Somatic mutation patterns in non-lymphoid cancers resemble the strand biased somatic hypermutation spectra of antibody genes

It has been long accepted that many types of B cell cancer (lymphomas, myelomas, plasmacytomas, etc.) are derived from the antigen-stimulated B cell Germinal Center (GC) reaction [1], [2], [3] and [4], i.e. they are aberrant products of the somatic hypermutation mechanism normally targeting rearranged immunoglobulin (Ig) variable genes (so-called V[D]J regions). Here we provide evidence that the somatic mutation patterns of some well-characterised cancer genomes [5] such as lung carcinomas, breast carcinomas and squamous cell carcinomas, strongly resemble in toto or in part the spectrum of somatic point mutations observed in normal physiological somatic hypermutation (SHM) in antibody variable genes [6]. This implies that whilst SHM itself is a tightly regulated and beneficial mutational process for B lymphocytes of the immune system, aberrant mutations (or “crises”) or inadvertent activation of this complex activation-induced cytidine deaminase (AID)-dependent mechanism in a range of somatic tissue types could result, as often speculated [7], in cancer

Genesis of ancestral haplotypes: RNA modifications and reverse transcription–mediated polymorphisms

Understanding the genesis of the block haplotype structure of the genome is a major challenge. With the completion of the sequencing of the Human Genome and the initiation of the HapMap project the concept that the chromosomes of the mammalian genome are a mosaic, or patchwork, of conserved extended block haplotype sequences is now accepted by the mainstream genomics research community. Ancestral Haplotypes (AHs) can be viewed as a recombined string of smaller Polymorphic Frozen Blocks (PFBs). How have such variant extended DNA sequence tracts emerged in evolution? Here the relevant literature on the problem is reviewed from various fields of molecular and cell biology particularly molecular immunology and comparative and functional genomics. Based on our synthesis we then advance a testable molecular and cellular model. A critical part of the analysis concerns the origin of the strand biased mutation signatures in the transcribed regions of the human and higher primate genome, A-to-G versus T-to-C (ratio ~1.5 fold) and C-to-T versus G-to-A (≥1.5 fold). A comparison and evaluation of the current state of the fields of immunoglobulin Somatic Hypermutation (SHM) and Transcription-Coupled DNA Repair focused on how mutations in newly synthesized RNA might be copied back to DNA thus accounting for some of the genome-wide strand biases (e.g., the A-to-G vs T-to-C component of the strand biased spectrum). We hypothesize that the genesis of PFBs and extended AHs occurs during mutagenic episodes in evolution (e.g., retroviral infections) and that many of the critical DNA sequence diversifying events occur first at the RNA level, e.g., recombination between RNA strings resulting in tandem and dispersed RNA duplications (retroduplications), RNA mutations via adenosine-to-inosine pre-mRNA editing events as well as error prone RNA synthesis. These are then copied back into DNA by a cellular reverse transcription process (also likely to be error-prone) that we have called "reverse transcription-mediated long DNA conversion." Finally we suggest that all these activities and others can be envisaged as being brought physically under the umbrella of special sites in the nucleus involved in transcription known as "transcription factories."

Plausibility functions and exact frequentist inference

In the frequentist program, inferential methods with exact control on error rates are a primary focus. The standard approach, however, is to rely on asymptotic approximations, which may not be suitable. This paper presents a general framework for the construction of exact frequentist procedures based on plausibility functions. It is shown that the plausibility function-based tests and confidence regions have the desired frequentist properties in finite samples---no large-sample justification needed. An extension of the proposed method is also given for problems involving nuisance parameters. Examples demonstrate that the plausibility function-based method is both exact and efficient in a wide variety of problems.Comment: 21 pages, 5 figures, 3 table

Astrophysical constraints on primordial black holes in Brans-Dicke theory

We consider cosmological evolution in Brans-Dicke theory with a population of primordial black holes. Hawking radiation from the primordial black holes impacts various astrophysical processes during the evolution of the Universe. The accretion of radiation by the black holes in the radiation dominated era may be effective in imparting them a longer lifetime. We present a detailed study of how this affects various standard astrophysical constraints coming from the evaporation of primordial black holes. We analyze constraints from the present density of the Universe, the present photon spectrum, the distortion of the cosmic microwave background spectrum and also from processes affecting light element abundances after nucleosynthesis. We find that the constraints on the initial primordial black hole mass fractions are tightened with increased accretion efficiency.Comment: 15 page

