28 research outputs found
Cancellable elements of the lattice of semigroup varieties
We completely determine all commutative semigroup varieties that are cancellable elements of the lattice SEM of all semigroup varieties. In particular, we verify that a commutative semigroup variety is a cancellable element of the lattice SEM if and only if it is a modular element of this lattice
Photonic molecules and spectral engineering
This chapter reviews the fundamental optical properties and applications of
pho-tonic molecules (PMs) - photonic structures formed by electromagnetic
coupling of two or more optical microcavities (photonic atoms). Controllable
interaction between light and matter in photonic atoms can be further modified
and en-hanced by the manipulation of their mutual coupling. Mechanical and
optical tunability of PMs not only adds new functionalities to
microcavity-based optical components but also paves the way for their use as
testbeds for the exploration of novel physical regimes in atomic physics and
quantum optics. Theoretical studies carried on for over a decade yielded novel
PM designs that make possible lowering thresholds of semiconductor microlasers,
producing directional light emission, achieving optically-induced transparency,
and enhancing sensitivity of microcavity-based bio-, stress- and
rotation-sensors. Recent advances in material science and nano-fabrication
techniques make possible the realization of optimally-tuned PMs for cavity
quantum electrodynamic experiments, classical and quantum information
processing, and sensing.Comment: A review book chapter: 29 pages, 19 figure
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