MicroRNAome of Porcine Pre- and Postnatal Development

The domestic pig is of enormous agricultural significance and valuable models for many human diseases. Information concerning the pig microRNAome (miRNAome) has been long overdue and elucidation of this information will permit an atlas of microRNA (miRNA) regulation functions and networks to be constructed. Here we performed a comprehensive search for porcine miRNAs on ten small RNA sequencing libraries prepared from a mixture of tissues obtained during the entire pig lifetime, from the fetal period through adulthood. The sequencing results were analyzed using mammalian miRNAs, the precursor hairpins (pre-miRNAs) and the first release of the high-coverage porcine genome assembly (Sscrofa9, April 2009) and the available expressed sequence tag (EST) sequences. Our results extend the repertoire of pig miRNAome to 867 pre-miRNAs (623 with genomic coordinates) encoding for 1,004 miRNAs, of which 777 are unique. We preformed real-time quantitative PCR (q-PCR) experiments for selected 30 miRNAs in 47 tissue-specific samples and found agreement between the sequencing and q-PCR data. This broad survey provides detailed information about multiple variants of mature sequences, precursors, chromosomal organization, development-specific expression, and conservation patterns. Our data mining produced a broad view of the pig miRNAome, consisting of miRNAs and isomiRs and a wealth of information of pig miRNA characteristics. These results are prelude to the advancement in pig biology as well the use of pigs as model organism for human biological and biomedical studies

Statistics on Lefschetz thimbles: Bell/Leggett-Garg inequalities and the classical-statistical approximation

Inspired by Lefschetz thimble theory, we treat Quantum Field Theory as a statistical theory with a complex Probability Distribution Function (PDF). Such complex-valued PDFs permit the violation of Bell-type inequalities, which cannot be violated by a real-valued, non-negative PDF. In this paper, we consider the Classical-Statistical approximation in the context of Bell-type inequalities, viz. the familiar (spatial) Bell inequalities and the temporal Leggett-Garg inequalities. We show that the Classical-Statistical approximation does not violate temporal Bell-type inequalities, even though it is in some sense exact for a free theory, whereas the full quantum theory does. We explain the origin of this discrepancy, and point out the key difference between the spatial and temporal Bell-type inequalities. We comment on the import of this work for applications of the Classical-Statistical approximation