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

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

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

Dissociative adsorption of NO upon AI(111): Orientation dependent charge transfer and chemisorption reaction dynamics.

In order to clarify the underlying mechanism of the initial oxidation of aluminum, the reaction between a heteronuclear diatomic molecule, nitric oxide, and the Al(111) surface was studied. It was shown that the reaction of NO with aluminum is a two-step process including a change of the orientation of the molecule with respect to the surface

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

Advances in ab-initio theory of Multiferroics. Materials and mechanisms: modelling and understanding

Within the broad class of multiferroics (compounds showing a coexistence of magnetism and ferroelectricity), we focus on the subclass of "improper electronic ferroelectrics", i.e. correlated materials where electronic degrees of freedom (such as spin, charge or orbital) drive ferroelectricity. In particular, in spin-induced ferroelectrics, there is not only a {\em coexistence} of the two intriguing magnetic and dipolar orders; rather, there is such an intimate link that one drives the other, suggesting a giant magnetoelectric coupling. Via first-principles approaches based on density functional theory, we review the microscopic mechanisms at the basis of multiferroicity in several compounds, ranging from transition metal oxides to organic multiferroics (MFs) to organic-inorganic hybrids (i.e. metal-organic frameworks, MOFs)Comment: 22 pages, 9 figure

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

Evidence for a Massive Post-Starburst Galaxy at z ~ 6.5

We present results from a search for high-redshift J--band ``dropout'' galaxies in the portion of the GOODS southern field that is covered by extremely deep imaging from the Hubble Ultradeep Field (HUDF).Using observations at optical, near-infrared and mid-infrared wavelengths from the Hubble and Spitzer Space Telescopes and the ESO-VLT, we search for very massive galaxies at high redshifts and find one particularly remarkable candidate. Its spectral energy distribution is consistent with a galaxy at z ~ 6.5 and a stellar mass of 6x10e11 M(sun) (for a Salpeter IMF). We interpret a prominent photometric break between the near-infrared and Spitzer bandpasses as the 3646A Balmer discontinuity. The best-fitting models have low reddening and ages of several hundred Myr, placing the formation of the bulk of the stars at z > 9. Alternative models of dusty galaxies at z ~ 2.5 are possible but provide significantly poorer fits. The object is detected with Spitzer at 24 micron. This emission originats from an obscured active nucleus or star formation. We present optical and near-infrared spectroscopy which has, thus far, failed to detect any spectral features. This helps limit the solution in which the galaxy is a starburst or active galaxy at z ~ 2.5. If the high-redshift interpretation is correct, this object would be an example of a galaxy that formed by a process strongly resembling traditional models of monolithic collapse, in a way which a very large mass of stars formed within a remarkably short period of time, at very high redshift.Comment: Accepted for publication in Ap.J. 31 pages, 6 diagram

anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data

Background: Compared to other omics techniques, quantitative metabolomics is still at its infancy. Complex sample preparation and analytical procedures render exact quantification extremely difficult. Furthermore, not only the actual measurement but also the subsequent interpretation of quantitative metabolome data to obtain mechanistic insights is still lacking behind the current expectations. Recently, the method of network-embedded thermodynamic (NET) analysis was introduced to address some of these open issues. Building upon principles of thermodynamics, this method allows for a quality check of measured metabolite concentrations and enables to spot metabolic reactions where active regulation potentially controls metabolic flux. So far, however, widespread application of NET analysis in metabolomics labs was hindered by the absence of suitable software. Results: We have developed in Matlab a generalized software called 'anNET' that affords a user-friendly implementation of the NET analysis algorithm. anNET supports the analysis of any metabolic network for which a stoichiometric model can be compiled. The model size can span from a single reaction to a complete genome-wide network reconstruction including compartments. anNET can (i) test quantitative data sets for thermodynamic consistency, (ii) predict metabolite concentrations beyond the actually measured data, (iii) identify putative sites of active regulation in the metabolic reaction network, and (iv) help in localizing errors in data sets that were found to be thermodynamically infeasible. We demonstrate the application of anNET with three published Escherichia coli metabolome data sets. Conclusion: Our user-friendly and generalized implementation of the NET analysis method in the software anNET allows users to rapidly integrate quantitative metabolome data obtained from virtually any organism. We envision that use of anNET in labs working on quantitative metabolomics will provide the systems biology and metabolic engineering communities with a mean to proof the quality of metabolome data sets and with all further benefits of the NET analysis approach.