Kosterlitz-Thouless Transition Line for the Two Dimensional Coulomb Gas

With a rigorous renormalization group approach, we study the pressure of the two dimensional Coulomb Gas along a small piece of the Kosterlitz-Thouless transition line, i.e. the boundary of the dipole region in the activity-temperature phase-space.Comment: 61 pages, 2 figure

Nonlocal Conductivity in the Vortex-Liquid Regime of a Two-Dimensional Superconductor

We have simulated the time-dependent Ginzburg-Landau equation with thermal fluctuations, to study the nonlocal dc conductivity of a superconducting film. Having examined points in the phase diagram at a wide range of temperatures and fields below the mean-field upper critical field, we find a portion of the vortex-liquid regime in which the nonlocal ohmic conductivity in real space is negative over a distance several times the spacing between vortices. The effect is suppressed when driven beyond linear response. Earlier work had predicted the existence of such a regime, due to the high viscosity of a strongly-correlated vortex liquid. This behavior is clearly distinguishable from the monotonic spatial fall-off of the conductivity in the higher temperature or field regimes approaching the normal state. The possibilities for experimental study of the nonlocal transport properties are discussed.Comment: 18 pages, revtex, 6 postscript figure

Interstitials, Vacancies and Dislocations in Flux-Line Lattices: A Theory of Vortex Crystals, Supersolids and Liquids

We study a three dimensional Abrikosov vortex lattice in the presence of an equilibrium concentration of vacancy, interstitial and dislocation loops. Vacancies and interstitials renormalize the long-wavelength bulk and tilt elastic moduli. Dislocation loops lead to the vanishing of the long-wavelength shear modulus. The coupling to vacancies and interstitials - which are always present in the liquid state - allows dislocations to relax stresses by climbing out of their glide plane. Surprisingly, this mechanism does not yield any further independent renormalization of the tilt and compressional moduli at long wavelengths. The long wavelength properties of the resulting state are formally identical to that of the ``flux-line hexatic'' that is a candidate ``normal'' hexatically ordered vortex liquid state.Comment: 21 RevTeX pgs, 7 eps figures uuencoded; corrected typos, published versio

NMR and NQR Fluctuation Effects in Layered Superconductors

We study the effect of thermal fluctuations of the s-wave order parameter of a quasi two dimensional superconductor on the nuclear spin relaxation rate near the transition temperature Tc. We consider both the effects of the amplitude fluctuations and the Berezinskii-Kosterlitz-Thouless (BKT) phase fluctuations in weakly coupled layered superconductors. In the treatment of the amplitude fluctuations we employ the Gaussian approximation and evaluate the longitudinal relaxation rate 1/T1 for a clean s-wave superconductor, with and without pair breaking effects, using the static pair fluctuation propagator D. The increase in 1/T1 due to pair breaking in D is overcompensated by the decrease arising from the single particle Green's functions. The result is a strong effect on 1/T1 for even a small amount of pair breaking. The phase fluctuations are described in terms of dynamical BKT excitations in the form of pancake vortex-antivortex (VA) pairs. We calculate the effect of the magnetic field fluctuations caused by the translational motion of VA excitations on 1/T1 and on the transverse relaxation rate 1/T2 on both sides of the BKT transitation temperature T(BKT)<Tc. The results for the NQR relaxation rates depend strongly on the diffusion constant that governs the motion of free and bound vortices as well as the annihilation of VA pairs. We discuss the relaxation rates for real multilayer systems where the diffusion constant can be small and thus increase the lifetime of a VA pair, leading to an enhancement of the rates. We also discuss in some detail the experimental feasibility of observing the effects of amplitude fluctuations in layered s-wave superconductors such as the dichalcogenides and the effects of phase fluctuations in s- or d-wave superconductors such as the layered cuprates.Comment: 38 pages, 12 figure

In utero exposure to benzo[a]pyrene increases mutation burden in the soma and sperm of adult mice

Background: Mosaicism, the presence of genetically distinct cell populations within an organism, has emerged as an important contributor to disease. Mutational events occurring during embryonic development can cause mosaicism in any tissue, but the influence of environmental factors on levels of mosaicism is unclear. Objectives: We investigated whether in utero exposure to the widespread environmental mutagen benzo[a]pyrene (BaP) has an impact on the burden and distribution of mutations in adult mice. Methods: We used the Muta™Mouse transgenic rodent model to quantify and characterize mutations in the offspring of pregnant mice exposed to BaP during postconception days 7 through 16, covering the major period of organogenesis in mice. Next-generation DNA sequencing was then used to determine the spectrum of mutations induced in adult mice that were exposed to BaP during fetal development. Results: Mutation frequency was significantly increased in the bone marrow, liver, brain, and sperm of first filial generation (F1) males. Developing embryos accumulated more mutations and exhibited higher proportions of mosaicism than exposed adults, particularly in the brain. Decreased sperm count and motility revealed additional negative impacts on the reproductive function of F1 males. Conclusion: In utero exposure to environmental mutagens contributes to somatic and germline mosaicism, permanently affecting both the genetic health of the F1 and the population gene pool. Citation: Meier MJ, O’Brien JM, Beal MA, Allan B, Yauk CL, Marchetti F. 2017. In utero exposure to benzo[a]pyrene increases mutation burden in the soma and sperm of adult mice

