in conserved regulatory networks in primates. Our study highlights how exonized Alus could nucleate large-scale mRNA-miRNA interactions. Using a functional genomics approach, we characterize a transcript isoform of an orphan gene, CYP20A1 (CYP20A1_Alu-LT) that has exonization of 23 Alus in its 3’UTR. CYP20A1_Alu-LT, confirmed by 3’RACE, is an outlier in length (9 kb 3’UTR) and widely expressed. Using publically available datasets, we demonstrate its expression in higher primates and presence in single nucleus RNA-seq of 15928 human cortical neurons. miRanda predicts ∼4700 miRNA recognition elements (MREs) for ∼1000 miRNAs, primarily originated within these 3’UTR-Alus. CYP20A1_Alu-LT could be a potential multi-miRNA sponge as it harbors ≥10 MREs for 140 miRNAs and has cytosolic localization. We further tested whether expression of CYP20A1_Alu-LT correlates with mRNAs harboring similar MRE targets. RNA-seq with conjoint miRNA-seq analysis was done in primary human neurons where we observed CYP20A1_Alu-LT to be downregulated during heat shock response and upregulated in HIV1-Tat treatment. 380 genes were positively correlated with its expression (significantly downregulated in heat shock and upregulated in Tat) and they harbored MREs for nine expressed miRNAs which were also enriched in CYP20A1_Alu-LT. MREs were significantly enriched in these 380 genes compared to random sets of differentially expressed genes (p = 8.134e-12). Gene ontology suggested involvement of these genes in neuronal development and hemostasis pathways thus proposing a novel component of Alu-miRNA mediated transcriptional modulation that could govern specific physiological outcomes in higher primates.

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A harmonically weighted filter for cyclical long memory processes

AStA Advances in Statistical Analysis ◽

10.1007/s10182-021-00394-9 ◽

2021 ◽

Author(s):

Federico Maddanu

Keyword(s):

Spectral Density ◽

Long Memory ◽

Convergence In Probability ◽

Simulation Methods ◽

Integrated Process ◽

Paleoclimatic Data ◽

Memory Time ◽

Long Memory Processes ◽

Short Memory ◽

Memory Parameter

AbstractThe estimation of the long memory parameter d is a widely discussed issue in the literature. The harmonically weighted (HW) process was recently introduced for long memory time series with an unbounded spectral density at the origin. In contrast to the most famous fractionally integrated process, the HW approach does not require the estimation of the d parameter, but it may be just as able to capture long memory as the fractionally integrated model, if the sample size is not too large. Our contribution is a generalization of the HW model, denominated the Generalized harmonically weighted (GHW) process, which allows for an unbounded spectral density at $$k \ge 1$$ k ≥ 1 frequencies away from the origin. The convergence in probability of the Whittle estimator is provided for the GHW process, along with a discussion on simulation methods. Fit and forecast performances are evaluated via an empirical application on paleoclimatic data. Our main conclusion is that the above generalization is able to model long memory, as well as its classical competitor, the fractionally differenced Gegenbauer process, does. In addition, the GHW process does not require the estimation of the memory parameter, simplifying the issue of how to disentangle long memory from a (moderately persistent) short memory component. This leads to a clear advantage of our formulation over the fractional long memory approach.

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