Evolution of String-Wall Networks and Axionic Domain Wall Problem

We study the cosmological evolution of domain walls bounded by strings which arise naturally in axion models. If we introduce a bias in the potential, walls become metastable and finally disappear. We perform two dimensional lattice simulations of domain wall networks and estimate the decay rate of domain walls. By using the numerical results, we give a constraint for the bias parameter and the Peccei-Quinn scale. We also discuss the possibility to probe axion models by direct detection of gravitational waves produced by domain walls.Comment: 19 pages, 7 figures; revised version of the manuscript, accepted for publication in JCA

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism

The gravitational wave spectrum from cosmological B - L breaking

Cosmological B-L breaking is a natural and testable mechanism to generate the initial conditions of the hot early universe. If B-L is broken at the grand unification scale, the false vacuum phase drives hybrid inflation, ending in tachyonic preheating. The decays of heavy B-L Higgs bosons and heavy neutrinos generate entropy, baryon asymmetry and dark matter and also control the reheating temperature. The different phases in the transition from inflation to the radiation dominated phase produce a characteristic spectrum of gravitational waves. We calculate the complete gravitational wave spectrum due to inflation, preheating and cosmic strings, which turns out to have several features. The production of gravitational waves from cosmic strings has large uncertainties, with lower and upper bounds provided by Abelian Higgs strings and Nambu-Goto strings, implying ΩGWh2 ~ 10−13–10−8, much larger than the spectral amplitude predicted by inflation. Forthcoming gravitational wave detectors such as eLISA, advanced LIGO, ET, BBO and DECIGO will reach the sensitivity needed to test the predictions from cosmological B-L breaking

A promoter-level mammalian expression atlas

Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal. Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body. We find that few genes are truly ‘housekeeping’, whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles. TSSs specific to different cell types evolve at different rates, whereas promoters of broadly expressed genes are the most conserved. Promoter-based expression analysis reveals key transcription factors defining cell states and links them to binding-site motifs. The functions of identified novel transcripts can be predicted by coexpression and sample ontology enrichment analyses. The functional annotation of the mammalian genome 5 (FANTOM5) project provides comprehensive expression profiles and functional annotation of mammalian cell-type-specific transcriptomes with wide applications in biomedical research

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

10.1038/s41467-021-23143-7Nature Communications121329

First joint oscillation analysis of Super-Kamiokande atmospheric and T2K accelerator neutrino data

The Super-Kamiokande and T2K collaborations present a joint measurement of neutrino oscillation parameters from their atmospheric and beam neutrino data. It uses a common interaction model for events overlapping in neutrino energy and correlated detector systematic uncertainties between the two datasets, which are found to be compatible. Using 3244.4 days of atmospheric data and a beam exposure of $19.7(16.3) \times 10^{20}$ protons on target in (anti)neutrino mode, the analysis finds a 1.9$\sigma$ exclusion of CP-conservation (defined as $J_{CP}=0$) and a preference for the normal mass ordering