Velocity-force characteristics of an interface driven through a periodic potential

We study the creep dynamics of a two-dimensional interface driven through a periodic potential using dynamical renormalization group methods. We find that the nature of weak-drive transport depends qualitatively on whether the temperature $T$ is above or below the equilibrium roughening transition temperature $T_c$. Above $T_c$, the velocity-force characteristics is Ohmic, with linear mobility exhibiting a jump discontinuity across the transition. For $T \le T_c$, the transport is highly nonlinear, exhibiting an interesting crossover in temperature and weak external force $F$. For intermediate drive, $F>F_*$, we find near $T_c^{-}$ a power-law velocity-force characteristics $v(F)\sim F^\sigma$, with $\sigma-1\propto \tilde{t}$, and well-below $T_c$, $v(F)\sim e^{-(F_*/F)^{2\tilde{t}}}$, with $\tilde{t}=(1-T/T_c)$. In the limit of vanishing drive ($F\ll F_*$) the velocity-force characteristics crosses over to $v(F)\sim e^{-(F_0/F)}$, and is controlled by soliton nucleation.Comment: 18 pages, submitted to Phys. Rev.

Complete genomic characterization in patients with cancer of unknown primary origin in routine diagnostics

Background: In ∼3%-5% of patients with metastatic disease, tumor origin remains unknown despite modern imaging techniques and extensive pathology work-up. With long diagnostic delays and limited and ineffective therapy options, the clinical outcome of patients with cancer of unknown primary (CUP) remains poor. Large-scale genome sequencing studies have revealed that tumor types can be predicted based on distinct patterns of somatic variants and other genomic characteristics. Moreover, actionable genomic events are present in almost half of CUP patients. This study investigated the clinical value of whole genome sequencing (WGS) in terms of primary tumor identification and detection of actionable events, in the routine diagnostic work-up of CUP patients. Patients and methods: A WGS-based tumor type ‘cancer of unknown primary prediction algorithm’ (CUPPA) was developed based on previously described principles and validated on a large pan-cancer WGS database of metastatic cancer patients (>4000 samples) and 254 independent patients, respectively. We assessed the clinical value of this prediction algorithm as part of routine WGS-based diagnostic work-up for 72 CUP patients. Results: CUPPA correctly predicted the primary tumor type in 78% of samples in the independent validation cohort (194/254 patients). High-confidence predictions (>95% precision) were obtained for 162/254 patients (64%). When integrated in the diagnostic work-up of CUP patients, CUPPA could identify a primary tumor type for 49/72 patients (68%). Most common diagnoses included non-small-cell lung (n = 7), gastroesophageal (n = 4), pancreatic (n = 4), and colorectal cancer (n = 3). Actionable events with matched therapy options in clinical trials were identified in 47% of patients. Conclusions: Genome-based tumor type prediction can predict cancer diagnoses with high accuracy when integrated in the routine diagnostic work-up of patients with metastatic cancer. With identification of the primary tumor type in the majority of patients and detection of actionable events, WGS is a valuable diagnostic tool for patients with CUP

The On-orbit Calibrations for the Fermi Large Area Telescope

The Large Area Telescope (LAT) on--board the Fermi Gamma ray Space Telescope began its on--orbit operations on June 23, 2008. Calibrations, defined in a generic sense, correspond to synchronization of trigger signals, optimization of delays for latching data, determination of detector thresholds, gains and responses, evaluation of the perimeter of the South Atlantic Anomaly (SAA), measurements of live time, of absolute time, and internal and spacecraft boresight alignments. Here we describe on orbit calibration results obtained using known astrophysical sources, galactic cosmic rays, and charge injection into the front-end electronics of each detector. Instrument response functions will be described in a separate publication. This paper demonstrates the stability of calibrations and describes minor changes observed since launch. These results have been used to calibrate the LAT datasets to be publicly released in August 2009.Comment: 60 pages, 34 figures, submitted to Astroparticle Physic