Primordial black holes in braneworld cosmologies: astrophysical constraints

In two recent papers we explored the modifications to primordial black hole physics when one moves to the simplest braneworld model, Randall--Sundrum type II. Both the evaporation law and the cosmological evolution of the population can be modified, and additionally accretion of energy from the background can be dominant over evaporation at high energies. In this paper we present a detailed study of how this impacts upon various astrophysical constraints, analyzing constraints from the present density, from the present high-energy photon background radiation, from distortion of the microwave background spectrum, and from processes affecting light element abundances both during and after nucleosynthesis. Typically, the constraints on the formation rate of primordial black holes weaken as compared to the standard cosmology if black hole accretion is unimportant at high energies, but can be strengthened in the case of efficient accretion.Comment: 17 pages RevTeX4 file with three figures incorporated; final paper in series astro-ph/0205149 and astro-ph/0208299. Minor changes to match version accepted by Physical Review

Search for single vector-like B quark production and decay via B → bH(b¯b) in pp collisions at √s = 13 TeV with the ATLAS detector

A search is presented for single production of a vector-like B quark decaying into a Standard Model b-quark and a Standard Model Higgs boson, which decays into a b¯b pair. The search is carried out in 139 fb−1 of √s = 13 TeV proton-proton collision data collected by the ATLAS detector at the LHC between 2015 and 2018. No significant deviation from the Standard Model background prediction is observed, and mass-dependent exclusion limits at the 95% confidence level are set on the resonance production cross-section in several theoretical scenarios determined by the couplings cW, cZ and cH between the B quark and the Standard Model W, Z and Higgs bosons, respectively. For a vector-like B occurring as an isospin singlet, the search excludes values of cW greater than 0.45 for a B resonance mass (mB) between 1.0 and 1.2 TeV. For 1.2 TeV < mB < 2.0 TeV, cW values larger than 0.50–0.65 are excluded. If the B occurs as part of a (B, Y) doublet, the smallest excluded cZ coupling values range between 0.3 and 0.5 across the investigated resonance mass range 1.0 TeV < mB < 2.0 TeV

Search for resonances decaying into photon pairs in 139 fb−1 of pp collisions at √s = 13 TeV with the ATLAS detector

Searches for new resonances in the diphoton final state, with spin 0 as predicted by theories with an extended Higgs sector and with spin 2 using a warped extra-dimension benchmark model, are presented using 139 fb−1 of √s = 13 TeV pp collision data collected by the ATLAS experiment at the LHC. No significant deviation from the Standard Model is observed and upper limits are placed on the production cross-section times branching ratio to two photons as a function of the resonance mass

Search for pair production of boosted Higgs bosons via vector-boson fusion in the bb¯bb¯ final state using pp collisions at √s = 13 TeV with the ATLAS detector

A search for Higgs boson pair production via vector-boson fusion is performed in the Lorentz-boosted regime, where a Higgs boson candidate is reconstructed as a single large-radius jet, using 140 fb−1 of proton–proton collision data at √s = 13 TeV recorded by the ATLAS detector at the Large Hadron Collider. Only Higgs boson decays into bottom quark pairs are considered. The search is particularly sensitive to the quartic coupling between two vector bosons and two Higgs bosons relative to its Standard Model prediction, K2V . This study constrains K2V to 0.55 &lt; K2V &lt; 1.49 at the 95% confidence level. The value K2V = 0 is excluded with a significance of 3.8 standard deviations with other Higgs boson couplings fixed to their Standard Model values. A search for new heavy spin-0 resonances that would mediate Higgs boson pair production via vector-boson fusion is carried out in the mass range of 1–5 TeV for the first time under several model and decay-width assumptions. No significant deviation from the Standard Model hypothesis is observed and exclusion limits at the 95% confidence level are derived

Evidence for the charge asymmetry in pp → tt¯ production at s√ = 13 TeV with the ATLAS detector

Inclusive and differential measurements of the top–antitop (tt¯) charge asymmetry Att¯C and the leptonic asymmetry Aℓℓ¯C are presented in proton–proton collisions at s√ = 13 TeV recorded by the ATLAS experiment at the CERN Large Hadron Collider. The measurement uses the complete Run 2 dataset, corresponding to an integrated luminosity of 139 fb−1, combines data in the single-lepton and dilepton channels, and employs reconstruction techniques adapted to both the resolved and boosted topologies. A Bayesian unfolding procedure is performed to correct for detector resolution and acceptance effects. The combined inclusive tt¯ charge asymmetry is measured to be Att¯C = 0.0068 ± 0.0015, which differs from zero by 4.7 standard deviations. Differential measurements are performed as a function of the invariant mass, transverse momentum and longitudinal boost of the tt¯ system. Both the inclusive and differential measurements are found to be compatible with the Standard Model predictions, at next-to-next-to-leading order in quantum chromodynamics perturbation theory with next-to-leading-order electroweak corrections. The measurements are interpreted in the framework of the Standard Model effective field theory, placing competitive bounds on several Wilson coefficients