CosmoDM and its application to Pan-STARRS data

The Cosmology Data Management system (CosmoDM) is an automated and flexible data management system for the processing and calibration of data from optical photometric surveys. It is designed to run on supercomputers and to minimize disk I/O to enable scaling to very high throughput during periods of reprocessing. It serves as an early prototype for one element of the ground-based processing required by the Euclid mission and will also be employed in the preparation of ground based data needed in the eROSITA X-ray all sky survey mission. CosmoDM consists of two main pipelines. The first is the single-epoch or detrending pipeline, which is used to carry out the photometric and astrometric calibration of raw exposures. The second is the co- addition pipeline, which combines the data from individual exposures into deeper coadd images and science ready catalogs. A novel feature of CosmoDM is that it uses a modified stack of As- tromatic software which can read and write tile compressed images. Since 2011, CosmoDM has been used to process data from the DECam, the CFHT MegaCam and the Pan-STARRS cameras. In this paper we shall describe how processed Pan-STARRS data from CosmoDM has been used to optically confirm and measure photometric redshifts of Planck-based Sunyaev-Zeldovich effect selected cluster candidates.Comment: 11 pages, 4 figures. Proceedings of Precision Astronomy with Fully Depleted CCDs Workshop (2014). Accepted for publication in JINS

A systematic review and meta-analysis on the effect of neoadjuvant chemotherapy on complications following immediate breast reconstruction

Background The impact of neoadjuvant chemotherapy (NACT) on surgical outcomes following immediate breast reconstruction (IBR) remains unclear. While it is generally considered safe practice to perform an IBR post NACT, reported complication rates in published data are highly variable with the majority of studies including fewer than 50 patients in the NACT and IBR arm. To evaluate this further, we conducted a systematic review and meta-analysis on the effect of NACT on autologous and implant based immediate breast reconstructions. We aimed to assess for differences in the post-operative course following IBR between patients who received NACT with those who did not. Methods PubMed, EMBASE, and Cochrane Library were searched from 1995 to Sept 2, 2020 to identify articles that assessed the impact of NACT on IBR. All included studies assessed outcomes following IBR. Only studies comparing reconstructed patients receiving NACT to a control group of women who did not receive NACT were included. Unadjusted relative risk of outcomes between patients who received or did not receive NACT were synthesized using a fixed-effect meta-analysis. The evidence was assessed using the Newcastle Ottawa Scale scores and GRADE. Primary effect measures were risk ratios (RRs) with 95% confidence intervals. Results A total 17 studies comprising 3249 patients were included in the meta-analyses. Overall, NACT did not increase the risk of complications after immediate breast reconstructions (risk ratio [RR]: 0.91, 95% CI 0.74 to 1.11, p = 0.34). There was a moderate, but not significant, increase in flap loss following NACT compared with controls (RR: 1.23, 95% CI 0.70 to 2.18, p = 0.47; I2 = 0%). Most notably, there was a statistically significant increase in implant/expander loss after NACT (RR: 1.54, 95% CI 1.04 to 2.29, p = 0.03; I2 = 34%). NACT was not shown to significantly increase the incidence of hematomas, seromas or wound complications, or result in a significant delay to commencing adjuvant therapy (RR: 1.59, 95% CI 0.66 to 3.87, p = 0.30). Conclusion Immediate breast reconstruction after NACT is a safe procedure with an acceptable post-operative complication profile. It may result in a slight increase in implant loss rates, but it does not delay commencing adjuvant therapy

J- and Ks-band Galaxy Counts and Color Distributions in the AKARI North Ecliptic Pole Field

We present the J- and Ks-band galaxy counts and galaxy colors covering 750 square arcminutes in the deep AKARI North Ecliptic Pole (NEP) field, using the FLoridA Multi-object Imaging Near-ir Grism Observational Spectrometer (FLAMINGOS) on the Kitt Peak National Observatory (KPNO) 2.1m telescope. The limiting magnitudes with a signal-to-noise ratio of three in the deepest regions are 21.85 and 20.15 in the J- and Ks-bands respectively in the Vega magnitude system. The J- and Ks-band galaxy counts in the AKARI NEP field are broadly in good agreement with those of other results in the literature, however we find some indication of a change in the galaxy number count slope at J~19.5 and over the magnitude range 18.0 < Ks < 19.5. We interpret this feature as a change in the dominant population at these magnitudes because we also find an associated change in the B - Ks color distribution at these magnitudes where the number of blue samples in the magnitude range 18.5 < Ks < 19.5 is significantly larger than that of Ks < 17.5

Chiral symmetry breaking in Hamiltonian QCD in Coulomb gauge

Spontaneous breaking of chiral symmetry is investigated in the Hamiltonian approach to QCD in Coulomb gauge. The quark wave functional is determined by the variational principle using an ansatz which goes beyond the commonly used BCS-type of wave functionals and includes the coupling of the quarks to the transversal spatial gluons. Using the lattice gluon propagator as input it is shown that the low energy chiral properties of the quarks, like the quark condensate and the constituent quark mass, are substantially increased by the coupling of the quarks to the spatial gluons. Our results compare favourably with the phenomenological values.Comment: 4 pages, 2 figure

