Price-and-verify: a new algorithm for recursive circle packing using Dantzig–Wolfe decomposition

This is the author accepted manuscript. The final version is available from Springer via the DOI in this record Packing rings into a minimum number of rectangles is an optimization problem which appears naturally in the logistics operations of the tube industry. It encompasses two major difficulties, namely the positioning of rings in rectangles and the recursive packing of rings into other rings. This problem is known as the Recursive Circle Packing Problem (RCPP). We present the first dedicated method for solving RCPP that provides strong dual bounds based on an exact Dantzig–Wolfe reformulation of a nonconvex mixed-integer nonlinear programming formulation. The key idea of this reformulation is to break symmetry on each recursion level by enumerating one-level packings, i.e., packings of circles into other circles, and by dynamically generating packings of circles into rectangles. We use column generation techniques to design a “price-and-verify” algorithm that solves this reformulation to global optimality. Extensive computational experiments on a large test set show that our method not only computes tight dual bounds, but often produces primal solutions better than those computed by heuristics from the literature.Federal Ministry of Education and Researc

Stratosphere troposphere coupling: the influence of volcanic eruptions

Stratospheric sulfate aerosols produced by major volcanic eruptions modify the radiative and dynamical properties of the troposphere and stratosphere through their reflection of solar radiation and absorption of infrared radiation. At the Earth's surface, the primary consequence of a large eruption is cooling, however, it has long been known that major tropical eruptions tend to be followed by warmer than usual winters over the Northern Hemisphere (NH) continents. This volcanic "winter-warming" effect in the NH is understood to be the result of changes in atmospheric circulation patterns resulting from heating in the stratosphere, and is often described as positive anomalies of the Northern Annular Mode (NAM) that propagate downward from the stratosphere to the troposphere. In the southern hemisphere, climate models tend to also predict a positive Southern Annular Mode (SAM) response to volcanic eruptions, but this is generally inconsistent with post-eruption observations during the 20th century. We review present understanding of the influence of volcanic eruptions on the large scale modes of atmospheric variability in both the Northern and Southern Hemispheres. Using models of varying complexity, including an aerosol-climate model, an Earth system model, and CMIP5 simulations, we assess the ability of climate models to reproduce the observed post-eruption climatic and dynamical anomalies. We will also address the parametrization of volcanic eruptions in simulations of the past climate, and identify possibilities for improvemen

Extensive transcriptional complexity during hypoxia-regulated expression of the myoglobin gene in cancer

Recently, the ectopic expression of myoglobin (MB) was reported in human epithelial cancer cell lines and breast tumor tissues, where MB expression increased with hypoxia. The better prognosis of MB-positive breast cancer patients suggested that the globin exerts a tumor-suppressive role, possibly by impairing mitochondrial activity in hypoxic breast carcinoma cells. To better understand MB gene regulation in cancer, we systematically investigated the architecture of the human MB gene, its transcripts and promoters. In silico analysis of transcriptome data from normal human tissues and cancer cell lines, followed by RACE-PCR verification, revealed seven novel exons in the MB gene region, most of which are untranslated exons located 5′-upstream of the coding DNA sequence (CDS). Sixteen novel alternatively spliced MB transcripts were detected, most of which predominantly occur in tumor tissue or cell lines. Quantitative RT-PCR analyses of MB expression in surgical breast cancer specimen confirmed the preferential usage of a hitherto unknown, tumor-associated MB promoter, which was functionally validated by luciferase reporter gene assays. In line with clinical observations of MB up-regulation in avascular breast tumors, the novel cancer-associated MB splice variants exhibited increased expression in tumor cells subjected to experimental hypoxia. The novel gene regulatory mechanisms unveiled in this study support the idea of a non-canonical role of MB during carcinogenesi

Rhizosphere bacterial carbon turnover is higher in nucleic acids than membrane lipids : Implications for understanding soil carbon cycling

