Mapping Bias Overestimates Reference Allele Frequencies at the HLA Genes in the 1000 Genomes Project Phase I Data.

Next-generation sequencing (NGS) technologies have become the standard for data generation in studies of population genomics, as the 1000 Genomes Project (1000G). However, these techniques are known to be problematic when applied to highly polymorphic genomic regions, such as the human leukocyte antigen (HLA) genes. Because accurate genotype calls and allele frequency estimations are crucial to population genomics analyses, it is important to assess the reliability of NGS data. Here, we evaluate the reliability of genotype calls and allele frequency estimates of the single-nucleotide polymorphisms (SNPs) reported by 1000G (phase I) at five HLA genes (HLA-A, -B, -C, -DRB1, and -DQB1). We take advantage of the availability of HLA Sanger sequencing of 930 of the 1092 1000G samples and use this as a gold standard to benchmark the 1000G data. We document that 18.6% of SNP genotype calls in HLA genes are incorrect and that allele frequencies are estimated with an error greater than ±0.1 at approximately 25% of the SNPs in HLA genes. We found a bias toward overestimation of reference allele frequency for the 1000G data, indicating mapping bias is an important cause of error in frequency estimation in this dataset. We provide a list of sites that have poor allele frequency estimates and discuss the outcomes of including those sites in different kinds of analyses. Because the HLA region is the most polymorphic in the human genome, our results provide insights into the challenges of using of NGS data at other genomic regions of high diversity

Outskirts of Distant Galaxies In Absorption

QSO absorption spectroscopy provides a sensitive probe of both the neutral medium and diffuse ionized gas in the distant Universe. It extends 21cm maps of gaseous structures around low-redshift galaxies both to lower gas column densities and to higher redshifts. Combining galaxy surveys with absorption-line observations of gas around galaxies enables comprehensive studies of baryon cycles in galaxy outskirts over cosmic time. This Chapter presents a review of the empirical understanding of the cosmic neutral gas reservoir from studies of damped Lya absorbers (DLAs). It describes the constraints on the star formation relation and chemical enrichment history in the outskirts of distant galaxies from DLA studies. A brief discussion of available constraints on the ionized circumgalactic gas from studies of lower column density Lya absorbers and associated ionic absorption transitions is presented at the end.Comment: 45 pages, 7 figures, invited review, Book chapter in "Outskirts of Galaxies", Eds. J. H. Knapen, J. C. Lee and A. Gil de Paz, Astrophysics and Space Science Library, Springer, in pres

Magnetotunneling spectroscopy of mesoscopic correlations in two-dimensional electron systems

An approach to experimentally exploring electronic correlation functions in mesoscopic regimes is proposed. The idea is to monitor the mesoscopic fluctuations of a tunneling current flowing between the two layers of a semiconductor double-quantum-well structure. From the dependence of these fluctuations on external parameters, such as in-plane or perpendicular magnetic fields, external bias voltages, etc., the temporal and spatial dependence of various prominent correlation functions of mesoscopic physics can be determined. Due to the absence of spatially localized external probes, the method provides a way to explore the interplay of interaction and localization effects in two-dimensional systems within a relatively unperturbed environment. We describe the theoretical background of the approach and quantitatively discuss the behavior of the current fluctuations in diffusive and ergodic regimes. The influence of both various interaction mechanisms and localization effects on the current is discussed. Finally a proposal is made on how, at least in principle, the method may be used to experimentally determine the relevant critical exponents of localization-delocalization transitions.Comment: 15 pages, 3 figures include

Survey response in colorectal surgery:A systematic review

Background: Survey research is widely used for developing value-based management strategies in colorectal surgery. However, declining response rates threaten the validity of results. Our aim is to identify factors that influence response rate in colorectal surgical surveys and provide recommendations for future survey design.Methods: We performed a (MEDLINE) search between 2007 and 2020 for survey studies in colorectal surgery providing response rates.Results: Our search revealed 5693 studies, of which 128 studies were included. Patients with colorectal cancer have a lower mean response rate than patients with benign pathology (62.8% vs 75.5%, p &lt; 0.001). Response rate depends on the mode of survey; conducted in person (76%), postal (68%), email (61%) and web-based (44%). Patients participate more often than doctors (P &lt; 0.001). Reminders can positively influence response rates in postal patient surveys (p = 0.03). The proportion of web-based doctor surveys has grown over time (p &lt; 0.01) and overall survey response is declining over time (p = &lt; 0.01).Conclusion: In-person surveying should be explored first in colorectal surgery, especially when addressing colorectal cancer patients and doctors. Reminders are useful to boost response rate in postal surveys directed at patients. Web-based doctor surveys generate the lowest response rate. As response rate is declining, it is important to address these factors when designing and reviewing colorectal surgical survey studies.</p

Resonant nonstationary amplification of polychromatic laser pulses and conical emission in an optically dense ensemble of neon metastable atoms

Experimental and numerical investigation of single-beam and pump-probe interaction with a resonantly absorbing dense extended medium under strong and weak field-matter coupling is presented. Significant probe beam amplification and conical emission were observed. Under relatively weak pumping and high medium density, when the condition of strong coupling between field and resonant matter is fulfilled, the probe amplification spectrum has a form of spectral doublet. Stronger pumping leads to the appearance of a single peak of the probe beam amplification at the transition frequency. The greater probe intensity results in an asymmetrical transmission spectrum with amplification at the blue wing of the absorption line and attenuation at the red one. Under high medium density, a broad band of amplification appears. Theoretical model is based on the solution of the Maxwell-Bloch equations for a two-level system. Different types of probe transmission spectra obtained are attributed to complex dynamics of a coherent medium response to broadband polychromatic radiation of a multimode dye laser.Comment: 9 pages, 13 figures, corrected, Fig.8 was changed, to be published in Phys. Rev.