Inelastic Quantum Transport

We solve a Schrodinger equation for inelastic quantum transport that retains full quantum coherence, in contrast to previous rate or Boltzmann equation approaches. The model Hamiltonian is the zero temperature 1d Holstein model for an electron coupled to optical phonons (polaron), in a strong electric field. The Hilbert space grows exponentially with electron position, forming a non-standard Bethe lattice. We calculate nonperturbatively the transport current, electron-phonon correlations, and quantum diffusion. This system is a toy model for the constantly branching ``wavefunction of the universe''.Comment: revtex, 13 pages, 4 figure

Spectral Properties of Quasiparticle Excitations Induced by Magnetic Moments in Superconductors

The consequences of localized, classical magnetic moments in superconductors are explored and their effect on the spectral properties of the intragap bound states is studied. Above a critical moment, a localized quasiparticle excitation in an s-wave superconductor is spontaneously created near a magnetic impurity, inducing a zero-temperature quantum transition. In this transition, the spin quantum number of the ground state changes from zero to 1/2, while the total charge remains the same. In contrast, the spin-unpolarized ground state of a d-wave superconductor is found to be stable for any value of the magnetic moment when the normal-state energy spectrum possesses particle-hole symmetry. The effect of impurity scattering on the quasiparticle states is interpreted in the spirit of relevant symmetries of the clean superconductor. The results obtained by the non-self-consistent (T matrix) and the self-consistent mean-field approximations are compared and qualitative agreement between the two schemes is found in the regime where the coherence length is longer than the Fermi length.Comment: to appear in Phys. Rev. B55, May 1st (1997

Local Electronic Structure of a Single Magnetic Impurity in a Superconductor

The electronic structure near a single classical magnetic impurity in a superconductor is determined using a fully self-consistent Koster-Slater algorithm. Localized excited states are found within the energy gap which are half electron and half hole. Within a jellium model we find the new result that the spatial structure of the positive-frequency (electron-like) spectral weight (or local density of states), can differ strongly from that of the negative frequency (hole-like) spectral weight. The effect of the impurity on the continuum states above the energy gap is calculated with good spectral resolution for the first time. This is also the first three-dimensional self-consistent calculation for a strong magnetic impurity potential.Comment: 13 pages, RevTex, change in heuristic picture, no change in numerical result

Local Electronic Structure of Defects in Superconductors

The electronic structure near defects (such as impurities) in superconductors is explored using a new, fully self-consistent technique. This technique exploits the short-range nature of the impurity potential and the induced change in the superconducting order parameter to calculate features in the electronic structure down to the atomic scale with unprecedented spectral resolution. Magnetic and non-magnetic static impurity potentials are considered, as well as local alterations in the pairing interaction. Extensions to strong-coupling superconductors and superconductors with anisotropic order parameters are formulated.Comment: RevTex source, 20 pages including 22 figures in text with eps

Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks

<p>Abstract</p> <p>Background</p> <p>In recent years, constrained optimization – usually referred to as flux balance analysis (FBA) – has become a widely applied method for the computation of stationary fluxes in large-scale metabolic networks. The striking advantage of FBA as compared to kinetic modeling is that it basically requires only knowledge of the stoichiometry of the network. On the other hand, results of FBA are to a large degree hypothetical because the method relies on plausible but hardly provable optimality principles that are thought to govern metabolic flux distributions.</p> <p>Results</p> <p>To augment the reliability of FBA-based flux calculations we propose an additional side constraint which assures thermodynamic realizability, i.e. that the flux directions are consistent with the corresponding changes of Gibb's free energies. The latter depend on metabolite levels for which plausible ranges can be inferred from experimental data. Computationally, our method results in the solution of a mixed integer linear optimization problem with quadratic scoring function. An optimal flux distribution together with a metabolite profile is determined which assures thermodynamic realizability with minimal deviations of metabolite levels from their expected values. We applied our novel approach to two exemplary metabolic networks of different complexity, the metabolic core network of erythrocytes (30 reactions) and the metabolic network iJR904 of <it>Escherichia coli </it>(931 reactions). Our calculations show that increasing network complexity entails increasing sensitivity of predicted flux distributions to variations of standard Gibb's free energy changes and metabolite concentration ranges. We demonstrate the usefulness of our method for assessing critical concentrations of external metabolites preventing attainment of a metabolic steady state.</p> <p>Conclusion</p> <p>Our method incorporates the thermodynamic link between flux directions and metabolite concentrations into a practical computational algorithm. The weakness of conventional FBA to rely on intuitive assumptions about the reversibility of biochemical reactions is overcome. This enables the computation of reliable flux distributions even under extreme conditions of the network (e.g. enzyme inhibition, depletion of substrates or accumulation of end products) where metabolite concentrations may be drastically altered.</p