f(R)f(R) gravity constrained by PPN parameters and stochastic background of gravitational waves

We analyze seven different viable $f(R)$-gravities towards the Solar System tests and stochastic gravitational waves background. The aim is to achieve experimental bounds for the theory at local and cosmological scales in order to select models capable of addressing the accelerating cosmological expansion without cosmological constant but evading the weak field constraints. Beside large scale structure and galactic dynamics, these bounds can be considered complimentary in order to select self-consistent theories of gravity working at the infrared limit. It is demonstrated that seven viable $f(R)$-gravities under consideration not only satisfy the local tests, but additionally, pass the above PPN-and stochastic gravitational waves bounds for large classes of parameters.Comment: 23 pages, 8 figure

f(R,L_m) gravity

We generalize the $f(R)$ type gravity models by assuming that the gravitational Lagrangian is given by an arbitrary function of the Ricci scalar $R$ and of the matter Lagrangian $L_m$. We obtain the gravitational field equations in the metric formalism, as well as the equations of motion for test particles, which follow from the covariant divergence of the energy-momentum tensor. The equations of motion for test particles can also be derived from a variational principle in the particular case in which the Lagrangian density of the matter is an arbitrary function of the energy-density of the matter only. Generally, the motion is non-geodesic, and takes place in the presence of an extra force orthogonal to the four-velocity. The Newtonian limit of the equation of motion is also considered, and a procedure for obtaining the energy-momentum tensor of the matter is presented. The gravitational field equations and the equations of motion for a particular model in which the action of the gravitational field has an exponential dependence on the standard general relativistic Hilbert--Einstein Lagrange density are also derived.Comment: 6 pages, no figures; minor modifications, references added; accepted for publication in EPJ

Retrotransposon instability dominates the acquired mutation landscape of mouse induced pluripotent stem cells.

Induced pluripotent stem cells (iPSCs) can in principle differentiate into any cell of the body, and have revolutionized biomedical research and regenerative medicine. Unlike their human counterparts, mouse iPSCs (miPSCs) are reported to silence transposable elements and prevent transposable element-mediated mutagenesis. Here we apply short-read or Oxford Nanopore Technologies long-read genome sequencing to 38 bulk miPSC lines reprogrammed from 10 parental cell types, and 18 single-cell miPSC clones. While single nucleotide variants and structural variants restricted to miPSCs are rare, we find 83 de novo transposable element insertions, including examples intronic to Brca1 and Dmd. LINE-1 retrotransposons are profoundly hypomethylated in miPSCs, beyond other transposable elements and the genome overall, and harbor alternative protein-coding gene promoters. We show that treatment with the LINE-1 inhibitor lamivudine does not hinder reprogramming and efficiently blocks endogenous retrotransposition, as detected by long-read genome sequencing. These experiments reveal the complete spectrum and potential significance of mutations acquired by miPSCs.Patricia Gerdes, SueMei Lim, AdamD. Ewing, Michael R. Larcombe, Dorothy Chan, Francisco J. Sanchez-Luque, Lucinda Walker, Alexander L. Carleton, Cini James, Anja S. Knaupp, Patricia E. Carreira, Christian M. Nefzger, Ryan Lister, Sandra R. Richardson, Jose M. Polo, Geoffrey J. Faulkne

Study of Charm Fragmentation into D^{*\pm} Mesons in Deep-Inelastic Scattering at HERA

The process of charm quark fragmentation is studied using $D^{*\pm}$ meson production in deep-inelastic scattering as measured by the H1 detector at HERA. Two different regions of phase space are investigated defined by the presence or absence of a jet containing the $D^{*\pm}$ meson in the event. The parameters of fragmentation functions are extracted for QCD models based on leading order matrix elements and DGLAP or CCFM evolution of partons together with string fragmentation and particle decays. Additionally, they are determined for a next-to-leading order QCD calculation in the fixed flavour number scheme using the independent fragmentation of charm quarks to $D^{*\pm}$ mesons.Comment: 33 pages, submitted to EPJ

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

A proposed method for ship routing using long range weather forecasts

Two advances in the calculus of variations method for minimal time ship routing are described. The first is a scheme for constructing ocean wave field forecasts which may be expected to have considerable skill for perhaps a week. The second is an improved technique for varying time extremal ship tracks toward admissibility. Both ideas are illustrated by calculating the optimum track ship route of a VC2AP3 vessel on a transpacific voyage. Possible future developments are discussed.This work was supported by the Naval Air Systems Command under the administration of the Navy Weather Research Facility, Norfolk, Va