Deep Inelastic Scattering from off-Shell Nucleons

We derive the general structure of the hadronic tensor required to describe deep-inelastic scattering from an off-shell nucleon within a covariant formalism. Of the large number of possible off-shell structure functions we find that only three contribute in the Bjorken limit. In our approach the usual ambiguities encountered when discussing problems related to off-shellness in deep-inelastic scattering are not present. The formulation therefore provides a clear framework within which one can discuss the various approximations and assumptions which have been used in earlier work. As examples, we investigate scattering from the deuteron, nuclear matter and dressed nucleons. The results of the full calculation are compared with those where various aspects of the off-shell structure are neglected, as well as with those of the convolution model.Comment: 36 pages RevTeX, 9 figures (available upon request), ADP-93-210/T128, PSI-PR-93-13, accepted for publication in Physical Review

Nucleosynthesis Constraints on a Massive Gravitino in Neutralino Dark Matter Scenarios

The decays of massive gravitinos into neutralino dark matter particles and Standard Model secondaries during or after Big-Bang nucleosynthesis (BBN) may alter the primordial light-element abundances. We present here details of a new suite of codes for evaluating such effects, including a new treatment based on PYTHIA of the evolution of showers induced by hadronic decays of massive, unstable particles such as a gravitino. We also develop an analytical treatment of non-thermal hadron propagation in the early universe, and use this to derive analytical estimates for light-element production and in turn on decaying particle lifetimes and abundances. We then consider specifically the case of an unstable massive gravitino within the constrained minimal supersymmetric extension of the Standard Model (CMSSM). We present upper limits on its possible primordial abundance before decay for different possible gravitino masses, with CMSSM parameters along strips where the lightest neutralino provides all the astrophysical cold dark matter density. We do not find any CMSSM solution to the cosmological Li7 problem for small m_{3/2}. Discounting this, for m_{1/2} ~ 500 GeV and tan beta = 10 the other light-element abundances impose an upper limit m_{3/2} n_{3/2}/n_\gamma < 3 \times 10^{-12} GeV to < 2 \times 10^{-13} GeV for m_{3/2} = 250 GeV to 1 TeV, which is similar in both the coannihilation and focus-point strips and somewhat weaker for tan beta = 50, particularly for larger m_{1/2}. The constraints also weaken in general for larger m_{3/2}, and for m_{3/2} > 3 TeV we find a narrow range of m_{3/2} n_{3/2}/n_\gamma, at values which increase with m_{3/2}, where the Li7 abundance is marginally compatible with the other light-element abundances.Comment: 74 pages, 40 Figure

Nucleon-deuteron elastic scattering as a tool to probe properties of three-nucleon forces

Faddeev equations for elastic Nd scattering have been solved using modern NN forces combined with the Tucson-Melbourne two-pion exchange three-nucleon force, with a modification thereof closer to chiral symmetry and the Urbana IX three-nucleon force. Theoretical predictions for the differential cross section and several spin observables using NN forces only and NN forces combined with three-nucleon force models are compared to each other and to the existing data. A wide range of energies from 3 to 200 MeV is covered. Especially at the higher energies striking three-nucleon force effects are found, some of which are supported by the still rare set of data, some are in conflict with data and thus very likely point to defects in those three-nucleon force models.Comment: 30 pages, 14 Postscript figures; now minor changes in figures and reference

Asymptotic Expansions for Stationary Distributions of Perturbed Semi-Markov Processes

New algorithms for computing of asymptotic expansions for stationary distributions of nonlinearly perturbed semi-Markov processes are presented. The algorithms are based on special techniques of sequential phase space reduction, which can be applied to processes with asymptotically coupled and uncoupled finite phase spaces.Comment: 83 page

Dynamical Renormalization Group Approach to Quantum Kinetics in Scalar and Gauge Theories

We derive quantum kinetic equations from a quantum field theory implementing a diagrammatic perturbative expansion improved by a resummation via the dynamical renormalization group. The method begins by obtaining the equation of motion of the distribution function in perturbation theory. The solution of this equation of motion reveals secular terms that grow in time, the dynamical renormalization group resums these secular terms in real time and leads directly to the quantum kinetic equation. We used this method to study the relaxation in a cool gas of pions and sigma mesons in the O(4) chiral linear sigma model. We obtain in relaxation time approximation the pion and sigma meson relaxation rates. We also find that in large momentum limit emission and absorption of massless pions result in threshold infrared divergence in sigma meson relaxation rate and lead to a crossover behavior in relaxation. We then study the relaxation of charged quasiparticles in scalar electrodynamics (SQED). While longitudinal, Debye screened photons lead to purely exponential relaxation, transverse photons, only dynamically screened by Landau damping lead to anomalous relaxation, thus leading to a crossover between two different relaxational regimes. We emphasize that infrared divergent damping rates are indicative of non-exponential relaxation and the dynamical renormalization group reveals the correct relaxation directly in real time. Finally we also show that this method provides a natural framework to interpret and resolve the issue of pinch singularities out of equilibrium and establish a direct correspondence between pinch singularities and secular terms. We argue that this method is particularly well suited to study quantum kinetics and transport in gauge theories.Comment: RevTeX, 40 pages, 4 eps figures, published versio