Acknowledgments We thank Agnes Fastnacht, Karl Kuebler, Steffen Ruehlow, Iris Kuhlmann, Heike Geilmann, Petra Linke, and Willi Brand for technical support in establishing the experimental setup and/or with stable isotope analyses. We also thank Bernhard Ahrens and Daniel Read for helpful discussions. This project was funded by the Max-Planck-Gesellschaft. We acknowledge Deutsche Forschungsgemeinschaft (DFG) for the fellowship to AAM in the research training group 1257 ‘Alteration and element mobility at microbe-mineral interface’ that is part of the Jena School for Microbial Communication (JSMC). AAM was also supported by the International Max Planck Research School for Global Biogeochemical Cycles (IMPRS-gBGC).Peer reviewedPublisher PD

The stable isotopic signature of biologically produced molecular hydrogen (H₂)

Biologically produced molecular hydrogen (H₂) is characterised by a very strong depletion in deuterium. Although the biological source to the atmosphere is small compared to photochemical or combustion sources, it makes an important contribution to the global isotope budget of H₂. Large uncertainties exist in the quantification of the individual production and degradation processes that contribute to the atmospheric budget, and isotope measurements are a tool to distinguish the contributions from the different sources. Measurements of &delta; D from the various H₂ sources are scarce and for biologically produced H₂ only very few measurements exist. <br><br> Here the first systematic study of the isotopic composition of biologically produced H₂ is presented. In a first set of experiments, we investigated &delta; D of H₂ produced in a biogas plant, covering different treatments of biogas production. In a second set of experiments, we investigated pure cultures of several H₂ producing microorganisms such as bacteria or green algae. A Keeling plot analysis provides a robust overall source signature of &delta; D = &minus;712&permil; (±13&permil;) for the samples from the biogas reactor (at 38 °C, &delta; D_H2O= +73.4&permil;), with a fractionation constant &varepsilon;_H2-H2O of −689&permil; (±20&permil;) between H₂ and the water. The five experiments using pure culture samples from different microorganisms give a mean source signature of &delta; D = &minus;728&permil; (±28&permil;), and a fractionation constant &varepsilon;_H2-H2O of −711&permil; (±34&permil;) between H₂ and the water. The results confirm the massive deuterium depletion of biologically produced H₂ as was predicted by the calculation of the thermodynamic fractionation factors for hydrogen exchange between H₂ and water vapour. Systematic errors in the isotope scale are difficult to assess in the absence of international standards for &delta; D of H₂. <br><br> As expected for a thermodynamic equilibrium, the fractionation factor is temperature dependent, but largely independent of the substrates used and the H₂ production conditions. The equilibrium fractionation coefficient is positively correlated with temperature and we measured a rate of change of 2.3&permil; / °C between 45 °C and 60 °C, which is in general agreement with the theoretical prediction of 1.4&permil; / °C. Our best experimental estimate for &varepsilon;_H2-H2O at a temperature of 20 °C is −731&permil; (±20&permil;) for biologically produced H₂. This value is close to the predicted value of −722&permil;, and we suggest using these values in future global H₂ isotope budget calculations and models with adjusting to regional temperatures for calculating &delta; D values

Plants with arbuscular mycorrhizal fungi efficiently acquire Nitrogen from substrate additions by shaping the decomposer community composition and their net plant carbon demand

Acknowledgements SC received funding from long term DAAD scholarship to carry out the research. ML is funded by the German Research Foundation (DFG; FOR 456, FOR 1451 – “The Jena Experiment”) and by the “Zwillenberg-Tietz Stiftung”. We acknowledge help from Agnes Fastnacht with greenhouse resources and monitoring of the experiment. Special thanks to Karl Kübler for construction and deployment of the pulse labelling setup in the greenhouse. We acknowledge Heike Geilmann and Steffen Ruehlow for help with stable isotope measurements, and Maria Foerster for helping with fatty acid analysis. We also thank Erika Kothe, Ruchira Mukherji, Elisa Catao and Huei Ying Gan for helpful comments and discussions and Simon Benk for proof reading the MS. Funding Open Access funding enabled and organized by Projekt DEAL.Peer reviewedPublisher PD