The rapid transition between spherical and γ-soft shapes in Ba and Xe nuclei in the mass region A ≥ 130 is analyzed using excitation spectra and collective wave functions obtained by diagonalization of a five-dimensional Hamiltonian for quadrupole vibrational and rotational degrees of freedom, with parameters determined by constrained self-consistent relativistic mean-field calculations for triaxial shapes. The results reproduce the characteristic evolution of excitation spectra and E2 transition probabilities and, in general, a good agreement with available data is obtained. The calculated spectra display fingerprints of a second-order shape phase transition that can approximately be described by analytic solutions corresponding to the E(5) dynamical symmetry.
Clinical applications of precision oncology require accurate tests that can distinguish true cancer specific mutations from errors introduced at each step of next-generation sequencing (NGS). To date, no bulk sequencing study has addressed the effects of cross-site reproducibility, nor the biological, technical and computational factors that influence variant identification. Here we report a systematic interrogation of somatic mutations in paired tumor-normal cell lines to identify factors affecting detection reproducibility and accuracy at six different centers. Using whole genome sequencing (WGS) and whole-exome sequencing (WES), we evaluated the reproducibility of different sample types with varying input amount and tumor purity, and multiple library construction protocols, followed by processing with nine bioinformatics pipelines. We found that read coverage and callers affected both WGS and WES reproducibility, but WES performance was influenced by insert fragment size, genomic copy content and the global imbalance score (GIV; G > T/C > A). Finally, taking into account library preparation protocol, tumor content, read coverage and bioinformatics processes concomitantly, we recommend actionable practices to improve the reproducibility and accuracy of NGS experiments for cancer mutation detection.
There has been much recent interest in nuclear fission, due in part to a new appreciation of its relevance to astrophysics, stability of superheavy elements, and fundamental theory of neutrino interactions. At the same time, there have been important developments on a conceptual and computational level for the theory. The promising new theoretical avenues were the subject of a workshop held at the University of York in October 2019; this report summarises its findings and recommendations.
SummaryThe precisionFDA Truth Challenge V2 aimed to assess the state-of-the-art of variant calling in difficult-to-map regions and the Major Histocompatibility Complex (MHC). Starting with FASTQ files, 20 challenge participants applied their variant calling pipelines and submitted 64 variant callsets for one or more sequencing technologies (~35X Illumina, ~35X PacBio HiFi, and ~50X Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with the new GIAB benchmark sets and genome stratifications. Challenge submissions included a number of innovative methods for all three technologies, with graph-based and machine-learning methods scoring best for short-read and long-read datasets, respectively. New methods out-performed the 2016 Truth Challenge winners, and new machine-learning approaches combining multiple sequencing technologies performed particularly well. Recent developments in sequencing and variant calling have enabled benchmarking variants in challenging genomic regions, paving the way for the identification of previously unknown clinically relevant variants.
A quantitative analysis of the evolution of nuclear shapes and shape phase transitions, including regions of short-lived nuclei that are becoming accessible in experiments at radioactive-beam facilities, necessitate accurate modeling of the underlying nucleonic dynamics. Important theoretical advances have recently been made in studies of complex shapes and the corresponding excitation spectra and electromagnetic decay patterns, especially in the "beyond mean-field" framework based on nuclear density functionals. Interesting applications include studies of shape evolution and coexistence in N = 28 isotones, the structure of lowest 0 + excitations in deformed N ≈ 90 rare-earth nuclei, and quadrupole and octupole shape transitions in thorium isotopes.Coexistence of nuclear shapes: self-consistent mean-field and beyond 2
Static and dynamic aspects of the fission process of 226 Th are analyzed in a self-consistent framework based on relativistic energy density functionals. Constrained relativistic mean-field (RMF) calculations in the collective space of axially symmetric quadrupole and octupole deformations, based on the energy density functional PC-PK1 and a δ-force pairing, are performed to determine the potential energy surface of the fissioning nucleus, the scission line, the single-nucleon wave functions, energies and occupation probabilities, as functions of deformation parameters. Induced fission dynamics is described using the time-dependent generator coordinate method in the Gaussian overlap approximation. A collective Schrödinger equation, determined entirely by the microscopic single-nucleon degrees of freedom, propagates adiabatically in time the initial wave packet built by boosting the ground-state solution of the collective Hamiltonian for 226 Th. The position of the scission line and the microscopic input for the collective Hamiltonian are analyzed as functions of the strength of the pairing interaction. The effect of static pairing correlations on the pre-neutron emission charge yields and total kinetic energy of fission fragments is examined in comparison with available data, and the distribution of fission fragments is analyzed for different values of the initial excitation energy. * Electronic address: zpliphy@swu.edu.cn A microscopic description of fission presents one of the most complex problems in lowenergy theoretical nuclear physics [1, 2]. For a comprehensive recent review and an exhaustive list of references, we refer the reader to Ref. [1]. The spontaneous or induced fission process in which a heavy nucleus splits into fragments is out of reach for ab initio methods and, therefore, modern microscopic approaches are based on the framework of nuclear energy density functionals (NEDFs). Nuclear density functional theory (DFT) and its timedependent (TD) generalization have enabled a self-consistent treatment of both static and dynamic aspects of fission [3-11]. The slow large-amplitude collective motion of the compound system that eventually leads to the formation of the final fragments can be described, in a first approximation, as an adiabatic process in which the intrinsic nucleonic degrees of freedom are decoupled from macroscopic collective degrees of freedom such as multipole moments (deformations) of the mass distribution and pairing fields [1].Numerous studies of spontaneous fission, based on NEDFs, have analyzed the effects of the choice of collective coordinates (shape degrees of freedom), approximations used to calculate the collective inertia, and coupling between shape and pairing degrees of freedom on fission half-lives [12][13][14][15][16][17][18]. A quantitative description of induced fission is, in this framework, conceptually and computationally more challenging and this process has been explored less systematically. In particular, several recent studies have used the time-dependent gener...
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